Merge pull request #1296 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:1.10/master to 1.10/master

* commit 'f3f29dc7df5f3cc41a5e9462d8c415e540cda3d6': (42 commits)
  Commit version string changes for HDF5 1.10.4 release.
  Merge hdf5_1_10 changes to hdf5_1_10_4.
  Merge in changes from hdf5_1_10.
  Commit release date change.
  Update RELEASE.txt for HDF5 1.10.4 release.
  Add notes about unsupported options
  Add contents of HDF5 1.10.3 RELEASE.txt to HISTORY-1_10.txt and update RELEASE.txt for continuing development.
  Switch maintainer mode to disable, build mode to production, version to 1.10.4, and commit files generated by autogen.sh for release branch hdf5_1_10_4.
  HDFFV-10568 fix hdf5_java library dependency
  Fix Java library location for testing
  Java groups example fix
  Update system commands with HD prefix and whitespace
  Merge pull request #1224 in HDFFV/hdf5 from ~JHENDERSON/hdf5:develop to develop
  Disable failing tests because of execution issue
  Add testfiles to data copy
  Same changes needed for examples as test
  Correct name of test jar
  Only remove test jars
  Remove obsolete var
  Change prefix in example scripts to relative path to bin. This was done for 1.8, and works wherever installed without the need to replace the original prefix.
  ...

1 files changed, 22 insertions, 12 deletions

diff --git a/java/src/jni/h5pImp.c b/java/src/jni/h5pImp.c
index 3ff7436..52008ce 100644
--- a/java/src/jni/h5pImp.c
+++ b/java/src/jni/h5pImp.c
@@ -27,7 +27,6 @@ extern "C" {
 #include "h5pImp.h"
 
 extern JavaVM *jvm;
-extern jobject visit_callback;
 extern jobject copy_callback;
 extern jobject close_callback;
 extern jobject create_callback;
@@ -36,6 +35,11 @@ extern jobject get_callback;
 extern jobject set_callback;
 extern jobject delete_callback;
 
+typedef struct _cb_wrapper {
+    jobject visit_callback;
+    jobject op_data;
+} cb_wrapper;
+
 /********************/
 /* Local Prototypes */
 /********************/
@@ -52,7 +56,7 @@ static herr_t H5P_prp_get_func_cb(hid_t prop_id, const char *name, size_t size,
 static herr_t H5P_prp_set_func_cb(hid_t prop_id, const char *name, size_t size, void *value);
 static herr_t H5P_prp_delete_func_cb(hid_t prop_id, const char *name, size_t size, void *value);
 
-static herr_t H5P_iterate_cb(hid_t prop_id, const char *name, void *op_data);
+static herr_t H5P_iterate_cb(hid_t prop_id, const char *name, void *cb_data);
 
 /*
  * Class:     hdf_hdf5lib_H5
@@ -3877,7 +3881,7 @@ Java_hdf_hdf5lib_H5_H5Pset_1fapl_1multi
                 const char *utf8 = ENVPTR->GetStringUTFChars(ENVPAR obj, 0);
 
                 if (utf8) {
-                    member_name[i] = (char*)HDmalloc(strlen(utf8) + 1);
+                    member_name[i] = (char*)HDmalloc(HDstrlen(utf8) + 1);
                     if (member_name[i]) {
                         strcpy(member_name[i], utf8);
                     } /* end if */
@@ -4185,7 +4189,7 @@ Java_hdf_hdf5lib_H5_H5Pset_1mdc_1config
         h5JNIFatalError(env, "H5Pset_mdc_config: out of memory trace_file_name");
         return;
     } /* end if */
-    strncpy(cacheinfo.trace_file_name, str, 1025);
+    HDstrncpy(cacheinfo.trace_file_name, str, 1025);
     ENVPTR->ReleaseStringUTFChars(ENVPAR j_str, str);
     if(ENVPTR->ExceptionOccurred(ENVONLY)) {
         h5JNIFatalError(env, "H5Pset_mdc_config: loading trace_file_name failed");
@@ -5042,7 +5046,7 @@ H5P_cls_copy_cb
     } /* end if */
     JVMPTR->DetachCurrentThread(JVMPAR);
     return (herr_t)status;
-} /* end H5P_cls_ccopy_cb */
+} /* end H5P_cls_copy_cb */
 
 static herr_t
 H5P_cls_close_cb
@@ -5158,13 +5162,16 @@ Java_hdf_hdf5lib_H5_H5Pget_1mdc_1log_1options
 
 static herr_t
 H5D_append_cb
-    (hid_t dataset_id, hsize_t *cur_dims, void *op_data)
+    (hid_t dataset_id, hsize_t *cur_dims, void *cb_data)
 {
     JNIEnv    *cbenv;
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
     jlongArray cur_dimsArray;
+    cb_wrapper *wrapper = (cb_wrapper *)cb_data;
+    void *op_data = (void *)wrapper->op_data;
+    jobject visit_callback = wrapper->visit_callback;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) {
         JVMPTR->DetachCurrentThread(JVMPAR);
@@ -5199,9 +5206,9 @@ Java_hdf_hdf5lib_H5_H5Pset_1append_1flush
     (JNIEnv *env, jclass clss, jlong plist_id, jint ndims, jlongArray boundary, jobject callback_op, jobject op_data)
 {
     herr_t   status = -1;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if (op_data == NULL) {
         h5nullArgument(env, "H5Pset_append_flush:  op_data is NULL");
@@ -5210,7 +5217,7 @@ Java_hdf_hdf5lib_H5_H5Pset_1append_1flush
         h5nullArgument(env, "H5Pset_append_flush:  callback_op is NULL");
     } /* end if */
     else {
-        status = H5Pset_append_flush((hid_t)plist_id, (unsigned)ndims, (const hsize_t*)boundary, (H5D_append_cb_t)H5D_append_cb, (void*)op_data);
+        status = H5Pset_append_flush((hid_t)plist_id, (unsigned)ndims, (const hsize_t*)boundary, (H5D_append_cb_t)H5D_append_cb, (void*)&wrapper);
 
         if (status < 0)
             h5libraryError(env);
@@ -5603,13 +5610,16 @@ Java_hdf_hdf5lib_H5_H5Pinsert2
 
 static herr_t
 H5P_iterate_cb
-    (hid_t prop_id, const char *name, void *op_data)
+    (hid_t prop_id, const char *name, void *cb_data)
 {
     JNIEnv    *cbenv;
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
     jstring    str;
+    cb_wrapper *wrapper = (cb_wrapper *)cb_data;
+    void *op_data = (void *)wrapper->op_data;
+    jobject visit_callback = wrapper->visit_callback;
 
     /* fprintf(stderr, "\nJNI H5P_iterate_cb entered\n"); fflush(stderr); */
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) {
@@ -5656,9 +5666,9 @@ Java_hdf_hdf5lib_H5_H5Piterate
     herr_t   status = -1;
     jint    *theArray = NULL;
     jboolean isCopy;
+    cb_wrapper wrapper = {callback_op, op_data};
 
     ENVPTR->GetJavaVM(ENVPAR &jvm);
-    visit_callback = callback_op;
 
     if (op_data == NULL) {
         h5nullArgument(env, "H5Piterate:  op_data is NULL");
@@ -5668,7 +5678,7 @@ Java_hdf_hdf5lib_H5_H5Piterate
     } /* end else if */
     else {
         if (idx == NULL) {
-            status = H5Piterate((hid_t)prop_id, NULL, (H5P_iterate_t)H5P_iterate_cb, (void*)op_data);
+            status = H5Piterate((hid_t)prop_id, NULL, (H5P_iterate_t)H5P_iterate_cb, (void*)&wrapper);
         } /* end if */
         else {
             theArray = (jint *)ENVPTR->GetIntArrayElements(ENVPAR idx, &isCopy);
@@ -5676,7 +5686,7 @@ Java_hdf_hdf5lib_H5_H5Piterate
                 h5JNIFatalError(env, "H5Piterate:  idx not pinned");
             } /* end if */
             else
-                status = H5Piterate((hid_t)prop_id, (int*)&theArray[0], (H5P_iterate_t)H5P_iterate_cb, (void*)op_data);
+                status = H5Piterate((hid_t)prop_id, (int*)&theArray[0], (H5P_iterate_t)H5P_iterate_cb, (void*)&wrapper);
         } /* end else */
 
         if (status < 0) {