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develop JNI export references and java updates (#467)

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* OESS-98 convert plugin option to FetchContent, add tests

* Fixes for pkcfg files because of plugin option

* OESS-98 fix tools test for plugins

* Keep doxygen comments under 100 chars long - format hint

* Whitespace

* HDFFV-11144 - Reclassify CMake messages

* HDFFV-11099/11100 added help text

* Reworked switch statement to compare string instead

* Fix typo

* Update CDash mode

* Correct name of threadsafe

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace

* GH #359 implement and fix tools 1.6 API usage

* remove excessive comments

* Flip inits to correct ifdef section

* rework ifdef to be simpler

* format issue

* Reformat ifdef inits

* remove static attribute

* format compliance

* Update names

* Revert because logic relies on float not being int

* Changes noticed from creating merge of #412

* Double underscore change

* Correct compiler version variable used

* Remove header guard underscores

* Whitespace cleanup

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* correct window os name

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
This commit is contained in:
Allen Byrne
2021-03-12 07:47:47 -06:00
committed by GitHub
parent 6f760f200d
commit 748da20bbc
16 changed files with 562 additions and 229 deletions
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119
java/test/TestH5.java
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@@ -49,9 +49,13 @@ public class TestH5 {
@Rule public TestName testname = new TestName();
private static final String H5_FILE = "testData.h5";
private static final String EXPORT_FILE = "testExport.txt";
private static final String H5_DREG_FILE = "trefer_reg.h5";
private static final String EXPORT_DREG_FILE = "testExportReg.txt";
private static final String H5_AREG_FILE = "trefer_attr.h5";
private static final String H5_REGION_FILE = "trefer_reg.h5";
private static final String EXPORT_REGION_FILE = "testExportReg.txt";
private static final String H5_ATTR_FILE = "trefer_attr.h5";
private static final String EXPORT_ATTR_FILE = "testExportAttr.txt";
private static final String H5_DREG_FILE = "tdatareg.h5";
private static final String EXPORT_DREG_FILE = "testExportDReg.txt";
private static final String H5_AREG_FILE = "tattrreg.h5";
private static final String EXPORT_AREG_FILE = "testExportAReg.txt";
private static final int DIM_X = 4;
private static final int DIM_Y = 6;
@@ -129,7 +133,7 @@ public class TestH5 {
public void _openH5File(String filename, String dsetname) {
try {
H5fid = H5.H5Fopen(filename,
HDF5Constants.H5F_ACC_RDWR, HDF5Constants.H5P_DEFAULT);
HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
}
catch (Throwable err) {
err.printStackTrace();
@@ -162,6 +166,7 @@ public class TestH5 {
@After
public void closeH5File() throws HDF5LibraryException {
_closeH5File();
assertTrue("H5 open ids is 0", H5.getOpenIDCount()==0);
System.out.println();
}
@@ -415,8 +420,10 @@ public class TestH5 {
_closeH5File();
_openH5File(H5_FILE, "/dset");
try {
H5.H5export_dataset(EXPORT_FILE, H5_FILE, "/dset", 99);
H5.H5export_dataset(EXPORT_FILE, H5fid, "/dset", 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
@@ -453,6 +460,86 @@ public class TestH5 {
_deleteH5file();
}
@Test
public void testH5export_region() {
int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
int[] dset_indata = new int[DIM_BLKS+DIM_PNTS];
String objName = "/Dataset1";
_openH5File(H5_REGION_FILE, objName);
try {
H5.H5export_dataset(EXPORT_REGION_FILE, H5fid, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
}
File file = new File(EXPORT_REGION_FILE);
try {
Reader reader = new FileReader(EXPORT_REGION_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx] = (int)streamTokenizer.nval;
indx++;
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for(int row = 0; row < DIM_X; row++)
assertTrue("testH5export_region: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
}
@Test
public void testH5export_attribute() {
int[] dset_data_expect = {0, 3, 6, 9, 1, 4, 7, 10, 2, 5, 8, 11};
int[] dset_indata = new int[DIM_ATTR];
String objName = "/Dataset3";
_openH5File(H5_ATTR_FILE, objName);
try {
H5.H5export_dataset(EXPORT_ATTR_FILE, H5did, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
}
File file = new File(EXPORT_ATTR_FILE);
try {
Reader reader = new FileReader(EXPORT_ATTR_FILE);
StreamTokenizer streamTokenizer = new StreamTokenizer(reader);
int indx = 0;
int jndx = 0;
while(streamTokenizer.nextToken() != StreamTokenizer.TT_EOF){
if(streamTokenizer.ttype == StreamTokenizer.TT_NUMBER) {
dset_indata[indx] = (int)streamTokenizer.nval;
indx++;
}
}
reader.close();
}
catch (IOException err) {
err.printStackTrace();
fail("read file failed: " + err);
}
for(int row = 0; row < DIM_X; row++)
assertTrue("testH5export_attribute: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
}
@Test
public void testH5export_regdataset() {
int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
@@ -465,7 +552,7 @@ public class TestH5 {
_openH5File(H5_DREG_FILE, objName);
try {
H5.H5export_dataset(EXPORT_DREG_FILE, H5_DREG_FILE, objName, 99);
H5.H5export_dataset(EXPORT_DREG_FILE, H5fid, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
@@ -491,23 +578,27 @@ public class TestH5 {
fail("read file failed: " + err);
}
for(int row = 0; row < DIM_X; row++)
assertTrue("H5export_dataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
assertTrue("testH5export_regdataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
}
@Test
public void testH5export_attrdataset() {
int[] dset_data_expect = {0, 3, 6, 9, 1, 4, 7, 10, 2, 5, 8, 11};
int[] dset_indata = new int[DIM_ATTR];
String objName = "/Dataset3";
int[] dset_data_expect = {66, 69, 72, 75, 78, 81, 96, 99, 102, 105, 108,
111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
186, 189, 192, 195, 198, 201, 216, 219, 222, 225, 228, 231,
207, 66, 252, 48, 84, 96, 12, 14, 213, 99};
int[] dset_indata = new int[DIM_BLKS+DIM_PNTS];
String dsetName = "/Dataset1";
String objName = "Attribute1";
_openH5File(H5_AREG_FILE, objName);
_openH5File(H5_AREG_FILE, dsetName);
try {
H5.H5export_dataset(EXPORT_AREG_FILE, H5_AREG_FILE, objName, 99);
H5.H5export_attribute(EXPORT_AREG_FILE, H5did, objName, 99);
}
catch (HDF5LibraryException err) {
err.printStackTrace();
fail("H5export_dataset failed: " + err);
fail("H5export_attribute failed: " + err);
}
File file = new File(EXPORT_AREG_FILE);
@@ -530,6 +621,6 @@ public class TestH5 {
fail("read file failed: " + err);
}
for(int row = 0; row < DIM_X; row++)
assertTrue("H5export_dataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
assertTrue("testH5export_attrdataset: <"+row+">"+dset_indata[row], dset_indata[row]==dset_data_expect[row]);
}
}