1 12 JNI export references and java updates (#464)

* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge serval small changes from dev

* fix typo

* Minor non-space formatting changes

* GH #386 copyright corrections for java folder

* revert because logic requires false return

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Remove case statement for H5I_EVENTSET

* Correct call with versioning

* Remove tabs

* Double underscore change

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
Remove more underscores from header guards

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* 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>

1 files changed, 105 insertions, 14 deletions

diff --git a/java/test/TestH5.java b/java/test/TestH5.java
index a6b60d3..bef0627 100644
--- a/java/test/TestH5.java
+++ b/java/test/TestH5.java
@@ -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();
@@ -454,6 +461,86 @@ public class TestH5 {
     }
 
     @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,
                 111, 126, 129, 132, 135, 138, 141, 156, 159, 162, 165, 168, 171,
@@ -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]);
     }
 }