add overwriting functionality for unsafe mode [HDF5]

src/templates_hdf5/templator_hdf5.org

@@ -218,29 +218,38 @@ trexio_hdf5_write_$group_num$ (trexio_t* const file, const $group_num_dtype_doub
 
   trexio_hdf5_t* const f = (trexio_hdf5_t*) file;
 
- /* Write the dimensioning variables */
+ /* Delete the attribute if it exists and if the file is open in UNSAFE mode */
-  const hid_t dtype = H5Tcopy(H5T_$GROUP_NUM_H5_DTYPE$);
+  if (trexio_hdf5_has_$group_num$(file) == TREXIO_SUCCESS && file->mode == 'u') {
-  const hid_t dspace = H5Screate(H5S_SCALAR);
+    herr_t status_del = H5Adelete(f->$group$_group, $GROUP_NUM$_NAME);
+    if (status_del < 0) return TREXIO_FAILURE;
+  }
 
-  const hid_t num_id = H5Acreate(f->$group$_group, $GROUP_NUM$_NAME,
+ /* Setup the dataspace */
-                                 dtype, dspace, H5P_DEFAULT, H5P_DEFAULT);
+  const hid_t dtype_id = H5Tcopy(H5T_$GROUP_NUM_H5_DTYPE$);
-  if (num_id <= 0) {
+  if (dtype_id <= 0) return TREXIO_INVALID_ID;
-    H5Sclose(dspace);
+
-    H5Tclose(dtype);
+  const hid_t dspace_id = H5Screate(H5S_SCALAR);
+  if (dspace_id <= 0) {
+    H5Tclose(dtype_id);
     return TREXIO_INVALID_ID;
   }
 
-  const herr_t status = H5Awrite(num_id, dtype, &(num));
+  const hid_t num_id = H5Acreate(f->$group$_group,
-  if (status < 0) {
+                                 $GROUP_NUM$_NAME,
-    H5Aclose(num_id);
+                                 dtype_id, dspace_id,
-    H5Sclose(dspace);
+                                 H5P_DEFAULT, H5P_DEFAULT);
-    H5Tclose(dtype);
+  if (num_id <= 0) {
-    return TREXIO_FAILURE;
+    H5Sclose(dspace_id);
+    H5Tclose(dtype_id);
+    return TREXIO_INVALID_ID;
   }
 
-  H5Sclose(dspace);
+  const herr_t status = H5Awrite(num_id, dtype_id, &num);
+
+  H5Sclose(dspace_id);
   H5Aclose(num_id);
-  H5Tclose(dtype);
+  H5Tclose(dtype_id);
+  if (status < 0) return TREXIO_FAILURE;
 
   return TREXIO_SUCCESS;
 }
@@ -340,30 +349,41 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file, const $group_dset_dtype$*
 
   trexio_hdf5_t* f = (trexio_hdf5_t*) file;
 
-  if ( H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) != 1 ) {
+  /*
-
+     Try to delete an existing dataset by unlinking it from the group (UNSAFE mode).
-    const herr_t status = H5LTmake_dataset(f->$group$_group,
+     NOTE: In principle, HDF5 should see the deallocated (unused) file space and free it,
-                                           $GROUP_DSET$_NAME,
+     thus reducing the size of the HDF5 file. In practic, this is not always the case.
-                                           (int) rank, (const hsize_t*) dims,
-                                           H5T_$GROUP_DSET_H5_DTYPE$,
-                                           $group_dset$);
-    if (status < 0) return TREXIO_FAILURE;
-
-  } else {
-
-    hid_t dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
-    if (dset_id <= 0) return TREXIO_INVALID_ID;
-
-    const herr_t status = H5Dwrite(dset_id,
-                                   H5T_$GROUP_DSET_H5_DTYPE$,
-                                   H5S_ALL, H5S_ALL, H5P_DEFAULT,
-                                   $group_dset$);
-
-    H5Dclose(dset_id);
-    if (status < 0) return TREXIO_FAILURE;
 
+     Consider using HDF5-native h5repack utility after deleting/overwriting big datasets.
+  ,*/
+  if (H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) == 1 && file->mode == 'u') {
+    herr_t status_del = H5Ldelete(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
+    if (status_del < 0) return TREXIO_FAILURE;
   }
 
+  hid_t dspace_id = H5Screate_simple( (int) rank, (const hsize_t*) dims, NULL);
+  if (dspace_id <= 0) return TREXIO_INVALID_ID;
+
+  hid_t dset_id = H5Dcreate (f->$group$_group,
+                             $GROUP_DSET$_NAME,
+                             H5T_$GROUP_DSET_H5_DTYPE$,
+                             dspace_id,
+                             H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+  if (dset_id <= 0) {
+    H5Sclose(dspace_id);
+    return TREXIO_INVALID_ID;
+  }
+
+  herr_t status = H5Dwrite(dset_id,
+                           H5T_$GROUP_DSET_H5_DTYPE$,
+                           H5S_ALL,
+                           dspace_id,
+                           H5P_DEFAULT,
+                           $group_dset$);
+  H5Dclose(dset_id);
+  H5Sclose(dspace_id);
+  if (status < 0) return TREXIO_FAILURE;
+
   return TREXIO_SUCCESS;
 
 }
@@ -716,6 +736,18 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file, const char** $group_dset$,
 
   trexio_hdf5_t* f = (trexio_hdf5_t*) file;
 
+  /*
+     Try to delete an existing dataset by unlinking it from the group (UNSAFE mode).
+     NOTE: In principle, HDF5 should see the deallocated (unused) file space and free it,
+     thus reducing the size of the HDF5 file. In practic, this is not always the case.
+
+     Consider using HDF5-provided h5repack utility after deleting/overwriting big datasets.
+  ,*/
+  if (H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) == 1 && file->mode == 'u') {
+    herr_t status_del = H5Ldelete(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
+    if (status_del < 0) return TREXIO_FAILURE;
+  }
+
   herr_t status;
   hid_t dset_id;
 
@@ -726,49 +758,30 @@ trexio_hdf5_write_$group_dset$ (trexio_t* const file, const char** $group_dset$,
   status = H5Tset_size (memtype, H5T_VARIABLE);
   if (status < 0) return TREXIO_FAILURE;
 
-  if ( H5LTfind_dataset(f->$group$_group, $GROUP_DSET$_NAME) != 1 ) {
+  hid_t dspace = H5Screate_simple( (int) rank, (const hsize_t*) dims, NULL);
+  if (dspace <= 0) return TREXIO_INVALID_ID;
 
- /* code to create dataset */
+ /* code to create dataset */
-    hid_t filetype = H5Tcopy (H5T_FORTRAN_S1);
+  hid_t filetype = H5Tcopy (H5T_FORTRAN_S1);
-    if (filetype <= 0) return TREXIO_INVALID_ID;
+  if (filetype <= 0) return TREXIO_INVALID_ID;
 
-    status = H5Tset_size (filetype, H5T_VARIABLE);
+  status = H5Tset_size (filetype, H5T_VARIABLE);
-    if (status < 0) return TREXIO_FAILURE;
+  if (status < 0) return TREXIO_FAILURE;
 
-    hid_t dspace = H5Screate_simple( (int) rank, (const hsize_t*) dims, NULL);
+  dset_id = H5Dcreate (f->$group$_group, $GROUP_DSET$_NAME, filetype, dspace,
-    if (dspace <= 0) return TREXIO_INVALID_ID;
+                       H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+  if (dset_id <= 0) return TREXIO_INVALID_ID;
 
-    dset_id = H5Dcreate (f->$group$_group, $GROUP_DSET$_NAME, filetype, dspace,
+  status = H5Dwrite (dset_id, memtype,
-                         H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+                     H5S_ALL, H5S_ALL, H5P_DEFAULT,
-    if (dset_id <= 0) return TREXIO_INVALID_ID;
+                     $group_dset$);
 
-    status = H5Dwrite (dset_id, memtype,
+  H5Dclose (dset_id);
-                       H5S_ALL, H5S_ALL, H5P_DEFAULT,
+  H5Sclose (dspace);
-                       $group_dset$);
+  H5Tclose (filetype);
+  H5Tclose (memtype);
 
-    H5Dclose (dset_id);
+  if (status < 0) return TREXIO_FAILURE;
-    H5Sclose (dspace);
-    H5Tclose (filetype);
-    H5Tclose (memtype);
-
-    if (status < 0) return TREXIO_FAILURE;
-
-  } else {
-
-    dset_id = H5Dopen(f->$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
-    if (dset_id <= 0) return TREXIO_INVALID_ID;
-
- /* code to write dataset */
-    status = H5Dwrite(dset_id, memtype,
-                      H5S_ALL, H5S_ALL, H5P_DEFAULT,
-                      $group_dset$);
-
-    H5Dclose(dset_id);
-    H5Tclose(memtype);
-
-    if (status < 0) return TREXIO_FAILURE;
-
-  }
 
   return TREXIO_SUCCESS;
 
@@ -857,8 +870,13 @@ trexio_hdf5_write_$group_str$ (trexio_t* const file, const char* str)
 
   trexio_hdf5_t* const f = (trexio_hdf5_t*) file;
 
+ /* Delete the attribute if it exists and if the file is open in UNSAFE mode */
+  if (trexio_hdf5_has_$group_str$(file) == TREXIO_SUCCESS && file->mode == 'u') {
+    herr_t status_del = H5Adelete(f->$group$_group, $GROUP_STR$_NAME);
+    if (status_del < 0) return TREXIO_FAILURE;
+  }
 
- /* Setup the dataspace */
+ /* Setup the datatype for variable length string */
   const hid_t dtype_id = H5Tcopy(H5T_C_S1);
   if (dtype_id <= 0) return TREXIO_INVALID_ID;
 
@@ -871,12 +889,15 @@ trexio_hdf5_write_$group_str$ (trexio_t* const file, const char* str)
   status = H5Tset_strpad(dtype_id, H5T_STR_NULLTERM);
   if (status < 0) return TREXIO_FAILURE;
 
+ /* Setup the dataspace */
   const hid_t dspace_id = H5Screate(H5S_SCALAR);
   if (dspace_id <= 0) return TREXIO_INVALID_ID;
 
  /* Create the $group_str$ attribute of $group$ group */
-  const hid_t str_id = H5Acreate(f->$group$_group, $GROUP_STR$_NAME, dtype_id, dspace_id,
+  const hid_t str_id = H5Acreate(f->$group$_group,
-                       H5P_DEFAULT, H5P_DEFAULT);
+                                 $GROUP_STR$_NAME,
+                                 dtype_id, dspace_id,
+                                 H5P_DEFAULT, H5P_DEFAULT);
 
   if (str_id <= 0) {
     H5Sclose(dspace_id);
@@ -885,18 +906,14 @@ trexio_hdf5_write_$group_str$ (trexio_t* const file, const char* str)
   }
 
   status = H5Awrite(str_id, dtype_id, str);
-  if (status < 0) {
-    H5Aclose(str_id);
-    H5Sclose(dspace_id);
-    H5Tclose(dtype_id);
-    return TREXIO_FAILURE;
-  }
 
   H5Aclose(str_id);
   H5Sclose(dspace_id);
   H5Tclose(dtype_id);
-  return TREXIO_SUCCESS;
 
+  if (status < 0) return TREXIO_FAILURE;
+
+  return TREXIO_SUCCESS;
 }
     #+end_src
 

tests/overwrite_all_hdf5.c

@@ -2,10 +2,11 @@
 #include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
 
 #define TEST_BACKEND 	TREXIO_HDF5
 #define TREXIO_FILE 	"test_over.h5"
-#define RM_COMMAND 	"rm -rf " TREXIO_FILE
+#define RM_COMMAND 	"rm -f -- " TREXIO_FILE
 
 static int test_write (const char* file_name, const back_end_t backend) {
 
@@ -56,13 +57,13 @@ static int test_write (const char* file_name, const back_end_t backend) {
 
   rc = trexio_write_nucleus_coord(file, coord);
   assert (rc == TREXIO_SUCCESS);
-  
+
   rc = trexio_write_nucleus_point_group(file, sym, 4);
   assert (rc == TREXIO_SUCCESS);
-  
+
   rc = trexio_write_nucleus_label(file, labels, 2);
   assert (rc == TREXIO_SUCCESS);
-  
+
   // close current session
   rc = trexio_close(file);
   assert (rc == TREXIO_SUCCESS);
@@ -73,9 +74,61 @@ static int test_write (const char* file_name, const back_end_t backend) {
 }
 
 
-static int test_overwrite (const char* file_name, const back_end_t backend) {
+static int test_overwrite_unsafe (const char* file_name, const back_end_t backend) {
 
-/* Try to overwrite the data that already exists in the TREXIO file */
+/* Try to overwrite the data that already exists in the TREXIO file which is open in UNSAFE mode*/
+
+  trexio_t* file = NULL;
+  trexio_exit_code rc;
+
+  // parameters to be written
+  int num = 5;
+  double coord[15] = {
+  0.00000000 ,  666.666    ,  0.00000000 ,
+ -1.20594314 ,  0.69625160 ,  0.00000000 ,
+ -1.20594314 , -0.69625160 ,  0.00000000 ,
+  0.00000000 , -1.39250319 ,  0.00000000 ,
+  1.20594314 , -0.69625160 ,  0.00000000
+  };
+  const char* sym = "Unknown";
+  const char* labels[] = {"Ru" ,
+                          "U"  ,
+                          "Cl" ,
+                          "Na" ,
+                          "H" };
+
+/*================= START OF TEST ==================*/
+
+  // open file in 'write' mode
+  file = trexio_open(file_name, 'u', backend, &rc);
+  assert (file != NULL);
+
+  // check that the previously written data cannot be overwritten
+  rc = trexio_write_nucleus_num(file, num);
+  assert (rc == TREXIO_SUCCESS);
+
+  rc = trexio_write_nucleus_coord(file, coord);
+  assert (rc == TREXIO_SUCCESS);
+
+  rc = trexio_write_nucleus_point_group(file, sym, 16);
+  assert (rc == TREXIO_SUCCESS);
+
+  rc = trexio_write_nucleus_label(file, labels, 4);
+  assert (rc == TREXIO_SUCCESS);
+
+  // close current session
+  rc = trexio_close(file);
+  assert (rc == TREXIO_SUCCESS);
+
+/*================= END OF TEST ==================*/
+
+  return 0;
+}
+
+
+static int test_overwrite_safe (const char* file_name, const back_end_t backend) {
+
+/* Try to overwrite the data that already exists in the TREXIO file which is open in SAFE mode*/
 
   trexio_t* file = NULL;
   trexio_exit_code rc;
@@ -104,10 +157,10 @@ static int test_overwrite (const char* file_name, const back_end_t backend) {
 
   rc = trexio_write_nucleus_coord(file, coord);
   assert (rc == TREXIO_DSET_ALREADY_EXISTS);
-  
+
   rc = trexio_write_nucleus_point_group(file, sym, 16);
   assert (rc == TREXIO_ATTR_ALREADY_EXISTS);
-  
+
   rc = trexio_write_nucleus_label(file, labels, 4);
   assert (rc == TREXIO_DSET_ALREADY_EXISTS);
 
@@ -121,6 +174,78 @@ static int test_overwrite (const char* file_name, const back_end_t backend) {
 }
 
 
+int test_read(const char* file_name, const back_end_t backend) {
+
+/*========= Test read ===========*/
+
+  trexio_t* file = NULL;
+  trexio_exit_code rc;
+
+  int num;
+  double* coord;
+  char** label;
+  char* point_group;
+
+/*================= START OF TEST ==================*/
+
+  // open existing file on 'read' mode
+  file = trexio_open(file_name, 'r', backend, &rc);
+  assert (file != NULL);
+
+  // read nucleus_num
+  rc = trexio_read_nucleus_num(file,&num);
+  assert (rc == TREXIO_SUCCESS);
+  assert (num == 5);
+
+  // read nucleus_coord
+  coord = (double*) calloc(3*num, sizeof(double));
+  rc = trexio_read_nucleus_coord(file,coord);
+  assert (rc == TREXIO_SUCCESS);
+
+  double x = coord[1] - 666.666;
+  assert( x*x < 1.e-14);
+  free(coord);
+
+  // read nucleus_label
+  label = (char**) malloc(num*sizeof(char*));
+  for (int i=0; i<num; i++){
+    label[i] = (char*) malloc(32*sizeof(char));
+  }
+
+  rc = trexio_read_nucleus_label(file, label, 2);
+  assert (rc == TREXIO_SUCCESS);
+  assert (strcmp(label[0], "Ru")  == 0);
+  assert (strcmp(label[3], "Na") == 0);
+
+  for (int i=0; i<num; i++){
+    free(label[i]);
+  }
+  free(label);
+
+  point_group = (char*) malloc(32*sizeof(char));
+
+  rc = trexio_read_nucleus_point_group(file, point_group, 10);
+  assert (rc == TREXIO_SUCCESS);
+
+  char * pch;
+  pch = strtok(point_group, " ");
+  assert (strcmp(pch, "Unknown") == 0);
+  /* alternative test when 3 symbols are read from the file to point_group */
+  /*rc = trexio_read_nucleus_point_group(file, point_group, 3);
+  assert (rc == TREXIO_SUCCESS);
+  assert (strcmp(point_group, "B3U") == 0 );*/
+  free(point_group);
+
+  // close current session
+  rc = trexio_close(file);
+  assert (rc == TREXIO_SUCCESS);
+
+/*================= END OF TEST =====================*/
+
+  return 0;
+}
+
+
 int main(void) {
 
 /*============== Test launcher ================*/
@@ -129,13 +254,13 @@ int main(void) {
   rc = system(RM_COMMAND);
   assert (rc == 0);
 
-  test_write     (TREXIO_FILE, TEST_BACKEND);
+  test_write            (TREXIO_FILE, TEST_BACKEND);
-  test_overwrite (TREXIO_FILE, TEST_BACKEND);
+  test_overwrite_safe   (TREXIO_FILE, TEST_BACKEND);
+  test_overwrite_unsafe (TREXIO_FILE, TEST_BACKEND);
+  test_read             (TREXIO_FILE, TEST_BACKEND);
 
   rc = system(RM_COMMAND);
   assert (rc == 0);
 
   return 0;
 }
-
-