1.12 Merge Add tests for H5Ocopy of new object refs (#1339)

* Add tests for H5Ocopy of new object refs

* Correct class name

* Skip test because of issue with debug assertions

* Update reference file

* Fix object examples for new refs and spelling fixs

* Fix ref try-catch blocks
This commit is contained in:
Allen Byrne
2022-01-13 22:17:59 -06:00
committed by GitHub
parent 94fd05b974
commit a0c2b2e8d4
20 changed files with 912 additions and 505 deletions

View File

@@ -70,7 +70,7 @@ public class H5Ex_T_ObjectReference {
long group_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM0 };
byte[][] dset_data = new byte[DIM0][8];
byte[][] dset_data = new byte[DIM0][HDF5Constants.H5R_REF_BUF_SIZE];
// Create a new file using default properties.
try {
@@ -111,50 +111,58 @@ public class H5Ex_T_ObjectReference {
e.printStackTrace();
}
// Create references to the previously created objects. Passing -1
// as space_id causes this parameter to be ignored. Other values
// besides valid dataspaces result in an error.
try {
if (file_id >= 0) {
byte rbuf0[] = H5.H5Rcreate(file_id, GROUPNAME, HDF5Constants.H5R_OBJECT, -1);
byte rbuf1[] = H5.H5Rcreate(file_id, DATASETNAME2, HDF5Constants.H5R_OBJECT, -1);
for (int indx = 0; indx < 8; indx++) {
dset_data[0][indx] = rbuf0[indx];
dset_data[1][indx] = rbuf1[indx];
try {
dset_data[0] = H5.H5Rcreate_object(file_id, GROUPNAME, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
}
try {
dset_data[1] = H5.H5Rcreate_object(file_id, DATASETNAME2, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
}
}
// Create dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
try {
filespace_id = H5.H5Screate_simple(RANK, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the dataset.
try {
if ((file_id >= 0) && (filespace_id >= 0))
dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_REF, filespace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the object references to it.
try {
if (dataset_id >= 0)
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
}
catch (Exception e) {
e.printStackTrace();
catch (Exception ex) {
ex.printStackTrace();
}
// Create dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
try {
filespace_id = H5.H5Screate_simple(RANK, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the dataset.
try {
if ((file_id >= 0) && (filespace_id >= 0))
dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_REF_OBJ, filespace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the object references to it.
try {
if (dataset_id >= 0)
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data);
}
catch (Exception e) {
e.printStackTrace();
finally {
try {H5.H5Rdestroy(dset_data[1]);} catch (Exception ex) {}
try {H5.H5Rdestroy(dset_data[0]);} catch (Exception ex) {}
}
// End access to the dataset and release resources used by it.
@@ -192,140 +200,91 @@ public class H5Ex_T_ObjectReference {
int object_type = -1;
long object_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM0 };
byte[][] dset_data;
byte[][] dset_data = new byte[DIM0][HDF5Constants.H5R_REF_BUF_SIZE];
// Open an existing file.
try {
file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Open an existing dataset.
try {
if (file_id >= 0)
dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Get dataspace and allocate memory for read buffer.
try {
if (dataset_id >= 0)
dataspace_id = H5.H5Dget_space(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataspace_id >= 0)
H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Allocate array of pointers to two-dimensional arrays (the
// elements of the dataset.
dset_data = new byte[(int)dims[0]][8];
// Read the data using the default properties.
try {
if (dataset_id >= 0) {
H5.H5Dread(dataset_id, HDF5Constants.H5T_STD_REF_OBJ, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data);
}
}
catch (Exception e) {
e.printStackTrace();
}
// Output the data to the screen.
for (int indx = 0; indx < dims[0]; indx++) {
System.out.println(DATASETNAME + "[" + indx + "]:");
System.out.print(" ->");
// Open the referenced object, get its name and type.
// Open an existing dataset.
try {
if (dataset_id >= 0) {
object_id = H5.H5Rdereference(dataset_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT, dset_data[indx]);
object_type = H5.H5Rget_obj_type(dataset_id, HDF5Constants.H5R_OBJECT, dset_data[indx]);
}
String obj_name = null;
if (object_type >= 0) {
// Get the length of the name and retrieve the name.
obj_name = H5.H5Iget_name(object_id);
}
if ((object_id >= 0) && (object_type >= -1)) {
switch (H5G_obj.get(object_type)) {
case H5G_GROUP:
System.out.print("H5G_GROUP");
dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT);
try {
// Get dataspace and allocate memory for read buffer.
dataspace_id = H5.H5Dget_space(dataset_id);
H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
// Read data.
H5.H5Dread(dataset_id, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL, HDF5Constants.H5S_ALL,
HDF5Constants.H5P_DEFAULT, dset_data);
// Output the data to the screen.
for (int indx = 0; indx < dims[0]; indx++) {
System.out.println(DATASETNAME + "[" + indx + "]:");
System.out.print(" ->");
// Open the referenced object, get its name and type.
try {
if (object_id >= 0)
H5.H5Gclose(object_id);
object_id = H5.H5Ropen_object(dset_data[indx], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
try {
object_type = H5.H5Rget_obj_type3(dset_data[indx], HDF5Constants.H5R_OBJECT);
String obj_name = null;
if (object_type >= 0) {
// Get the name.
obj_name = H5.H5Iget_name(object_id);
}
if ((object_id >= 0) && (object_type >= -1)) {
switch (H5G_obj.get(object_type)) {
case H5G_GROUP:
System.out.print("H5G_GROUP");
break;
case H5G_DATASET:
System.out.print("H5G_DATASET");
break;
case H5G_TYPE:
System.out.print("H5G_TYPE");
break;
default:
System.out.print("UNHANDLED");
}
}
// Print the name.
System.out.println(": " + obj_name);
}
catch (Exception e) {
e.printStackTrace();
}
finally {
try {H5.H5Oclose(object_id);} catch (Exception e) {}
}
}
catch (Exception e) {
e.printStackTrace();
catch (Exception e4) {
e4.printStackTrace();
}
break;
case H5G_DATASET:
System.out.print("H5G_DATASET");
try {
if (object_id >= 0)
H5.H5Dclose(object_id);
finally {
try {H5.H5Rdestroy(dset_data[indx]);} catch (Exception e4) {}
}
catch (Exception e) {
e.printStackTrace();
}
break;
case H5G_TYPE:
System.out.print("H5G_TYPE");
try {
if (object_id >= 0)
H5.H5Tclose(object_id);
}
catch (Exception e) {
e.printStackTrace();
}
break;
default:
System.out.print("UNHANDLED");
}
} // end for
}
catch (Exception e3) {
e3.printStackTrace();
}
finally {
try {H5.H5Sclose(dataspace_id);} catch (Exception e3) {}
}
// Print the name.
System.out.println(": " + obj_name);
}
catch (Exception e) {
e.printStackTrace();
catch (Exception e2) {
e2.printStackTrace();
}
finally {
try {H5.H5Dclose(dataset_id);} catch (Exception e2) {}
}
}
// End access to the dataset and release resources used by it.
try {
if (dataspace_id >= 0)
H5.H5Sclose(dataspace_id);
catch (Exception e1) {
e1.printStackTrace();
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
finally {
try {H5.H5Fclose(file_id);} catch (Exception e1) {}
}
}

View File

@@ -18,7 +18,6 @@
Next, it reopens the file, dereferences the references,
and outputs the names of their targets to the screen.
************************************************************/
package examples.datatypes;
import java.util.EnumSet;
@@ -72,7 +71,7 @@ public class H5Ex_T_ObjectReferenceAttribute {
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long attribute_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM0 };
byte[][] dset_data = new byte[DIM0][8];
byte[][] dset_data = new byte[DIM0][HDF5Constants.H5R_REF_BUF_SIZE];
// Create a new file using default properties.
try {
@@ -86,7 +85,7 @@ public class H5Ex_T_ObjectReferenceAttribute {
// Create dataset with a scalar dataspace.
try {
dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR);
if (dataspace_id >= 0) {
if ((file_id >= 0) && (dataspace_id >= 0)) {
dataset_id = H5.H5Dcreate(file_id, DATASETNAME2, HDF5Constants.H5T_STD_I32LE, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
if (dataset_id >= 0)
@@ -113,64 +112,72 @@ public class H5Ex_T_ObjectReferenceAttribute {
e.printStackTrace();
}
// Create references to the previously created objects. Passing -1
// as space_id causes this parameter to be ignored. Other values
// besides valid dataspaces result in an error.
try {
if (file_id >= 0) {
byte rbuf0[] = H5.H5Rcreate(file_id, GROUPNAME, HDF5Constants.H5R_OBJECT, -1);
byte rbuf1[] = H5.H5Rcreate(file_id, DATASETNAME2, HDF5Constants.H5R_OBJECT, -1);
for (int indx = 0; indx < 8; indx++) {
dset_data[0][indx] = rbuf0[indx];
dset_data[1][indx] = rbuf1[indx];
try {
dset_data[0] = H5.H5Rcreate_object(file_id, GROUPNAME, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
}
try {
dset_data[1] = H5.H5Rcreate_object(file_id, DATASETNAME2, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
}
}
}
catch (Exception e) {
e.printStackTrace();
}
// Create dataset with a scalar dataspace to serve as the parent
// for the attribute.
try {
dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR);
if (dataspace_id >= 0) {
dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5.H5Sclose(dataspace_id);
dataspace_id = HDF5Constants.H5I_INVALID_HID;
// Create dataset with a scalar dataspace to serve as the parent
// for the attribute.
try {
dataspace_id = H5.H5Screate(HDF5Constants.H5S_SCALAR);
if (dataspace_id >= 0) {
dataset_id = H5.H5Dcreate(file_id, DATASETNAME, HDF5Constants.H5T_STD_I32LE, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
H5.H5Sclose(dataspace_id);
dataspace_id = HDF5Constants.H5I_INVALID_HID;
}
}
catch (Exception e) {
e.printStackTrace();
}
// Create dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
try {
dataspace_id = H5.H5Screate_simple(RANK, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the attribute and write the array data to it.
try {
if ((dataset_id >= 0) && (dataspace_id >= 0))
attribute_id = H5.H5Acreate(dataset_id, ATTRIBUTENAME, HDF5Constants.H5T_STD_REF, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the dataset.
try {
if (attribute_id >= 0)
H5.H5Awrite(attribute_id, HDF5Constants.H5T_STD_REF, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
}
catch (Exception e) {
e.printStackTrace();
catch (Exception ex) {
ex.printStackTrace();
}
// Create dataspace. Setting maximum size to NULL sets the maximum
// size to be the current size.
try {
dataspace_id = H5.H5Screate_simple(RANK, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Create the attribute and write the array data to it.
try {
if ((dataset_id >= 0) && (dataspace_id >= 0))
attribute_id = H5.H5Acreate(dataset_id, ATTRIBUTENAME, HDF5Constants.H5T_STD_REF_OBJ, dataspace_id,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Write the dataset.
try {
if (attribute_id >= 0)
H5.H5Awrite(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, dset_data);
}
catch (Exception e) {
e.printStackTrace();
finally {
try {H5.H5Rdestroy(dset_data[1]);} catch (Exception ex) {}
try {H5.H5Rdestroy(dset_data[0]);} catch (Exception ex) {}
}
// End access to the dataset and release resources used by it.
@@ -190,7 +197,6 @@ public class H5Ex_T_ObjectReferenceAttribute {
e.printStackTrace();
}
// Terminate access to the data space.
try {
if (dataspace_id >= 0)
H5.H5Sclose(dataspace_id);
@@ -207,7 +213,6 @@ public class H5Ex_T_ObjectReferenceAttribute {
catch (Exception e) {
e.printStackTrace();
}
}
private static void ReadDataset() {
@@ -218,158 +223,102 @@ public class H5Ex_T_ObjectReferenceAttribute {
int object_type = -1;
long object_id = HDF5Constants.H5I_INVALID_HID;
long[] dims = { DIM0 };
byte[][] dset_data;
byte[][] dset_data = new byte[DIM0][HDF5Constants.H5R_REF_BUF_SIZE];
// Open an existing file.
try {
file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Open an existing dataset.
try {
if (file_id >= 0)
dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataset_id >= 0)
attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
}
catch (Exception e) {
e.printStackTrace();
}
// Get dataspace and allocate memory for read buffer.
try {
if (attribute_id >= 0)
dataspace_id = H5.H5Aget_space(attribute_id);
}
catch (Exception e) {
e.printStackTrace();
}
try {
if (dataspace_id >= 0)
H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
}
catch (Exception e) {
e.printStackTrace();
}
// Allocate array of pointers to two-dimensional arrays (the
// elements of the dataset.
dset_data = new byte[(int) dims[0]][8];
// Read data.
try {
if (attribute_id >= 0)
H5.H5Aread(attribute_id, HDF5Constants.H5T_STD_REF_OBJ, dset_data);
}
catch (Exception e) {
e.printStackTrace();
}
// Output the data to the screen.
for (int indx = 0; indx < dims[0]; indx++) {
System.out.println(ATTRIBUTENAME + "[" + indx + "]:");
System.out.print(" ->");
// Open the referenced object, get its name and type.
// Open an existing dataset.
try {
if (dataset_id >= 0) {
object_id = H5.H5Rdereference(dataset_id, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5R_OBJECT, dset_data[indx]);
object_type = H5.H5Rget_obj_type(dataset_id, HDF5Constants.H5R_OBJECT, dset_data[indx]);
}
String obj_name = null;
if (object_type >= 0) {
// Get the length of the name and retrieve the name.
obj_name = H5.H5Iget_name(object_id);
}
if ((object_id >= 0) && (object_type >= -1)) {
switch (H5G_obj.get(object_type)) {
case H5G_GROUP:
System.out.print("H5G_GROUP");
try {
if (object_id >= 0)
H5.H5Gclose(object_id);
}
catch (Exception e) {
e.printStackTrace();
}
break;
case H5G_DATASET:
System.out.print("H5G_DATASET");
try {
if (object_id >= 0)
H5.H5Dclose(object_id);
}
catch (Exception e) {
e.printStackTrace();
}
break;
case H5G_TYPE:
System.out.print("H5G_TYPE");
try {
if (object_id >= 0)
H5.H5Tclose(object_id);
}
catch (Exception e) {
e.printStackTrace();
}
break;
default:
System.out.print("UNHANDLED");
dataset_id = H5.H5Dopen(file_id, DATASETNAME, HDF5Constants.H5P_DEFAULT);
try {
attribute_id = H5.H5Aopen_by_name(dataset_id, ".", ATTRIBUTENAME, HDF5Constants.H5P_DEFAULT,
HDF5Constants.H5P_DEFAULT);
// Get dataspace and allocate memory for read buffer.
try {
dataspace_id = H5.H5Aget_space(attribute_id);
H5.H5Sget_simple_extent_dims(dataspace_id, dims, null);
// Read data.
H5.H5Aread(attribute_id, HDF5Constants.H5T_STD_REF, dset_data);
// Output the data to the screen.
for (int indx = 0; indx < dims[0]; indx++) {
System.out.println(ATTRIBUTENAME + "[" + indx + "]:");
System.out.print(" ->");
// Open the referenced object, get its name and type.
try {
object_id = H5.H5Ropen_object(dset_data[indx], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
try {
object_type = H5.H5Rget_obj_type3(dset_data[indx], HDF5Constants.H5R_OBJECT);
String obj_name = null;
if (object_type >= 0) {
// Get the name.
obj_name = H5.H5Iget_name(object_id);
}
if ((object_id >= 0) && (object_type >= -1)) {
switch (H5G_obj.get(object_type)) {
case H5G_GROUP:
System.out.print("H5G_GROUP");
break;
case H5G_DATASET:
System.out.print("H5G_DATASET");
break;
case H5G_TYPE:
System.out.print("H5G_TYPE");
break;
default:
System.out.print("UNHANDLED");
}
}
// Print the name.
System.out.println(": " + obj_name);
}
catch (Exception e) {
e.printStackTrace();
}
finally {
try {H5.H5Oclose(object_id);} catch (Exception e) {}
}
}
catch (Exception e5) {
e5.printStackTrace();
}
finally {
try {H5.H5Rdestroy(dset_data[indx]);} catch (Exception e5) {}
}
} // end for
}
catch (Exception e4) {
e4.printStackTrace();
}
finally {
try {H5.H5Sclose(dataspace_id);} catch (Exception e3) {}
}
}
// Print the name.
System.out.println(": " + obj_name);
catch (Exception e3) {
e3.printStackTrace();
}
finally {
try {H5.H5Aclose(attribute_id);} catch (Exception e4) {}
}
}
catch (Exception e) {
e.printStackTrace();
catch (Exception e2) {
e2.printStackTrace();
}
finally {
try {H5.H5Dclose(dataset_id);} catch (Exception e2) {}
}
}
// End access to the dataset and release resources used by it.
try {
if (attribute_id >= 0)
H5.H5Aclose(attribute_id);
catch (Exception e1) {
e1.printStackTrace();
}
catch (Exception e) {
e.printStackTrace();
finally {
try {H5.H5Fclose(file_id);} catch (Exception e1) {}
}
try {
if (dataset_id >= 0)
H5.H5Dclose(dataset_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Terminate access to the data space.
try {
if (dataspace_id >= 0)
H5.H5Sclose(dataspace_id);
}
catch (Exception e) {
e.printStackTrace();
}
// Close the file.
try {
if (file_id >= 0)
H5.H5Fclose(file_id);
}
catch (Exception e) {
e.printStackTrace();
}
}
public static void main(String[] args) {