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Add java to format source (#1690)

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This commit is contained in:
Allen Byrne
2022-04-25 20:32:50 -05:00
committed by GitHub
parent d19d9b4c8a
commit 41a36efde1
155 changed files with 12051 additions and 9135 deletions
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349
java/test/TestH5Ocopy.java
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@@ -31,20 +31,22 @@ import org.junit.Test;
import org.junit.rules.TestName;
public class TestH5Ocopy {
@Rule public TestName testname = new TestName();
@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 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) {
private final void _deleteFile(String filename)
{
File file = new File(filename);
if (file.exists()) {
@@ -57,94 +59,119 @@ public class TestH5Ocopy {
}
}
private final long _createDataset(long fid, long dsid, String name, long dapl) {
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);
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);
assertTrue("TestH5O._createDataset: ", did >= 0);
return did;
}
private final long _createGroup(long fid, String name) {
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);
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);
assertTrue("TestH5O._createGroup: ", gid >= 0);
return gid;
}
@Before
public void createH5file()
throws NullPointerException, HDF5Exception {
assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0);
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);
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);
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 {
public void deleteH5file() throws HDF5LibraryException
{
if (H5gid > 0)
try {H5.H5Gclose(H5gid);} catch (Exception ex) {}
try {
H5.H5Gclose(H5gid);
}
catch (Exception ex) {
}
if (H5did2 > 0)
try {H5.H5Dclose(H5did2);} catch (Exception ex) {}
try {
H5.H5Dclose(H5did2);
}
catch (Exception ex) {
}
if (H5dsid > 0)
try {H5.H5Sclose(H5dsid);} catch (Exception ex) {}
try {
H5.H5Sclose(H5dsid);
}
catch (Exception ex) {
}
if (H5dsid2 > 0)
try {H5.H5Sclose(H5dsid2);} catch (Exception ex) {}
try {
H5.H5Sclose(H5dsid2);
}
catch (Exception ex) {
}
if (H5did1 > 0)
try {H5.H5Dclose(H5did1);} catch (Exception ex) {}
try {
H5.H5Dclose(H5did1);
}
catch (Exception ex) {
}
if (H5fid > 0)
try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
try {
H5.H5Fclose(H5fid);
}
catch (Exception ex) {
}
_deleteFile(FILENAME);
System.out.println();
}
@Test
public void testH5OcopyRefsAttr() {
public void testH5OcopyRefsAttr()
{
long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
byte rbuf0[]=null , rbuf1[] = null;
byte[] dset_data = new byte[16];
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(rbuf0, 0, dset_data, 0, 8);
System.arraycopy(rbuf1, 0, dset_data, 8, 8);
}
catch (Exception ex) {
@@ -152,7 +179,8 @@ public class TestH5Ocopy {
}
try {
attribute_id = H5.H5Acreate(H5did2, "A1", HDF5Constants.H5T_STD_REF_OBJ, H5dsid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
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);
@@ -162,7 +190,11 @@ public class TestH5Ocopy {
fail("testH5OcopyRefsAttr: H5Awrite failed");
}
finally {
try {H5.H5Aclose(attribute_id);} catch (Exception exx) {}
try {
H5.H5Aclose(attribute_id);
}
catch (Exception exx) {
}
}
try {
@@ -172,82 +204,103 @@ public class TestH5Ocopy {
H5.H5Ocopy(H5fid, ".", H5fid, "CPYREF", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
}
catch (Exception ex) {
fail("testH5OcopyRefsAttr: H5Ocopy failed");
fail("testH5OcopyRefsAttr: H5Ocopy failed");
}
finally {
try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
try {
H5.H5Pclose(ocp_plist_id);
}
catch (Exception ex) {
}
}
}
@Test
public void testH5OcopyRefsDatasettodiffFile() {
byte rbuf1[] = null;
byte[] dset_data = new byte[16];
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;
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);
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.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 {
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);
// 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) {}
try {
H5.H5Fclose(H5fid2);
}
catch (Exception exx) {
}
fail("testH5OcopyRefsDatasettodiffFile: H5Fcreate failed");
}
try {
//create object copy property list id and set the flags.
// 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.
// Perform copy function.
H5.H5Ocopy(H5fid, ".", H5fid2, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
}
catch (Exception ex){
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) {}
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];
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];
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);
@@ -255,19 +308,22 @@ public class TestH5Ocopy {
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);
// 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.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) {}
try {
H5.H5Dclose(dataset_id);
}
catch (Exception exx) {
}
fail("testH5OcopyRefsDatasettosameFile: create dataset failed");
}
@@ -277,37 +333,50 @@ public class TestH5Ocopy {
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) {}
try {
H5.H5Pclose(ocp_plist_id);
}
catch (Exception exx) {
}
fail("testH5OcopyRefsDatasettosameFile: H5Pset_copy_object failed");
}
//Perform copy function.
// 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) {}
catch (Exception ex) {
try {
H5.H5Pclose(ocp_plist_id);
}
catch (Exception exx) {
}
fail("testH5OcopyRefsDatasettosameFile: H5Ocopy failed");
}
//Open the dataset that has been copied
// 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) {}
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);
// 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.
// 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);
@@ -318,46 +387,54 @@ public class TestH5Ocopy {
ex.printStackTrace();
}
finally {
try {H5.H5Dclose(did);} catch (Exception ex) {}
try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
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 = 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) {}
// }
// }
}
// @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) {}
// }
// }
}