From f68a59417eee3e285f2da8bad1e7cb0333473a1b Mon Sep 17 00:00:00 2001
From: q-posev <posenitskiy@irsamc.ups-tlse.fr>
Date: Mon, 24 Jan 2022 16:13:27 +0100
Subject: [PATCH] add overwriting functionality for unsafe mode [TEXT]

---
 src/templates_front/templator_front.org |  18 +--
 src/templates_text/templator_text.org   |   2 +-
 tests/overwrite_all_text.c              | 147 ++++++++++++++++++++++--
 3 files changed, 146 insertions(+), 21 deletions(-)

diff --git a/src/templates_front/templator_front.org b/src/templates_front/templator_front.org
index 356e480..6f0622d 100644
--- a/src/templates_front/templator_front.org
+++ b/src/templates_front/templator_front.org
@@ -1426,7 +1426,7 @@ trexio_write_$group_num$_64 (trexio_t* const file, const $group_num_dtype_double
 {
   if (file == NULL) return TREXIO_INVALID_ARG_1;
   //if (num <= 0L) return TREXIO_INVALID_NUM; /* this line is uncommented by the generator for dimensioning variables; do NOT remove! */
-  if (trexio_has_$group_num$(file) == TREXIO_SUCCESS) return TREXIO_ATTR_ALREADY_EXISTS;
+  if (trexio_has_$group_num$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
 
   switch (file->back_end) {
 
@@ -1496,7 +1496,7 @@ trexio_write_$group_num$_32 (trexio_t* const file, const $group_num_dtype_single
 
   if (file == NULL) return TREXIO_INVALID_ARG_1;
   //if (num <= 0) return TREXIO_INVALID_NUM; /* this line is uncommented by the generator for dimensioning variables; do NOT remove! */
-  if (trexio_has_$group_num$(file) == TREXIO_SUCCESS) return TREXIO_ATTR_ALREADY_EXISTS;
+  if (trexio_has_$group_num$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
 
   switch (file->back_end) {
 
@@ -1844,7 +1844,7 @@ trexio_write_$group_dset$_64 (trexio_t* const file, const $group_dset_dtype_doub
   assert(file->back_end < TREXIO_INVALID_BACK_END);
 
   if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
-  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) return TREXIO_DSET_ALREADY_EXISTS;
+  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
 
 
   trexio_exit_code rc;
@@ -2015,7 +2015,7 @@ trexio_write_$group_dset$_32 (trexio_t* const file, const $group_dset_dtype_sing
 
   if (file  == NULL) return TREXIO_INVALID_ARG_1;
   if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
-  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) return TREXIO_DSET_ALREADY_EXISTS;
+  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
 
   trexio_exit_code rc;
   int64_t $group_dset_dim$ = 0;
@@ -2127,7 +2127,7 @@ trexio_write_safe_$group_dset$_32 (trexio_t* const file, const $group_dset_dtype
 
   if (file  == NULL) return TREXIO_INVALID_ARG_1;
   if (dset_in == NULL) return TREXIO_INVALID_ARG_2;
-  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) return TREXIO_DSET_ALREADY_EXISTS;
+  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
 
 <<dimCheck>>
 
@@ -2162,7 +2162,7 @@ trexio_write_safe_$group_dset$_64 (trexio_t* const file, const $group_dset_dtype
 
   if (file  == NULL) return TREXIO_INVALID_ARG_1;
   if (dset_in == NULL) return TREXIO_INVALID_ARG_2;
-  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) return TREXIO_DSET_ALREADY_EXISTS;
+  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
 
 <<dimCheck>>
 
@@ -3288,7 +3288,7 @@ trexio_write_$group_dset$_low (trexio_t* const file, char* dset_in, const int32_
   if (file  == NULL) return TREXIO_INVALID_ARG_1;
   if (dset_in == NULL) return TREXIO_INVALID_ARG_2;
   if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
-  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) return TREXIO_DSET_ALREADY_EXISTS;
+  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
 
   trexio_exit_code rc;
   int64_t $group_dset_dim$ = 0;
@@ -3372,7 +3372,7 @@ trexio_write_$group_dset$ (trexio_t* const file, const char** dset_in, const int
   if (file  == NULL) return TREXIO_INVALID_ARG_1;
   if (dset_in == NULL) return TREXIO_INVALID_ARG_2;
   if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
-  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) return TREXIO_DSET_ALREADY_EXISTS;
+  if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_DSET_ALREADY_EXISTS;
 
   assert(file->back_end < TREXIO_INVALID_BACK_END);
 
@@ -3694,7 +3694,7 @@ trexio_write_$group_str$ (trexio_t* const file, const char* str, const int32_t m
   if (file == NULL) return TREXIO_INVALID_ARG_1;
   if (str  == NULL) return TREXIO_INVALID_ARG_2;
   if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
-  if (trexio_has_$group_str$(file) == TREXIO_SUCCESS) return TREXIO_ATTR_ALREADY_EXISTS;
+  if (trexio_has_$group_str$(file) == TREXIO_SUCCESS && file->mode != 'u') return TREXIO_ATTR_ALREADY_EXISTS;
 
   size_t len_write = strlen(str);
   if ((size_t) max_str_len < len_write) return TREXIO_INVALID_STR_LEN;
diff --git a/src/templates_text/templator_text.org b/src/templates_text/templator_text.org
index 96f945a..7ad0ff9 100644
--- a/src/templates_text/templator_text.org
+++ b/src/templates_text/templator_text.org
@@ -578,7 +578,7 @@ trexio_text_flush_$group$ (trexio_text_t* const file)
 
   if ($group$->to_flush == 0) return TREXIO_SUCCESS;
 
-  assert (file->parent.mode == 'w');
+  assert (file->parent.mode == 'w' || file->parent.mode == 'u');
 
   FILE* f = fopen($group$->file_name, "w");
   if (f == NULL) return TREXIO_INVALID_ARG_1;
diff --git a/tests/overwrite_all_text.c b/tests/overwrite_all_text.c
index 11e5518..5baf99e 100644
--- a/tests/overwrite_all_text.c
+++ b/tests/overwrite_all_text.c
@@ -2,6 +2,7 @@
 #include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
 
 #define TEST_BACKEND 	TREXIO_TEXT
 #define TREXIO_FILE 	"test_over.dir"
@@ -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_overwrite (TREXIO_FILE, TEST_BACKEND);
+  test_write            (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;
 }
-
-