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HDFFV-10876 Merge from develop

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This commit is contained in:
Allen Byrne
2019-12-08 14:00:04 -06:00
parent dbd6fb0ba6
commit 310b42e35a
93 changed files with 6249 additions and 3916 deletions
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417
java/test/TestH5R.java
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@@ -14,6 +14,7 @@
package test;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
@@ -24,9 +25,11 @@ import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;
import hdf.hdf5lib.exceptions.HDF5Exception;
import hdf.hdf5lib.exceptions.HDF5LibraryException;
import hdf.hdf5lib.exceptions.HDF5FunctionArgumentException;
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;
@@ -42,6 +45,8 @@ public class TestH5R {
long H5gid = -1;
long H5did2 = -1;
long[] H5dims = { DIM_X, DIM_Y };
int[][] dset_data = new int[DIM_X][DIM_Y];
int FILLVAL = 99;
private final void _deleteFile(String filename) {
File file = null;
@@ -51,8 +56,9 @@ public class TestH5R {
catch (Throwable err) {}
if (file.exists()) {
try {file.delete();} catch (SecurityException e) {}
try {file.delete();} catch (SecurityException e) {e.printStackTrace();}
}
assertFalse("TestH5R._deleteFile file still exists ", file.exists());
}
private final long _createDataset(long fid, long dsid, String name, long dapl) {
@@ -66,7 +72,7 @@ public class TestH5R {
err.printStackTrace();
fail("H5.H5Dcreate: " + err);
}
assertTrue("TestH5R._createDataset: ",did > 0);
assertTrue("TestH5R._createDataset: ", did > 0);
return did;
}
@@ -100,6 +106,21 @@ public class TestH5R {
H5did2 = _createDataset(H5gid, H5dsid, "dset2", HDF5Constants.H5P_DEFAULT);
H5did = _createDataset(H5fid, H5dsid, "dset", HDF5Constants.H5P_DEFAULT);
// Initialize the dataset.
for (int indx = 0; indx < DIM_X; indx++)
for (int jndx = 0; jndx < DIM_Y; jndx++)
dset_data[indx][jndx] = FILLVAL;
try {
if (H5did >= 0)
H5.H5Dwrite(H5did, HDF5Constants.H5T_NATIVE_INT,
HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data[0]);
}
catch (Exception e) {
e.printStackTrace();
}
}
catch (Throwable err) {
err.printStackTrace();
@@ -129,13 +150,15 @@ public class TestH5R {
System.out.println();
}
@Test
// Test v1.8 APIs params
@Ignore
public void testH5Rget_name() {
long loc_id=H5fid;
int ref_type=HDF5Constants.H5R_OBJECT;
long ret_val=-1;
byte[] ref=null;
String[] name= {""};
long loc_id = H5fid;
int ref_type = HDF5Constants.H5R_OBJECT;
long ret_val = -1;
byte[] ref = null;
String[] name = {""};
String objName = "/dset";
try {
@@ -158,13 +181,13 @@ public class TestH5R {
assertTrue("The name of the object: ", objName.equals(name[0]));
}
@Test
@Ignore
public void testH5Rget_obj_type2() {
int ref_type=HDF5Constants.H5R_OBJECT;
byte[] ref=null;
String objName = "/dset";
int obj_type = -1;;
int obj_type = -1;
try {
ref = H5.H5Rcreate(H5fid, objName, ref_type, -1);
@@ -183,7 +206,7 @@ public class TestH5R {
assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET);
}
@Test
@Ignore
public void testH5Rcreate_refobj() {
byte[] ref = null;
@@ -197,7 +220,7 @@ public class TestH5R {
assertNotNull(ref);
}
@Test
@Ignore
public void testH5Rcreate_regionrefobj() {
byte[] ref = null;
try {
@@ -210,7 +233,7 @@ public class TestH5R {
assertNotNull(ref);
}
@Test
@Ignore
public void testH5Rdereference() {
byte[] ref1 = null;
byte[] ref2 = null;
@@ -226,8 +249,8 @@ public class TestH5R {
group_id= H5.H5Rdereference(H5gid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT, ref2);
assertNotNull(ref1);
assertNotNull(ref2);
assertTrue(dataset_id>=0);
assertTrue(group_id>=0);
assertTrue(dataset_id >= 0);
assertTrue(group_id >= 0);
}
catch (Throwable err) {
err.printStackTrace();
@@ -239,7 +262,7 @@ public class TestH5R {
}
}
@Test
@Ignore
public void testH5Rget_region() {
byte[] ref = null;
long dsid = -1;
@@ -247,7 +270,7 @@ public class TestH5R {
ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, H5dsid);
dsid = H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref);
assertNotNull(ref);
assertTrue(dsid>=0);
assertTrue(dsid >= 0);
}
catch (Throwable err) {
err.printStackTrace();
@@ -258,70 +281,70 @@ public class TestH5R {
}
}
@Test(expected = IllegalArgumentException.class)
@Ignore//(expected = IllegalArgumentException.class)
public void testH5Rget_name_Invalidreftype() throws Throwable {
byte[] ref = null;
String[] name= {""};
String[] name = {""};
ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_OBJECT, -1);
H5.H5Rget_name(H5fid, HDF5Constants.H5R_DATASET_REGION, ref, name, 16);
}
@Test(expected = NullPointerException.class)
@Ignore//(expected = NullPointerException.class)
public void testH5Rget_name_NULLreference() throws Throwable {
byte[] ref = null;
String[] name= {""};
String[] name = {""};
H5.H5Rget_name(H5fid, HDF5Constants.H5R_OBJECT, ref, name, 16);
}
@Test(expected = HDF5LibraryException.class)
@Ignore//(expected = HDF5LibraryException.class)
public void testH5Rget_obj_type2_Invalidreftype() throws Throwable {
byte[] ref = null;
ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_OBJECT, -1);
H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_DATASET_REGION, ref);
}
@Test(expected = HDF5LibraryException.class)
@Ignore//(expected = HDF5LibraryException.class)
public void testH5Rcreate_InvalidObjectName() throws Throwable {
H5.H5Rcreate(H5fid, "/GROUPS", HDF5Constants.H5R_OBJECT, -1);
byte[] ref=H5.H5Rcreate(H5fid, "/GROUPS", HDF5Constants.H5R_OBJECT, -1);
}
@Test(expected = HDF5LibraryException.class)
@Ignore//(expected = HDF5LibraryException.class)
public void testH5Rcreate_Invalidspace_id() throws Throwable {
H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, -1);
byte[] ref=H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_DATASET_REGION, -1);
}
@Test(expected = IllegalArgumentException.class)
@Ignore//(expected = IllegalArgumentException.class)
public void testH5Rcreate_Invalidreftype() throws Throwable {
H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_BADTYPE, -1);
byte[] ref=H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_BADTYPE, -1);
}
@Test(expected = IllegalArgumentException.class)
@Ignore//(expected = IllegalArgumentException.class)
public void testH5Rgetregion_Invalidreftype() throws Throwable {
byte[] ref = null;
ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_OBJECT, H5dsid);
H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref);
}
@Test(expected = IllegalArgumentException.class)
@Ignore//(expected = IllegalArgumentException.class)
public void testH5Rgetregion_Badreferencetype() throws Throwable {
byte[] ref = null;
ref = H5.H5Rcreate(H5fid, "/dset", HDF5Constants.H5R_OBJECT, H5dsid);
H5.H5Rget_region(H5fid, HDF5Constants.H5R_OBJECT, ref);
}
@Test(expected = NullPointerException.class)
@Ignore//(expected = NullPointerException.class)
public void testH5Rgetregion_Nullreference() throws Throwable {
byte[] ref = null;
H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref);
}
@Test(expected = NullPointerException.class)
@Ignore//(expected = NullPointerException.class)
public void testH5Rdereference_Nullreference() throws Throwable {
byte[] ref = null;
H5.H5Rdereference(H5did2, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT, ref);
}
@Test(expected = IllegalArgumentException.class)
@Ignore//(expected = IllegalArgumentException.class)
public void testH5Rdereference_Invalidreference() throws Throwable {
byte[] ref1 = null;
byte[] ref2 = null;
@@ -330,4 +353,332 @@ public class TestH5R {
H5.H5Rdereference(H5gid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT, ref1);
}
// Test v1.12 APIs params
@Test
public void testH5Rget_object() {
int ref_type = HDF5Constants.H5R_OBJECT2;
long ret_val = -1;
byte[] ref = null;
String name = "";
String objName = "/dset";
try {
ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Rcreate_object " + err);
}
try {
ret_val = H5.H5Rget_type(ref);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Rget_type: " + err);
}
assertTrue("testH5Rget_object: H5Rget_type", ret_val == ref_type);
try {
name = H5.H5Rget_file_name(ref);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Rget_file_name: " + err);
}
assertTrue("testH5Rget_object: H5Rget_file_name", H5_FILE.equals(name));
try {
name = H5.H5Rget_obj_name(ref, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Rget_obj_name: " + err);
}
assertTrue("The name of the object: ", objName.equals(name));
}
@Test
public void testH5Rget_obj_type3() {
int obj_type = -1;
byte[] ref = null;
String objName = "/dset";
try {
ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_obj_type3: H5Rcreate_object " + err);
}
try {
obj_type = H5.H5Rget_obj_type3(ref, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_obj_type3: H5.H5Rget_obj_type3: " + err);
}
assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET);
}
@Test
public void testH5Rcreate_regionref_object() {
byte[] ref = null;
String objName = "/dset";
long start[] = {2,2}; // Starting location of hyperslab
long stride[] = {1,1}; // Stride of hyperslab
long count[] = {1,1}; // Element count of hyperslab
long block[] = {3,3}; // Block size of hyperslab
// Select 3x3 hyperslab for reference
try {
H5.H5Sselect_hyperslab(H5dsid, HDF5Constants.H5S_SELECT_SET, start, stride, count, block);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Sselect_hyperslab " + err);
}
try {
ref = H5.H5Rcreate_region(H5fid, objName, H5dsid, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5Rget_object: H5Rcreate_region " + err);
}
assertNotNull(ref);
}
// These tests need to be updated with new APIs
// @Test//
// public void testH5Rget_group() {
// long loc_id = H5fid;
// int ref_type = HDF5Constants.H5R_OBJECT2;
// long ret_val = -1;
// byte[] ref = null;
// String name = "";
// String objName = "/dset";
//
// try {
// ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("testH5Rget_object: H5Rcreate_object " + err);
// }
// try {
// dataset_id= H5.H5Rdereference(H5fid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_DATASET_REGION, ref1);
//
// //Create reference on group
// ref2 = H5.H5Rcreate(H5gid, "/Group1", HDF5Constants.H5R_OBJECT, -1);
// group_id= H5.H5Rdereference(H5gid, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT, ref2);
// assertNotNull(ref1);
// assertNotNull(ref2);
// assertTrue(dataset_id >= 0);
// assertTrue(group_id >= 0);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("TestH5Rdereference " + err);
// }
// finally {
// try {H5.H5Dclose(dataset_id);} catch (Exception ex) {}
// try {H5.H5Gclose(group_id);} catch (Exception ex) {}
// }
// }
// @Test//
// public void testH5Rget_region_dataset() {
// long loc_id = H5fid;
// int ref_type = HDF5Constants.H5R_OBJECT2;
// long ret_val = -1;
// byte[] ref = null;
// String name = "";
// String objName = "/dset";
//
// try {
// ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("testH5Rget_object: H5Rcreate_object " + err);
// }
// try {
// dsid = H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref);
// assertNotNull(ref);
// assertTrue(dsid >= 0);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("TestH5Rget_region: " + err);
// }
// finally {
// try {H5.H5Sclose(dsid);} catch (Exception ex) {}
// }
// }
// @Test//
// public void testH5Rget_attr() {
// long loc_id = H5fid;
// int ref_type = HDF5Constants.H5R_OBJECT2;
// long ret_val = -1;
// byte[] ref = null;
// String name = "";
// String objName = "/dset";
//
// try {
// ref = H5.H5Rcreate_object(H5fid, objName, HDF5Constants.H5P_DEFAULT);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("testH5Rget_object: H5Rcreate_object " + err);
// }
// try {
// dsid = H5.H5Rget_region(H5fid, HDF5Constants.H5R_DATASET_REGION, ref);
// assertNotNull(ref);
// assertTrue(dsid >= 0);
// }
// catch (Throwable err) {
// err.printStackTrace();
// fail("TestH5Rget_region: " + err);
// }
// finally {
// try {H5.H5Sclose(dsid);} catch (Exception ex) {}
// }
// }
// Test parameters to H5Rcreate_object
@Test(expected = NullPointerException.class)
public void testH5Rcreate_object_Nullname() throws Throwable {
String name = null;
H5.H5Rcreate_object(H5fid, name, HDF5Constants.H5P_DEFAULT);
}
@Test(expected = HDF5FunctionArgumentException.class)
public void testH5Rget_name_Invalidloc() throws Throwable {
String name= "";
H5.H5Rcreate_object(-1, name, HDF5Constants.H5P_DEFAULT);
}
// Test parameters to H5Rcreate_region
@Test(expected = NullPointerException.class)
public void testH5Rcreate_region_Nullname() throws Throwable {
String name = null;
H5.H5Rcreate_region(H5fid, name, -1, HDF5Constants.H5P_DEFAULT);
}
@Test(expected = HDF5FunctionArgumentException.class)
public void testH5Rcreate_region_Invalidloc() throws Throwable {
String name= "";
H5.H5Rcreate_region(-1, name, -1, HDF5Constants.H5P_DEFAULT);
}
// Test parameters to H5Rcreate_attr
@Test(expected = NullPointerException.class)
public void testH5Rcreate_attr_Nullname() throws Throwable {
String name = null;
String attrname = "";
H5.H5Rcreate_attr(H5fid, name, attrname, HDF5Constants.H5P_DEFAULT);
}
@Test(expected = NullPointerException.class)
public void testH5Rcreate_attr_Nullattrname() throws Throwable {
String name = "";
String attrname = null;
H5.H5Rcreate_attr(H5fid, name, attrname, HDF5Constants.H5P_DEFAULT);
}
@Test(expected = HDF5FunctionArgumentException.class)
public void testH5Rcreate_attr_Invalidloc() throws Throwable {
String name= "";
String attrname= "";
H5.H5Rcreate_attr(-1, name, attrname, HDF5Constants.H5P_DEFAULT);
}
// Test parameters to H5Rdestroy
@Test(expected = NullPointerException.class)
public void testH5Rdestroy_Nullref() throws Throwable {
byte[] ref = null;
H5.H5Rdestroy(ref);
}
// Test parameters to H5Rget_type
@Test(expected = NullPointerException.class)
public void testH5Rget_type_Nullref() throws Throwable {
byte[] ref = null;
H5.H5Rget_type(ref);
}
// Test parameters to H5Requal
@Test(expected = NullPointerException.class)
public void testH5Requal_Nullref1() throws Throwable {
byte[] ref1 = null;
byte[] ref2 = {0,0,0,0};
H5.H5Requal(ref1, ref2);
}
@Test(expected = NullPointerException.class)
public void testH5Requal_Nullref2() throws Throwable {
byte[] ref1 = {0,0,0,0};
byte[] ref2 = null;
H5.H5Requal(ref1, ref2);
}
// Test parameters to H5Rcopy
@Test(expected = NullPointerException.class)
public void testH5Rcopy_Nullref1() throws Throwable {
byte[] ref1 = null;
byte[] ref2 = H5.H5Rcopy(ref1);
}
// Test parameters to H5Ropen_object
@Test(expected = NullPointerException.class)
public void testH5Ropen_object_Nullref() throws Throwable {
byte[] ref = null;
H5.H5Ropen_object(ref, -1, -1);
}
// Test parameters to H5Ropen_region
@Test(expected = NullPointerException.class)
public void testH5Ropen_region_Nullref() throws Throwable {
byte[] ref = null;
H5.H5Ropen_region(ref, -1, -1);
}
// Test parameters to H5Ropen_attr
@Test(expected = NullPointerException.class)
public void testH5Ropen_attr_Nullref() throws Throwable {
byte[] ref = null;
H5.H5Ropen_attr(ref, -1, -1);
}
// Test parameters to H5Rget_obj_type3
@Test(expected = NullPointerException.class)
public void testH5Rget_obj_type3_Nullref() throws Throwable {
byte[] ref = null;
H5.H5Rget_obj_type3(ref, -1);
}
// Test parameters to H5Rget_file_name
@Test(expected = NullPointerException.class)
public void testH5Rget_file_name_Nullref() throws Throwable {
byte[] ref = null;
H5.H5Rget_file_name(ref);
}
// Test parameters to H5Rget_obj_name
@Test(expected = NullPointerException.class)
public void testH5Rget_obj_name_Nullref() throws Throwable {
byte[] ref = null;
H5.H5Rget_obj_name(ref, -1);
}
// Test parameters to H5Rget_attr_name
@Test(expected = NullPointerException.class)
public void testH5Rget_attr_name_Nullref() throws Throwable {
byte[] ref = null;
H5.H5Rget_attr_name(ref);
}
}