mirror of
https://github.com/HDFGroup/hdf5.git
synced 2025-02-23 16:20:57 +08:00
216bff5778
* OESS-98 convert plugin option to FetchContent, add tests * Fixes for pkcfg files because of plugin option * OESS-98 fix tools test for plugins * Keep doxygen comments under 100 chars long - format hint * Whitespace * HDFFV-11144 - Reclassify CMake messages * HDFFV-11099/11100 added help text * Reworked switch statement to compare string instead * Fix typo * Update CDash mode * Correct name of threadsafe * Correct option name * Undo accidental commit * Note LLVM 10 to 11 format default changes * Update format plugin * Undo clang-format version 11 changes * One more correction * Update supported platforms * Revert whitespace changes * Correct whitespace * Changes from PR#3 * HDFFV-11213 added option to control gcc10 warnings diagnostics * HDFFV-11212 Use the new references correctly in JNI utility and tests * format source * Fix typo * Add new test file * HDFFV-11212 - update test and remove unused arg * Minor non-space formatting changes * Use H5I_INVALID_ID instead of "-1" * source formatting * add missing testfile, update jni function * Undo commit of debug code * remove mislocated file * Fix h5repack test for handling of fapls and id close * Update h5diff test files usage text * HDFFV-11212 add new ref tests for JNI export dataset * src format update * Remove blank line typo * src format typo * long double requires %Lg * Another long double foramt specifer S.B. %Lg * issue with t128bit test * Windows issue with h5dump and type. * Fix review issues * refactor function nesting and fix error checks * format fixes * Remove untested functions and javadoc quiet comments * Restore TRY block. * Change string append errors to memory exception * revert to H5_JNI_FATAL_ERROR - support functions need work * Add assertion error for h5util functions * remove duplicate function * format fix * Revert HD function error handling * Update copyright comments * GH #386 java folder copyright corrections * Whitespace
364 lines
15 KiB
Java
364 lines
15 KiB
Java
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the COPYING file, which can be found at the root of the source code *
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* distribution tree, or in https://www.hdfgroup.org/licenses. *
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* If you do not have access to either file, you may request a copy from *
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* help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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package test;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertTrue;
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import static org.junit.Assert.fail;
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import java.io.File;
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import hdf.hdf5lib.H5;
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import hdf.hdf5lib.HDF5Constants;
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import hdf.hdf5lib.exceptions.HDF5Exception;
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import hdf.hdf5lib.exceptions.HDF5LibraryException;
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import org.junit.After;
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import org.junit.Before;
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import org.junit.Ignore;
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import org.junit.Rule;
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import org.junit.Test;
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import org.junit.rules.TestName;
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public class TestH5Ocopy {
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@Rule public TestName testname = new TestName();
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private static final String FILENAME = "testRefsattribute.h5";
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private static final int DIM_X = 4;
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private static final int DIM_Y = 6;
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long H5fid = HDF5Constants.H5I_INVALID_HID;
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long H5dsid = HDF5Constants.H5I_INVALID_HID;
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long H5did1 = HDF5Constants.H5I_INVALID_HID;
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long H5did2 = HDF5Constants.H5I_INVALID_HID;
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long H5gcpl = HDF5Constants.H5I_INVALID_HID;
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long H5gid = HDF5Constants.H5I_INVALID_HID;
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long H5dsid2 = HDF5Constants.H5I_INVALID_HID;
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long[] dims = { 2 };
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private final void _deleteFile(String filename) {
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File file = new File(filename);
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if (file.exists()) {
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try {
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file.delete();
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}
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catch (Exception e) {
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e.printStackTrace();
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}
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}
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}
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private final long _createDataset(long fid, long dsid, String name, long dapl) {
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long did = HDF5Constants.H5I_INVALID_HID;
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try {
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did = H5.H5Dcreate(fid, name,
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HDF5Constants.H5T_STD_I32BE, dsid,
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HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, dapl);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Dcreate: " + err);
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}
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assertTrue("TestH5O._createDataset: ",did >= 0);
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return did;
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}
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private final long _createGroup(long fid, String name) {
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long gid = HDF5Constants.H5I_INVALID_HID;
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try {
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H5gcpl = HDF5Constants.H5P_DEFAULT;
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gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT,
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H5gcpl, HDF5Constants.H5P_DEFAULT);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("H5.H5Gcreate: " + err);
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}
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assertTrue("TestH5O._createGroup: ",gid >= 0);
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return gid;
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}
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@Before
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public void createH5file()
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throws NullPointerException, HDF5Exception {
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assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0);
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System.out.print(testname.getMethodName());
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try {
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H5fid = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC,
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HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
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H5dsid2 = H5.H5Screate(HDF5Constants.H5S_SCALAR);
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H5did1 = _createDataset(H5fid, H5dsid2, "DS2", HDF5Constants.H5P_DEFAULT);
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H5dsid = H5.H5Screate_simple(1, dims, null);
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H5gid = _createGroup(H5fid, "/G1");
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H5did2 = _createDataset(H5gid, H5dsid, "DS1", HDF5Constants.H5P_DEFAULT);
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}
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catch (Throwable err) {
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err.printStackTrace();
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fail("TestH5O.createH5file: " + err);
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}
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assertTrue("TestH5O.createH5file: H5.H5Fcreate: ",H5fid >= 0);
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assertTrue("TestH5O.createH5file: H5.H5Screate_simple: ",H5dsid >= 0);
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assertTrue("TestH5O.createH5file: H5.H5Gcreate: ",H5gid >= 0);
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H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
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}
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@After
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public void deleteH5file() throws HDF5LibraryException {
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if (H5gid > 0)
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try {H5.H5Gclose(H5gid);} catch (Exception ex) {}
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if (H5did2 > 0)
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try {H5.H5Dclose(H5did2);} catch (Exception ex) {}
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if (H5dsid > 0)
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try {H5.H5Sclose(H5dsid);} catch (Exception ex) {}
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if (H5dsid2 > 0)
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try {H5.H5Sclose(H5dsid2);} catch (Exception ex) {}
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if (H5did1 > 0)
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try {H5.H5Dclose(H5did1);} catch (Exception ex) {}
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if (H5fid > 0)
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try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
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_deleteFile(FILENAME);
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System.out.println();
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}
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@Test
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public void testH5OcopyRefsAttr() {
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long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
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byte rbuf0[]=null , rbuf1[] = null;
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byte[] dset_data = new byte[16];
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long attribute_id = HDF5Constants.H5I_INVALID_HID;
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try {
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rbuf0 = H5.H5Rcreate(H5fid, "/G1", HDF5Constants.H5R_OBJECT, -1);
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rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
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//System.arraycopy(rbuf0, 0, dset_data, 0, 8);
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System.arraycopy(rbuf1, 0, dset_data, 8, 8);
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}
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catch (Exception ex) {
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fail("testH5OcopyRefsAttr: H5Rcreate failed");
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}
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try {
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attribute_id = H5.H5Acreate(H5did2, "A1", HDF5Constants.H5T_STD_REF_OBJ, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
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assertTrue("testH5OcopyRefsAttr.H5Acreate: ", attribute_id >= 0);
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H5.H5Awrite(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, dset_data);
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H5.H5Aclose(attribute_id);
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}
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catch (Exception ex) {
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fail("testH5OcopyRefsAttr: H5Awrite failed");
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}
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finally {
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try {H5.H5Aclose(attribute_id);} catch (Exception exx) {}
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}
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try {
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ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
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assertTrue("testH5OcopyRefsAttr.H5Pcreate: ", ocp_plist_id >= 0);
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H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
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H5.H5Ocopy(H5fid, ".", H5fid, "CPYREF", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
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}
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catch (Exception ex) {
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fail("testH5OcopyRefsAttr: H5Ocopy failed");
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}
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finally {
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try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
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}
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}
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@Test
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public void testH5OcopyRefsDatasettodiffFile() {
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byte rbuf1[] = null;
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byte[] dset_data = new byte[16];
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long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
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long dataset_id = HDF5Constants.H5I_INVALID_HID;
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long H5fid2 = HDF5Constants.H5I_INVALID_HID;
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try {
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rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
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System.arraycopy(rbuf1, 0, dset_data, 8, 8);
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dataset_id = H5.H5Dcreate(H5fid, "DSREF",
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HDF5Constants.H5T_STD_REF_OBJ, H5dsid,
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HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
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assertTrue("testH5OcopyRefsDatasettodiffFile.H5Dcreate: ", dataset_id >= 0);
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H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ,
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HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
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HDF5Constants.H5P_DEFAULT, dset_data);
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H5.H5Dclose(dataset_id);
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}
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catch (Exception ex) {
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fail("testH5OcopyRefsDatasettodiffFile: create dataset failed");
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}
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finally {
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try {H5.H5Dclose(dataset_id);} catch (Exception exx) {}
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}
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try {
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//create new file
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H5fid2 = H5.H5Fcreate("copy.h5", HDF5Constants.H5F_ACC_TRUNC,
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HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
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assertTrue("testH5OcopyRefsDatasettodiffFile.H5Fcreate: ", H5fid2 >= 0);
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H5.H5Fflush(H5fid2, HDF5Constants.H5F_SCOPE_LOCAL);
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}
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catch (Exception ex) {
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try {H5.H5Fclose(H5fid2);} catch (Exception exx) {}
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fail("testH5OcopyRefsDatasettodiffFile: H5Fcreate failed");
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}
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try {
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//create object copy property list id and set the flags.
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ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
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assertTrue("testH5OcopyRefsDatasettodiffFile.H5Pcreate: ", ocp_plist_id >= 0);
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H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
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//Perform copy function.
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H5.H5Ocopy(H5fid, ".", H5fid2, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
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}
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catch (Exception ex){
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ex.printStackTrace();
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fail("testH5OcopyRefsDatasettodiffFile: H5Ocopy failed");
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}
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finally {
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try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
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try {H5.H5Fclose(H5fid2);} catch (Exception ex) {}
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}
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_deleteFile("copy.h5");
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}
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@Test
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public void testH5OcopyRefsDatasettosameFile() {
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byte rbuf0[]=null , rbuf1[] = null;
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byte[] dset_data = new byte[16];
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long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
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long dataset_id = HDF5Constants.H5I_INVALID_HID;
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long did = HDF5Constants.H5I_INVALID_HID;
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int obj_type = -1;
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byte[] read_data = new byte[16];
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try {
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rbuf0 = H5.H5Rcreate(H5fid, "/G1", HDF5Constants.H5R_OBJECT, -1);
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rbuf1 = H5.H5Rcreate(H5fid, "DS2", HDF5Constants.H5R_OBJECT, -1);
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System.arraycopy(rbuf0, 0, dset_data, 0, 8);
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System.arraycopy(rbuf1, 0, dset_data, 8, 8);
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//Create a dataset and write object references to it.
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dataset_id = H5.H5Dcreate(H5fid, "DSREF",
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HDF5Constants.H5T_STD_REF_OBJ, H5dsid,
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HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
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assertTrue("testH5OcopyRefsDatasettosameFile.H5Dcreate: ", dataset_id >= 0);
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H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ,
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HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
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HDF5Constants.H5P_DEFAULT, dset_data);
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//Close the dataset.
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H5.H5Dclose(dataset_id);
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}
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catch (Exception ex) {
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try {H5.H5Dclose(dataset_id);} catch (Exception exx) {}
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fail("testH5OcopyRefsDatasettosameFile: create dataset failed");
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}
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try {
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ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
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assertTrue("testH5OcopyRefsDatasettosameFile.H5Pcreate: ", ocp_plist_id >= 0);
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H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
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}
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catch (Exception ex) {
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try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
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fail("testH5OcopyRefsDatasettosameFile: H5Pset_copy_object failed");
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}
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//Perform copy function.
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try {
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H5.H5Ocopy(H5fid, "DSREF", H5fid, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
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}
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catch(Exception ex) {
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try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
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fail("testH5OcopyRefsDatasettosameFile: H5Ocopy failed");
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}
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//Open the dataset that has been copied
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try {
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did = H5.H5Dopen(H5fid, "DSREF", HDF5Constants.H5P_DEFAULT);
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assertTrue("testH5OcopyRefsDatasettosameFile.H5Dopen: ", did >= 0);
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}
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catch (Exception e) {
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try {H5.H5Dclose(did);} catch (Exception exx) {}
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e.printStackTrace();
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fail("testH5OcopyRefsDatasettosameFile: H5Dopen failed");
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}
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try {
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//Read the dataset object references in the read_data buffer.
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H5.H5Dread(did, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL,HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_data);
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System.arraycopy(read_data, 0, rbuf0, 0, 8);
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System.arraycopy(read_data, 8, rbuf1, 0, 8);
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//Get the type of object the reference points to.
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obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, rbuf1);
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assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET);
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obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, rbuf0);
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assertEquals(obj_type, HDF5Constants.H5O_TYPE_GROUP);
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}
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catch (Exception ex) {
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ex.printStackTrace();
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}
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finally {
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try {H5.H5Dclose(did);} catch (Exception ex) {}
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try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
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}
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}
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// @Ignore because of JIRA HDF5-9547
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// @Test(expected = HDF5LibraryException.class)
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// public void testH5OcopyInvalidRef() throws Throwable {
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// final long _pid_ = HDF5Constants.H5P_DEFAULT;
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// long sid = HDF5Constants.H5I_INVALID_HID;
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// long did = HDF5Constants.H5I_INVALID_HID;
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// long aid = HDF5Constants.H5I_INVALID_HID;
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//
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// try {
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// sid = H5.H5Screate_simple(1, new long[] {1}, null);
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// assertTrue("testH5OcopyInvalidRef.H5Screate_simple: ", sid >= 0);
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// did = H5.H5Dcreate(H5fid, "Dataset_with_invalid_Ref", HDF5Constants.H5T_NATIVE_INT, sid, _pid_, _pid_, _pid_);
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// assertTrue("testH5OcopyInvalidRef.H5Dcreate: ", did > 0);
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// aid = H5.H5Acreate(did, "Invalid_Ref", HDF5Constants.H5T_STD_REF_OBJ, sid, _pid_, _pid_);
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// assertTrue("testH5OcopyInvalidRef.H5Acreate: ", aid > 0);
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// H5.H5Awrite(aid, HDF5Constants.H5T_STD_REF_OBJ, new long[]{-1});
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// }
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// catch (Exception ex) {
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// ex.printStackTrace();
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// }
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// finally {
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// try {H5.H5Dclose(did);} catch (Exception exx) {}
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// try {H5.H5Aclose(aid);} catch (Exception exx) {}
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// try {H5.H5Sclose(sid);} catch (Exception exx) {}
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// }
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//
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// long ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
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// assertTrue("testH5OcopyInvalidRef.H5Pcreate: ", ocp_plist_id >= 0);
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// H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
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// try {
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// H5.H5Ocopy(H5fid, "/Dataset_with_invalid_Ref", H5fid, "/Dataset_with_invalid_Ref_cp", ocp_plist_id, _pid_);
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// }
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// finally {
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// try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
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// }
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// }
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}
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