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, 15 insertions, 14 deletions

diff --git a/src/H5Dint.c b/src/H5Dint.c
index 7eb1aaf..6fc02de 100644
--- a/src/H5Dint.c
+++ b/src/H5Dint.c
@@ -470,7 +470,7 @@ H5D__new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type)
         HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
 
     /* Copy the default dataset information */
-    HDmemcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t));
+    H5MM_memcpy(new_dset, &H5D_def_dset, sizeof(H5D_shared_t));
 
     /* If we are using the default dataset creation property list, during creation
      * don't bother to copy it, just increment the reference count
@@ -488,6 +488,9 @@ H5D__new(hid_t dcpl_id, hbool_t creating, hbool_t vl_type)
         new_dset->dcpl_id = H5P_copy_plist(plist, FALSE);
     } /* end else */
 
+    /* Set the DCPL for the API context */
+    H5CX_set_dcpl(new_dset->dcpl_id);
+
     /* Set return value */
     ret_value = new_dset;
 
@@ -678,7 +681,6 @@ done:
 static herr_t
 H5D__use_minimized_dset_headers(H5F_t *file, H5D_t *dset, hbool_t *minimize)
 {
-    H5P_genplist_t *plist     = NULL;
     herr_t          ret_value = SUCCEED;
 
     FUNC_ENTER_NOAPI_NOINIT;
@@ -687,11 +689,9 @@ H5D__use_minimized_dset_headers(H5F_t *file, H5D_t *dset, hbool_t *minimize)
     HDassert(dset);
     HDassert(minimize);
 
-    plist = H5P_object_verify(dset->shared->dcpl_id, H5P_DATASET_CREATE);
-    if(NULL == plist)
-        HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "problem getting dcpl")
-    if(H5P_get(plist, H5D_CRT_MIN_DSET_HDR_SIZE_NAME, minimize) == FAIL)
-        HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get minimize value from dcpl")
+    /* Get the dataset object header minimize flag for this call */
+    if(H5CX_get_dset_min_ohdr_flag(minimize) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset object header minimize flag from API context")
 
     if(FALSE == *minimize)
         *minimize = H5F_get_min_dset_ohdr(file);
@@ -774,7 +774,7 @@ H5D__calculate_minimum_header_size(H5F_t *file, H5D_t *dset, H5O_t *ohdr)
 
         /* Shallow copy the fill value property */
         /* guards against shared component modification */
-        HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop));
+        H5MM_memcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop));
 
         if (H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't reset the copied fill property")
@@ -1000,7 +1000,7 @@ H5D__update_oh_info(H5F_t *file, H5D_t *dset, hid_t dapl_id)
 
         /* Shallow copy the fill value property */
         /* (we only want to make certain that the shared component isn't modified) */
-        HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop));
+        H5MM_memcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop));
 
         /* Reset shared component info */
         H5O_msg_reset_share(H5O_FILL_ID, &old_fill_prop);
@@ -1642,7 +1642,7 @@ H5D__append_flush_setup(H5D_t *dset, hid_t dapl_id)
                 dset->shared->append_flush.ndims = info.ndims;
                 dset->shared->append_flush.func = info.func;
                 dset->shared->append_flush.udata = info.udata;
-                HDmemcpy(dset->shared->append_flush.boundary, info.boundary, sizeof(info.boundary));
+                H5MM_memcpy(dset->shared->append_flush.boundary, info.boundary, sizeof(info.boundary));
             } /* end if */
         } /* end if */
     } /* end if */
@@ -2778,7 +2778,7 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size)
 
     /* Keep the current dataspace dimensions for later */
     HDcompile_assert(sizeof(curr_dims) == sizeof(dset->shared->curr_dims));
-    HDmemcpy(curr_dims, dset->shared->curr_dims, H5S_MAX_RANK * sizeof(curr_dims[0]));
+    H5MM_memcpy(curr_dims, dset->shared->curr_dims, H5S_MAX_RANK * sizeof(curr_dims[0]));
 
     /* Modify the size of the dataspace */
     if((changed = H5S_set_extent(dset->shared->space, size)) < 0)
@@ -2898,7 +2898,8 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size)
          *-------------------------------------------------------------------------
          */
         if(H5D_CHUNKED == dset->shared->layout.type) {
-            if(shrink && (*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage))
+            if(shrink && ((*dset->shared->layout.ops->is_space_alloc)(&dset->shared->layout.storage)
+                    || (dset->shared->layout.ops->is_data_cached && (*dset->shared->layout.ops->is_data_cached)(dset->shared))))
                 /* Remove excess chunks */
                 if(H5D__chunk_prune_by_extent(dset, curr_dims) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to remove chunks")
@@ -3062,7 +3063,7 @@ H5D__format_convert(H5D_t *dataset)
             idx_info.storage = &dataset->shared->layout.storage.u.chunk;
 
             /* Copy the current layout info to the new layout */
-            HDmemcpy(newlayout, &dataset->shared->layout, sizeof(H5O_layout_t));
+            H5MM_memcpy(newlayout, &dataset->shared->layout, sizeof(H5O_layout_t));
 
             /* Set up info for version 1 B-tree in the new layout */
             newlayout->version = H5O_LAYOUT_VERSION_3;
@@ -3113,7 +3114,7 @@ H5D__format_convert(H5D_t *dataset)
                 HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info")
 
             /* Copy the new layout to the dataset's layout */
-            HDmemcpy(&dataset->shared->layout, newlayout, sizeof(H5O_layout_t));
+            H5MM_memcpy(&dataset->shared->layout, newlayout, sizeof(H5O_layout_t));
 
             break;