package test.hdf5lib; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import java.io.File; import ncsa.hdf.hdf5lib.H5; import ncsa.hdf.hdf5lib.HDF5Constants; import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException; import ncsa.hdf.hdf5lib.structs.H5G_info_t; import org.junit.After; import org.junit.Before; import org.junit.Test; @SuppressWarnings("all") public class TestH5G { private static final String H5_FILE = "test.h5"; private static final String H5_FILE2 = "test2.h5"; private static final String[] GROUPS = { "/G1", "/G1/G11", "/G1/G12", "/G1/G11/G111", "/G1/G11/G112", "/G1/G11/G113", "/G1/G11/G114" }; private static final String[] GROUPS2 = { "/G1", "/G1/G14", "/G1/G12", "/G1/G13", "/G1/G11"}; int H5fid = -1; int H5fid2 = -1; private final int _createGroup(int fid, String name) { int gid = -1; try { gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gcreate: " + err); } return gid; } private final int _createGroup2(int fid, String name) { int gid = -1; int gcpl = -1; try{ gcpl = H5.H5Pcreate(HDF5Constants.H5P_GROUP_CREATE); //create gcpl if (gcpl >= 0) { H5.H5Pset_link_creation_order(gcpl, HDF5Constants.H5P_CRT_ORDER_TRACKED + HDF5Constants.H5P_CRT_ORDER_INDEXED);//Set link creation order } } catch (final Exception ex) { fail("H5.H5Pcreate() failed. " + ex); } try { gid = H5.H5Gcreate(fid, name, HDF5Constants.H5P_DEFAULT, gcpl, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gcreate: " + err); } try {H5.H5Pclose(gcpl);} catch (final Exception ex) {} return gid; } private final int _openGroup(int fid, String name) { int gid = -1; try { gid = H5.H5Gopen(fid, name, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { gid = -1; err.printStackTrace(); fail("H5.H5Gopen: " + err); } return gid; } private final void _deleteFile(String filename) { File file = new File(filename); if (file.exists()) { try {file.delete();} catch (SecurityException e) {} } } @Before public void createH5file() throws HDF5LibraryException, NullPointerException { assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0); H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); H5fid2 = H5.H5Fcreate(H5_FILE2, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT); int gid = -1; for (int i = 0; i < GROUPS.length; i++) { gid = _createGroup(H5fid, GROUPS[i]); assertTrue(gid > 0); try {H5.H5Gclose(gid);} catch (Exception ex) {} } for (int i = 0; i < GROUPS2.length; i++) { gid = _createGroup2(H5fid2, GROUPS2[i]); assertTrue(gid > 0); try {H5.H5Gclose(gid);} catch (Exception ex) {} } H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL); H5.H5Fflush(H5fid2, HDF5Constants.H5F_SCOPE_LOCAL); } @After public void deleteH5file() throws HDF5LibraryException { if (H5fid > 0) { try {H5.H5Fclose(H5fid);} catch (Exception ex) {} } if (H5fid2 > 0) { try {H5.H5Fclose(H5fid2);} catch (Exception ex) {} } _deleteFile(H5_FILE); _deleteFile(H5_FILE2); } @Test public void testH5Gopen() { for (int i = 0; i < GROUPS.length; i++) { int gid = _openGroup(H5fid, GROUPS[i]); assertTrue(gid > 0); try { H5.H5Gclose(gid); } catch (Exception ex) { } } } @Test public void testH5Gget_create_plist() { int gid = -1; int pid = -1; for (int i = 0; i < GROUPS.length; i++) { gid = _openGroup(H5fid, GROUPS[i]); assertTrue(gid > 0); try { pid = H5.H5Gget_create_plist(gid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_create_plist: " + err); } assertTrue(pid > 0); try { H5.H5Gclose(gid); } catch (Exception ex) { } } } @Test public void testH5Gget_info() { H5G_info_t info = null; for (int i = 0; i < GROUPS.length; i++) { try { info = H5.H5Gget_info(H5fid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info: " + err); } assertNotNull(info); } } @Test public void testH5Gget_info_by_name() { H5G_info_t info = null; for (int i = 0; i < GROUPS.length; i++) { try { info = H5.H5Gget_info_by_name(H5fid, GROUPS[i], HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info_by_name: " + err); } assertNotNull(info); } } @Test public void testH5Gget_info_by_idx() { H5G_info_t info = null; for (int i = 0; i < 2; i++) { try { info = H5.H5Gget_info_by_idx(H5fid, "/G1", HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_INC, i, HDF5Constants.H5P_DEFAULT); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info_by_idx: " + err); } assertNotNull(info); } } @Test public void testH5Gget_obj_info_all() { H5G_info_t info = null; int gid = _openGroup(H5fid, GROUPS[0]); try { info = H5.H5Gget_info(gid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } assertNotNull(info); assertTrue("number of links is empty", info.nlinks > 0); String objNames[] = new String[(int) info.nlinks]; int objTypes[] = new int[(int) info.nlinks]; int lnkTypes[] = new int[(int) info.nlinks]; long objRefs[] = new long[(int) info.nlinks]; int names_found = 0; try { names_found = H5.H5Gget_obj_info_all(H5fid, GROUPS[0], objNames, objTypes, lnkTypes, objRefs, HDF5Constants.H5_INDEX_NAME); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_obj_info_all: " + err); } assertTrue("number found[" + names_found + "] different than expected[" + objNames.length + "]", names_found == objNames.length); for (int i = 0; i < objNames.length; i++) { assertNotNull("name #" + i + " does not exist", objNames[i]); assertTrue(objNames[i].length() > 0); } } @Test public void testH5Gget_obj_info_all_gid() { H5G_info_t info = null; int gid = _openGroup(H5fid, GROUPS[0]); try { info = H5.H5Gget_info(gid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info: " + err); } assertNotNull(info); assertTrue("number of links is empty", info.nlinks > 0); String objNames[] = new String[(int) info.nlinks]; long objRefs[] = new long[(int) info.nlinks]; int lnkTypes[] = new int[(int) info.nlinks]; int objTypes[] = new int[(int) info.nlinks]; int names_found = 0; try { names_found = H5.H5Gget_obj_info_all(gid, null, objNames, objTypes, lnkTypes, objRefs, HDF5Constants.H5_INDEX_NAME); } catch (Throwable err) { try { H5.H5Gclose(gid); } catch (Exception ex) { } err.printStackTrace(); fail("H5.H5Gget_obj_info_all: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } assertTrue("number found[" + names_found + "] different than expected[" + objNames.length + "]", names_found == objNames.length); for (int i = 0; i < objNames.length; i++) { assertNotNull("name #" + i + " does not exist", objNames[i]); assertTrue(objNames[i].length() > 0); } } @Test public void testH5Gget_obj_info_all_gid2() { H5G_info_t info = null; int gid = _openGroup(H5fid, GROUPS[1]); try { info = H5.H5Gget_info(gid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info: " + err); } assertNotNull(info); assertTrue("number of links is empty", info.nlinks > 0); String objNames[] = new String[(int) info.nlinks]; long objRefs[] = new long[(int) info.nlinks]; int lnkTypes[] = new int[(int) info.nlinks]; int objTypes[] = new int[(int) info.nlinks]; int names_found = 0; try { names_found = H5.H5Gget_obj_info_all(gid, null, objNames, objTypes, lnkTypes, objRefs, HDF5Constants.H5_INDEX_NAME); } catch (Throwable err) { try { H5.H5Gclose(gid); } catch (Exception ex) { } err.printStackTrace(); fail("H5.H5Gget_obj_info_all: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } assertTrue("number found[" + names_found + "] different than expected[" + objNames.length + "]", names_found == objNames.length); for (int i = 0; i < objNames.length; i++) { assertNotNull("name #" + i + " does not exist", objNames[i]); assertTrue(objNames[i].length() > 0); } } @Test public void testH5Gget_obj_info_max() { int gid = _openGroup(H5fid, GROUPS[0]); int groups_max_size = GROUPS.length + 1; String objNames[] = new String[groups_max_size]; int objTypes[] = new int[groups_max_size]; int lnkTypes[] = new int[groups_max_size]; long objRefs[] = new long[groups_max_size]; int names_found = 0; try { names_found = H5.H5Gget_obj_info_max(gid, objNames, objTypes, lnkTypes, objRefs, groups_max_size); } catch (Throwable err) { try { H5.H5Gclose(gid); } catch (Exception ex) { } err.printStackTrace(); fail("H5.H5Gget_obj_info_max: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } // expected number does not include root group assertTrue("number found[" + names_found + "] different than expected[" + (GROUPS.length - 1) + "]", names_found == (GROUPS.length - 1)); for (int i = 0; i < GROUPS.length-1; i++) { assertNotNull("name #"+i+" does not exist",objNames[i]); assertTrue(objNames[i].length()>0); } } @Test public void testH5Gget_obj_info_max_limit() { int gid = _openGroup(H5fid, GROUPS[0]); int groups_max_size = GROUPS.length - 3; String objNames[] = new String[groups_max_size]; int objTypes[] = new int[groups_max_size]; int lnkTypes[] = new int[groups_max_size]; long objRefs[] = new long[groups_max_size]; int names_found = 0; try { names_found = H5.H5Gget_obj_info_max(gid, objNames, objTypes, lnkTypes, objRefs, groups_max_size); } catch (Throwable err) { try { H5.H5Gclose(gid); } catch (Exception ex) { } err.printStackTrace(); fail("H5.H5Gget_obj_info_max: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } assertTrue("number found[" + names_found + "] different than expected[" + groups_max_size + "]", names_found == groups_max_size); for (int i = 0; i < objNames.length; i++) { assertNotNull("name #" + i + " does not exist", objNames[i]); assertTrue(objNames[i].length() > 0); } } @Test public void testH5Gget_obj_info_all_byIndexType() { H5G_info_t info = null; int gid = _openGroup(H5fid2, GROUPS2[0]); try { info = H5.H5Gget_info(gid); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_info: " + err); } try { H5.H5Gclose(gid); } catch (Exception ex) { } assertNotNull(info); assertTrue("number of links is empty", info.nlinks > 0); String objNames[] = new String[(int) info.nlinks]; int objTypes[] = new int[(int) info.nlinks]; int lnkTypes[] = new int[(int) info.nlinks]; long objRefs[] = new long[(int) info.nlinks]; try { H5.H5Gget_obj_info_all(H5fid2, GROUPS2[0], objNames, objTypes, lnkTypes, objRefs, HDF5Constants.H5_INDEX_CRT_ORDER); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_obj_info_all: " + err); } assertEquals("G12",objNames[1]); assertEquals("G13", objNames[2] ); assertEquals("G11", objNames[3] ); try { H5.H5Gget_obj_info_all(H5fid2, GROUPS2[0], objNames, objTypes, lnkTypes, objRefs, HDF5Constants.H5_INDEX_NAME); } catch (Throwable err) { err.printStackTrace(); fail("H5.H5Gget_obj_info_all: " + err); } assertEquals("G12",objNames[1]); assertEquals("G13", objNames[2] ); assertEquals("G14", objNames[3] ); } }