Merge pull request #1629 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:feature/json_vol to feature/json_vol

* commit '799a732650735b8ad05a0398781d2a26ec47b288': (185 commits)
  Updated the VOL struct. The json_vol test fails, though, because the plugin can't be found. Will diagnose later.
  Correct examples for packaging
  HDFFV-10738 Wrong INTENT for H5LTread_dataset_double_f
  Changes that show the right way to iterate over enums.
  Changes that show the right way to iterate over enums.
  Test improvement Description     Moved the new tests to a more appropriate test function. Platforms tested:     Linux/64 (jelly)
  Used the H5_INC_ENUM macro to squash enum value increment warnings.
  Fixed HDFFV-10210 and HDFFV-10587 Description:     - Added parameter validation (HDFFV-10210)     - Added detection of division by zero (HDFFV-10587 - CVE-2018-17438)     - Fixed typos in various tests Platforms tested:     Linux/64 (jelly)     Linux/64 (platypus)     Darwin (osx1011test)
  Fix CMake error in name
  Commented out memcpy overlap check while we investigate parallel filters issues.
  Yanked check for memcpy n > 0
  - Added H5MMprivate.h #includes where needed - Added casts to quiet H5MM_memcpy warnings - Removed char * casts from HDmemcpy
  Added an H5MM_memcpy call that checks for buffer overlap.
  Added the HDopen work-around on windows to pio_engine.c
  Adds _wopen support on Windows so that files with UTF-8 names can be opened.
  CMake: fix pthread linking to only be private
  Add API routines to retrieve, restore, reset, and free library state.
  Added a note of bug fix for HDFFV-10705.
  Fixed the MANIFEST
  Fix issue with direct chunk write not updating the "last chunk" index cache.  Fix issues involving datasets being "no allocated" when they contain cached raw data.
  ...

1 files changed, 227 insertions, 0 deletions

diff --git a/java/src/jni/h5pGCPLImp.c b/java/src/jni/h5pGCPLImp.c
new file mode 100644
index 0000000..2ba1c7d
--- /dev/null
+++ b/java/src/jni/h5pGCPLImp.c
@@ -0,0 +1,227 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ *  For details of the HDF libraries, see the HDF Documentation at:
+ *    http://hdfgroup.org/HDF5/doc/
+ *
+ */
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+#include <stdlib.h>
+#include "hdf5.h"
+#include "h5jni.h"
+#include "h5pGCPLImp.h"
+
+/*
+ * Pointer to the JNI's Virtual Machine; used for callback functions.
+ */
+/* extern JavaVM *jvm; */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_local_heap_size_hint
+ * Signature: (JJ)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1local_1heap_1size_1hint
+    (JNIEnv *env, jclass clss, jlong gcpl_id, jlong size_hint)
+{
+    herr_t retVal = FAIL;
+
+    UNUSED(clss);
+
+    if ((retVal = H5Pset_local_heap_size_hint((hid_t)gcpl_id, (size_t)size_hint)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1local_1heap_1size_1hint */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_local_heap_size_hint
+ * Signature: (J)J
+ */
+JNIEXPORT jlong JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1local_1heap_1size_1hint
+    (JNIEnv *env, jclass clss, jlong gcpl_id)
+{
+    size_t size_hint = 0;
+
+    UNUSED(clss);
+
+    if (H5Pget_local_heap_size_hint((hid_t)gcpl_id, &size_hint) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jlong)size_hint;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1local_1heap_1size_1hint */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_link_creation_order
+ * Signature: (JI)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1link_1creation_1order
+    (JNIEnv *env, jclass clss, jlong gcpl_id, jint crt_order_flags)
+{
+    herr_t retVal = FAIL;
+
+    UNUSED(clss);
+
+    if ((retVal = H5Pset_link_creation_order((hid_t)gcpl_id, (unsigned)crt_order_flags)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1link_1creation_1order */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_link_creation_order
+ * Signature: (J)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1link_1creation_1order
+    (JNIEnv *env, jclass clss, jlong gcpl_id)
+{
+    unsigned crt_order_flags;
+
+    UNUSED(clss);
+
+    if (H5Pget_link_creation_order((hid_t)gcpl_id, &crt_order_flags) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jint)crt_order_flags;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1link_1creation_1order */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_est_link_info
+ * Signature: (JII)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1est_1link_1info
+    (JNIEnv *env, jclass clss, jlong gcpl_id, jint est_num_entries, jint est_name_len)
+{
+    herr_t retVal = FAIL;
+
+    UNUSED(clss);
+
+    /* Range check values */
+    if ((est_num_entries > 65535) || (est_name_len > 65535))
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_est_link_info: est. name length or number of entries must be < 65536");
+
+    if ((retVal = H5Pset_est_link_info((hid_t)gcpl_id, (unsigned)est_num_entries, (unsigned)est_name_len)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1est_1link_1info */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_est_link_info
+ * Signature: (J[I)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1est_1link_1info
+    (JNIEnv *env, jclass clss, jlong gcpl_id, jintArray link_info)
+{
+    jboolean  isCopy;
+    jint     *theArray = NULL;
+    herr_t    retVal = FAIL;
+
+    UNUSED(clss);
+
+    if (NULL == link_info)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_est_link_info: link_info is NULL");
+
+    PIN_INT_ARRAY(ENVONLY, link_info, theArray, &isCopy, "H5Pget_est_link_info: input not pinned");
+
+    if ((retVal = H5Pget_est_link_info((hid_t)gcpl_id, (unsigned *)&(theArray[0]), (unsigned *)&(theArray[1]))) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    if (theArray)
+        UNPIN_INT_ARRAY(ENVONLY, link_info, theArray, (retVal < 0) ? JNI_ABORT : 0);
+
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1est_1link_1info */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pset_link_phase_change
+ * Signature: (JII)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pset_1link_1phase_1change
+    (JNIEnv *env, jclass clss, jlong gcpl_id, jint max_compact, jint min_dense)
+{
+    herr_t retVal = FAIL;
+
+    UNUSED(clss);
+
+    if (max_compact < min_dense)
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_link_phase_change: max compact value must be >= min dense value");
+    if (max_compact > 65535)
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_link_phase_change: max compact value must be < 65536");
+    if (min_dense > 65535)
+        H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_link_phase_change: min dense value must be < 65536");
+
+    if ((retVal = H5Pset_link_phase_change((hid_t)gcpl_id, (unsigned)max_compact, (unsigned)min_dense)) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pset_1link_1phase_1change */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Pget_link_phase_change
+ * Signature: (J[I)I
+ */
+JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_H5_H5Pget_1link_1phase_1change
+    (JNIEnv *env, jclass clss, jlong gcpl_id, jintArray links)
+{
+    jboolean  isCopy;
+    jint     *theArray = NULL;
+    herr_t    retVal = FAIL;
+
+    UNUSED(clss);
+
+    if (NULL == links)
+        H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Pget_link_phase_change: links is NULL");
+
+    PIN_INT_ARRAY(ENVONLY, links, theArray, &isCopy, "H5Pget_link_phase_change: input not pinned");
+
+    if ((retVal = H5Pget_link_phase_change((hid_t)gcpl_id, (unsigned *)&(theArray[0]), (unsigned *)&(theArray[1]))) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    if (theArray)
+        UNPIN_INT_ARRAY(ENVONLY, links, theArray, (retVal < 0) ? JNI_ABORT : 0);
+
+    return (jint)retVal;
+} /* end Java_hdf_hdf5lib_H5_H5Pget_1link_1phase_1change */
+
+#ifdef __cplusplus
+} /* end extern "C" */
+#endif /* __cplusplus */