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Develop java newrefs fixes for obj ref datasets (#1354)

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Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
This commit is contained in:
Allen Byrne
2022-01-18 14:02:53 -06:00
committed by GitHub
co-authored by github-actions Dana Robinson
parent 2f34c433dc
commit 8dc72928b8
3 changed files with 210 additions and 252 deletions
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java/examples/datatypes/H5Ex_T_ObjectReference.java
+69 -96
View File
@@ -205,113 +205,86 @@ public class H5Ex_T_ObjectReference {
// 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();
}
// Read data.
try {
if (dataset_id >= 0) {
H5.H5Dread(dataset_id, HDF5Constants.H5T_STD_REF, 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.H5Ropen_object(dset_data[indx], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
object_type = H5.H5Rget_obj_type(dataset_id, HDF5Constants.H5R_OBJECT, dset_data[indx]);
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 {
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 e4) {
e4.printStackTrace();
}
finally {
try {H5.H5Rdestroy(dset_data[indx]);} catch (Exception e4) {}
}
} // end for
}
String obj_name = null;
if (object_type >= 0) {
// Get the name.
obj_name = H5.H5Iget_name(object_id);
catch (Exception e3) {
e3.printStackTrace();
}
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");
}
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.H5Oclose(object_id);} catch (Exception ex) {}
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) {}
}
}
java/examples/datatypes/H5Ex_T_ObjectReferenceAttribute.java
+81 -115
View File
@@ -85,7 +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)
@@ -197,7 +197,6 @@ public class H5Ex_T_ObjectReferenceAttribute {
e.printStackTrace();
}
// Terminate access to the data space.
try {
if (dataspace_id >= 0)
H5.H5Sclose(dataspace_id);
@@ -229,129 +228,96 @@ public class H5Ex_T_ObjectReferenceAttribute {
// 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();
}
// Read data.
try {
if (attribute_id >= 0)
H5.H5Aread(attribute_id, HDF5Constants.H5T_STD_REF, 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.H5Ropen_object(dset_data[indx], HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
object_type = H5.H5Rget_obj_type(dataset_id, HDF5Constants.H5R_OBJECT, dset_data[indx]);
}
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");
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.H5Oclose(object_id);} catch (Exception ex) {}
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();
}
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();
finally {
try {H5.H5Fclose(file_id);} catch (Exception e1) {}
}
}
java/test/TestH5Ocopy.java
+60 -41
View File
@@ -136,18 +136,16 @@ public class TestH5Ocopy {
@Test
public void testH5OcopyRefsAttr() {
long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
byte[][] dset_data = null;
byte[][] read_data = null;
byte[][] dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE];
long attribute_id = HDF5Constants.H5I_INVALID_HID;
try {
dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE];
try {
dset_data[0] = H5.H5Rcreate_object(H5fid, "/G1", HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5OcopyInvalidRef: H5Rcreate_object " + err);
fail("testH5OcopyRefsAttr: H5Rcreate_object " + err);
}
try {
@@ -155,7 +153,7 @@ public class TestH5Ocopy {
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5OcopyInvalidRef: H5Rcreate_object " + err);
fail("testH5OcopyRefsAttr: H5Rcreate_object " + err);
}
try {
@@ -196,25 +194,30 @@ public class TestH5Ocopy {
@Test
public void testH5OcopyRefsDatasettodiffFile() {
byte[][] dset_data = null;
byte[][] read_data = null;
byte[][] dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE];
long ocp_plist_id = HDF5Constants.H5I_INVALID_HID;
long dataset_id = HDF5Constants.H5I_INVALID_HID;
long H5fid2 = HDF5Constants.H5I_INVALID_HID;
try {
dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE];
try {
dset_data[0] = H5.H5Rcreate_object(H5fid, "/G1", HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5OcopyRefsDatasettodiffFile: H5Rcreate_object " + err);
}
try {
dset_data[1] = H5.H5Rcreate_object(H5fid, "DS2", HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5OcopyInvalidRef: H5Rcreate_object " + err);
fail("testH5OcopyRefsDatasettodiffFile: H5Rcreate_object " + err);
}
try {
dataset_id = H5.H5Dcreate(H5fid, "DSREF",
HDF5Constants.H5T_STD_REF_OBJ, H5dsid,
HDF5Constants.H5T_STD_REF, H5dsid,
HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
assertTrue("testH5OcopyRefsDatasettodiffFile.H5Dcreate: ", dataset_id >= 0);
H5.H5Dwrite(dataset_id, HDF5Constants.H5T_STD_REF,
@@ -233,6 +236,7 @@ public class TestH5Ocopy {
ex.printStackTrace();
}
finally {
try {H5.H5Rdestroy(dset_data[0]);} catch (Exception ex) {}
try {H5.H5Rdestroy(dset_data[1]);} catch (Exception ex) {}
}
@@ -270,21 +274,20 @@ public class TestH5Ocopy {
@Test
public void testH5OcopyRefsDatasettosameFile() {
byte[][] dset_data = null;
byte[][] read_data = null;
byte[][] dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE];
byte[][] read_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE];
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;
try {
dset_data = new byte[2][HDF5Constants.H5R_REF_BUF_SIZE];
try {
dset_data[0] = H5.H5Rcreate_object(H5fid, "/G1", HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5OcopyInvalidRef: H5Rcreate_object " + err);
fail("testH5OcopyRefsDatasettosameFile: H5Rcreate_object " + err);
}
try {
@@ -292,7 +295,7 @@ public class TestH5Ocopy {
}
catch (Throwable err) {
err.printStackTrace();
fail("testH5OcopyInvalidRef: H5Rcreate_object " + err);
fail("testH5OcopyRefsDatasettosameFile: H5Rcreate_object " + err);
}
try {
@@ -308,9 +311,11 @@ public class TestH5Ocopy {
H5.H5Dclose(dataset_id);
}
catch (Exception ex) {
try {H5.H5Dclose(dataset_id);} catch (Exception exx) {}
fail("testH5OcopyRefsDatasettosameFile: create dataset failed");
}
finally {
try {H5.H5Dclose(dataset_id);} catch (Exception exx) {}
}
}
catch (Exception ex) {
ex.printStackTrace();
@@ -324,49 +329,63 @@ public class TestH5Ocopy {
ocp_plist_id = H5.H5Pcreate(HDF5Constants.H5P_OBJECT_COPY);
assertTrue("testH5OcopyRefsDatasettosameFile.H5Pcreate: ", ocp_plist_id >= 0);
H5.H5Pset_copy_object(ocp_plist_id, HDF5Constants.H5O_COPY_EXPAND_REFERENCE_FLAG);
//Perform copy function.
try {
H5.H5Ocopy(H5fid, "DSREF", H5fid, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
}
catch(Exception ex) {
fail("testH5OcopyRefsDatasettosameFile: H5Ocopy failed");
}
}
catch (Exception ex) {
try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
fail("testH5OcopyRefsDatasettosameFile: H5Pset_copy_object failed");
}
//Perform copy function.
try {
H5.H5Ocopy(H5fid, "DSREF", H5fid, "CPYREFD", ocp_plist_id, HDF5Constants.H5P_DEFAULT);
}
catch(Exception ex) {
finally {
try {H5.H5Pclose(ocp_plist_id);} catch (Exception exx) {}
fail("testH5OcopyRefsDatasettosameFile: H5Ocopy failed");
}
//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) {}
e.printStackTrace();
fail("testH5OcopyRefsDatasettosameFile: H5Dopen failed");
}
try {
//Open the dataset that has been copied
try {
did = H5.H5Dopen(H5fid, "DSREF", HDF5Constants.H5P_DEFAULT);
assertTrue("testH5OcopyRefsDatasettosameFile.H5Dopen: ", did >= 0);
}
catch (Exception e) {
e.printStackTrace();
fail("testH5OcopyRefsDatasettosameFile: H5Dopen failed");
}
//Read the dataset object references in the read_data buffer.
H5.H5Dread(did, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL,HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_data);
try {
H5.H5Dread(did, HDF5Constants.H5T_STD_REF, HDF5Constants.H5S_ALL,HDF5Constants.H5S_ALL, HDF5Constants.H5P_DEFAULT, read_data);
}
catch (Exception e) {
e.printStackTrace();
fail("testH5OcopyRefsDatasettosameFile: H5Dread failed");
}
}
catch (Exception ex) {
ex.printStackTrace();
fail("testH5OcopyRefsDatasettosameFile: open and read dataset failed");
}
finally {
try {H5.H5Dclose(did);} catch (Exception ex) {}
}
try {
//Get the type of object the reference points to.
obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, read_data[1]);
obj_type = H5.H5Rget_obj_type3(read_data[1], HDF5Constants.H5R_OBJECT);
assertEquals(obj_type, HDF5Constants.H5O_TYPE_DATASET);
obj_type = H5.H5Rget_obj_type(H5fid, HDF5Constants.H5R_OBJECT, read_data[0]);
obj_type = H5.H5Rget_obj_type3(read_data[0], HDF5Constants.H5R_OBJECT);
assertEquals(obj_type, HDF5Constants.H5O_TYPE_GROUP);
}
catch (Exception ex) {
ex.printStackTrace();
}
finally {
try {H5.H5Dclose(did);} catch (Exception ex) {}
try {H5.H5Pclose(ocp_plist_id);} catch (Exception ex) {}
try {H5.H5Rdestroy(read_data[1]);} catch (Exception ex) {}
try {H5.H5Rdestroy(read_data[0]);} catch (Exception ex) {}
}
}