Primary change is HDFFV-11212 - new refs and JNI (#372)

* 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
HDFGroup · Feb 25, 2021 · c7ffe68 · c7ffe68
1 parent c29e1b9
commit c7ffe68
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diff --git a/.clang-format b/.clang-format
@@ -1,10 +1,10 @@
 ---
 Language:        Cpp
 BasedOnStyle:  LLVM
-AlignConsecutiveMacros: true
 AlignConsecutiveAssignments: true
 #llvm11: AlignConsecutiveBitFields: false
 AlignConsecutiveDeclarations: true
+AlignConsecutiveMacros: true
 #llvm10-11: AlignOperands:   true - Align
 #llvm11: AllowShortEnumsOnASingleLine: true
 AlwaysBreakAfterReturnType: AllDefinitions

diff --git a/MANIFEST b/MANIFEST
@@ -2019,6 +2019,7 @@
 ./tools/testfiles/tintsnodata.h5
 ./tools/testfiles/tlarge_objname.ddl
 ./tools/testfiles/tlarge_objname.h5
+./tools/testfiles/tldouble.ddl
 ./tools/testfiles/tldouble.h5
 ./tools/testfiles/tlonglinks.ddl
 ./tools/testfiles/tlonglinks.h5
@@ -3428,6 +3429,7 @@
 ./java/test/testfiles/JUnit-TestH5Pvirtual.txt
 ./java/test/testfiles/JUnit-TestH5PL.txt
 ./java/test/testfiles/JUnit-TestH5R.txt
+./java/test/testfiles/JUnit-TestH5Rref.txt
 ./java/test/testfiles/JUnit-TestH5Sbasic.txt
 ./java/test/testfiles/JUnit-TestH5S.txt
 ./java/test/testfiles/JUnit-TestH5Tparams.txt
@@ -3468,6 +3470,7 @@
 ./java/test/TestH5Pvirtual.java
 ./java/test/TestH5PL.java
 ./java/test/TestH5R.java
+./java/test/TestH5Rref.java
 ./java/test/TestH5Sbasic.java
 ./java/test/TestH5S.java
 ./java/test/TestH5Tparams.java

diff --git a/java/examples/datasets/H5Ex_D_Alloc.java b/java/examples/datasets/H5Ex_D_Alloc.java
@@ -65,11 +65,11 @@ public static H5D_space_status get(int code) {
     }
 
     private static void allocation() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id1 = -1;
-        long dataset_id2 = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id1 = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id2 = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
         int space_status = 0;

diff --git a/java/examples/datasets/H5Ex_D_Checksum.java b/java/examples/datasets/H5Ex_D_Checksum.java
@@ -93,10 +93,10 @@ private static boolean checkFletcher32Filter() {
     }
 
     private static void writeChecksum() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -193,9 +193,9 @@ private static void writeChecksum() {
     }
 
     private static void readChecksum() {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_Chunk.java b/java/examples/datasets/H5Ex_D_Chunk.java
@@ -66,10 +66,10 @@ public static H5D_layout get(int code) {
     }
 
     private static void writeChunk() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -201,10 +201,10 @@ private static void writeChunk() {
     }
 
     private static void readChunk() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_Compact.java b/java/examples/datasets/H5Ex_D_Compact.java
@@ -60,10 +60,10 @@ public static H5D_layout get(int code) {
     }
 
     private static void writeCompact() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
@@ -163,10 +163,10 @@ private static void writeCompact() {
     }
 
     private static void readCompact() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open file and dataset using the default properties.

diff --git a/java/examples/datasets/H5Ex_D_External.java b/java/examples/datasets/H5Ex_D_External.java
@@ -34,10 +34,10 @@ public class H5Ex_D_External {
     private static final int NAME_BUF_SIZE = 32;
 
     private static void writeExternal() {
-        long file_id = -1;
-        long dcpl_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
@@ -138,9 +138,9 @@ private static void writeExternal() {
     }
 
     private static void readExternal() {
-        long file_id = -1;
-        long dcpl_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
         String[] Xname = new String[1];
 

diff --git a/java/examples/datasets/H5Ex_D_FillValue.java b/java/examples/datasets/H5Ex_D_FillValue.java
@@ -40,10 +40,10 @@ public class H5Ex_D_FillValue {
     private static final int FILLVAL = 99;
 
     private static void fillValue() {
-        long file_id = -1;
-        long dcpl_id = -1;
-        long dataspace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
+        long dataspace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] extdims = { EDIM_X, EDIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };

diff --git a/java/examples/datasets/H5Ex_D_Gzip.java b/java/examples/datasets/H5Ex_D_Gzip.java
@@ -95,10 +95,10 @@ private static boolean checkGzipFilter() {
     }
 
     private static void writeGzip() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -196,9 +196,9 @@ private static void writeGzip() {
     }
 
     private static void readGzip() {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_Hyperslab.java b/java/examples/datasets/H5Ex_D_Hyperslab.java
@@ -34,9 +34,9 @@ public class H5Ex_D_Hyperslab {
     private static final int RANK = 2;
 
     private static void writeHyperslab() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
@@ -142,10 +142,10 @@ private static void writeHyperslab() {
     }
 
     private static void readHyperslab() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_Nbit.java b/java/examples/datasets/H5Ex_D_Nbit.java
@@ -96,11 +96,11 @@ private static boolean checkNbitFilter() {
     }
 
     private static void writeData() throws Exception {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dtype_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dtype_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -157,9 +157,9 @@ private static void writeData() throws Exception {
     }
 
     private static void readData() throws Exception {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_ReadWrite.java b/java/examples/datasets/H5Ex_D_ReadWrite.java
@@ -32,9 +32,9 @@ public class H5Ex_D_ReadWrite {
     private static final int RANK = 2;
 
     private static void WriteDataset() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
@@ -109,8 +109,8 @@ private static void WriteDataset() {
     }
 
     private static void ReadDataset() {
-        long file_id = -1;
-        long dataset_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open file using the default properties.

diff --git a/java/examples/datasets/H5Ex_D_Shuffle.java b/java/examples/datasets/H5Ex_D_Shuffle.java
@@ -122,10 +122,10 @@ private static boolean checkShuffleFilter() {
     }
 
     private static void writeShuffle() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -229,9 +229,9 @@ private static void writeShuffle() {
     }
 
     private static void readShuffle() {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open an existing file.

diff --git a/java/examples/datasets/H5Ex_D_Sofloat.java b/java/examples/datasets/H5Ex_D_Sofloat.java
@@ -96,10 +96,10 @@ private static boolean checkScaleoffsetFilter() {
     }
 
     private static void writeData() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         double[][] dset_data = new double[DIM_X][DIM_Y];
@@ -213,9 +213,9 @@ private static void writeData() {
     }
 
     private static void readData() {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         double[][] dset_data = new double[DIM_X][DIM_Y];
 
         // Open file using the default properties.

diff --git a/java/examples/datasets/H5Ex_D_Soint.java b/java/examples/datasets/H5Ex_D_Soint.java
@@ -96,10 +96,10 @@ private static boolean checkScaleoffsetFilter() {
     }
 
     private static void writeData() {
-        long file_id = -1;
-        long filespace_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long filespace_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         long[] dims = { DIM_X, DIM_Y };
         long[] chunk_dims = { CHUNK_X, CHUNK_Y };
         int[][] dset_data = new int[DIM_X][DIM_Y];
@@ -195,9 +195,9 @@ private static void writeData() {
     }
 
     private static void readData() {
-        long file_id = -1;
-        long dataset_id = -1;
-        long dcpl_id = -1;
+        long file_id = HDF5Constants.H5I_INVALID_HID;
+        long dataset_id = HDF5Constants.H5I_INVALID_HID;
+        long dcpl_id = HDF5Constants.H5I_INVALID_HID;
         int[][] dset_data = new int[DIM_X][DIM_Y];
 
         // Open file using the default properties.