Merge branch 'master' into change_h5rw_datasets

src/test.c

@@ -120,15 +120,11 @@ int test_h5read() {
   file2 = trexio_open(file_name2, 'r', TREXIO_HDF5);
   assert (file2 == NULL);
 
-  // test appending non-existing file, should create it
-  const char* file_name3 = "test_append.h5";
+  // test appending non-existing file, should fail and return NULL
   trexio_t* file3 = NULL;
 
-  file3 = trexio_open(file_name3, 'a', TREXIO_HDF5);
-  assert (file3 != NULL);
-
-  rc = trexio_close(file3);
-  assert (rc == TREXIO_SUCCESS);
+  file3 = trexio_open(file_name2, 'a', TREXIO_HDF5);
+  assert (file3 == NULL);
 
   free(coord);
 

src/trexio.c

@@ -31,6 +31,7 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
 
   trexio_t* result = NULL;
   
+  /* Allocate data structures */
   switch (back_end) {
 
   case TREXIO_TEXT:
@@ -47,8 +48,10 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
 */      
   }
   
-  /* TODO: Error handling */
-  assert (result != NULL);
+  assert (result != NULL);    /* TODO: Error handling */
+
+
+  /* Data for the parent type */
 
   result->file_name   = (char*) calloc(strlen(file_name)+1,sizeof(char));
   strcpy(result->file_name, file_name);
@@ -57,7 +60,11 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
   int irc = pthread_mutex_init ( &(result->thread_lock), NULL);
   assert (irc == 0);
 
-  trexio_exit_code rc = TREXIO_FAILURE;
+  trexio_exit_code rc;
+  
+  /* Back end initialization */
+  
+  rc = TREXIO_FAILURE;
   
   switch (back_end) {
 
@@ -81,6 +88,32 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
     return NULL;
   }
 
+  /* File locking */
+  
+  rc = TREXIO_FAILURE;
+  
+  switch (back_end) {
+
+  case TREXIO_TEXT:
+    rc = trexio_text_lock(result);
+    break;
+
+  case TREXIO_HDF5:
+    rc = TREXIO_SUCCESS;
+    break;
+/*
+  case TREXIO_JSON:
+    rc = trexio_json_lock(result);
+    break;
+*/      
+  }
+  
+  if (rc != TREXIO_SUCCESS) {
+    free(result->file_name);
+    free(result);
+    return NULL;
+  }
+  
   return result;
 }
 
@@ -90,6 +123,7 @@ trexio_exit_code trexio_close(trexio_t* file) {
   
   trexio_exit_code rc;
   
+  /* Terminate the back end */
   switch (file->back_end) {
 
   case TREXIO_TEXT:
@@ -108,16 +142,44 @@ trexio_exit_code trexio_close(trexio_t* file) {
     assert (1 == 0);  /* Impossible case */
   }
 
+  if (rc != TREXIO_SUCCESS) {
+    free(file->file_name);
+    free(file);
+    return TREXIO_FAILURE;
+  }
+  
+  /* File unlocking */
+  
+  rc = TREXIO_FAILURE;
+  
+  switch (file->back_end) {
+
+  case TREXIO_TEXT:
+    rc = trexio_text_unlock(file);
+    break;
+
+  case TREXIO_HDF5:
+    rc = TREXIO_SUCCESS;
+    break;
+/*
+  case TREXIO_JSON:
+    rc = trexio_json_unlock(file);
+    break;
+*/      
+  }
+
+  /* Terminate front end */
+  
   free(file->file_name);
   file->file_name = NULL;
   
   int irc = pthread_mutex_destroy( &(file->thread_lock) );
-  assert (irc == 0);
-
-  free(file); 
-
-  if (rc != TREXIO_SUCCESS) return rc;
   
+  free(file);
+
+  if (irc != 0) return TREXIO_ERRNO;
+  if (rc != TREXIO_SUCCESS) return TREXIO_FAILURE;
+    
   return TREXIO_SUCCESS;
 }
 

src/trexio.h

@@ -21,6 +21,7 @@ typedef int32_t trexio_exit_code;
 #define TREXIO_INVALID_ARG_5 ( (trexio_exit_code)  5 )
 #define TREXIO_END           ( (trexio_exit_code) 10 )
 #define TREXIO_READONLY      ( (trexio_exit_code) 11 )
+#define TREXIO_ERRNO         ( (trexio_exit_code) 12 )
 #define TREXIO_INVALID_ID    ( (trexio_exit_code) 20 )
 #define TREXIO_INVALID_NUM   ( (trexio_exit_code) 21 )
 

src/trexio.org

@@ -78,6 +78,7 @@ typedef int32_t trexio_exit_code;
 #define TREXIO_INVALID_ARG_5 ( (trexio_exit_code)  5 )
 #define TREXIO_END           ( (trexio_exit_code) 10 )
 #define TREXIO_READONLY      ( (trexio_exit_code) 11 )
+#define TREXIO_ERRNO         ( (trexio_exit_code) 12 )
 #define TREXIO_INVALID_ID    ( (trexio_exit_code) 20 )
 #define TREXIO_INVALID_NUM   ( (trexio_exit_code) 21 )
    #+end_src
@@ -170,6 +171,7 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
 
   trexio_t* result = NULL;
   
+ /* Allocate data structures */
   switch (back_end) {
 
   case TREXIO_TEXT:
@@ -186,8 +188,10 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
 ,*/      
   }
   
- /* TODO: Error handling */
-  assert (result != NULL);
+  assert (result != NULL); /* TODO: Error handling */
+
+
+ /* Data for the parent type */
 
   result->file_name   = (char*) calloc(strlen(file_name)+1,sizeof(char));
   strcpy(result->file_name, file_name);
@@ -196,7 +200,11 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
   int irc = pthread_mutex_init ( &(result->thread_lock), NULL);
   assert (irc == 0);
 
-  trexio_exit_code rc = TREXIO_FAILURE;
+  trexio_exit_code rc;
+  
+ /* Back end initialization */
+  
+  rc = TREXIO_FAILURE;
   
   switch (back_end) {
 
@@ -220,6 +228,32 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
     return NULL;
   }
 
+ /* File locking */
+  
+  rc = TREXIO_FAILURE;
+  
+  switch (back_end) {
+
+  case TREXIO_TEXT:
+    rc = trexio_text_lock(result);
+    break;
+
+  case TREXIO_HDF5:
+    rc = TREXIO_SUCCESS;
+    break;
+/*
+  case TREXIO_JSON:
+    rc = trexio_json_lock(result);
+    break;
+*/      
+  }
+  
+  if (rc != TREXIO_SUCCESS) {
+    free(result->file_name);
+    free(result);
+    return NULL;
+  }
+  
   return result;
 }
    #+end_src
@@ -237,6 +271,7 @@ trexio_exit_code trexio_close(trexio_t* file) {
   
   trexio_exit_code rc;
   
+ /* Terminate the back end */
   switch (file->back_end) {
 
   case TREXIO_TEXT:
@@ -255,17 +290,47 @@ trexio_exit_code trexio_close(trexio_t* file) {
     assert (1 == 0); /* Impossible case */
   }
 
+  if (rc != TREXIO_SUCCESS) {
+    free(file->file_name);
+    free(file);
+    return TREXIO_FAILURE;
+  }
+  
+ /* File unlocking */
+  
+  rc = TREXIO_FAILURE;
+  
+  switch (file->back_end) {
+
+  case TREXIO_TEXT:
+    rc = trexio_text_unlock(file);
+    break;
+
+  case TREXIO_HDF5:
+    rc = TREXIO_SUCCESS;
+    break;
+/*
+  case TREXIO_JSON:
+    rc = trexio_json_unlock(file);
+    break;
+*/      
+  }
+
+ /* Terminate front end */
+  
   free(file->file_name);
   file->file_name = NULL;
   
   int irc = pthread_mutex_destroy( &(file->thread_lock) );
-  assert (irc == 0);
-
-  free(file); 
-
-  if (rc != TREXIO_SUCCESS) return rc;
   
+  free(file);
+
+  if (irc != 0) return TREXIO_ERRNO;
+  if (rc != TREXIO_SUCCESS) return TREXIO_FAILURE;
+    
   return TREXIO_SUCCESS;
+}
+
 }
    #+end_src
 ** Reading/writing data
@@ -629,5 +694,4 @@ trexio_exit_code trexio_buffered_write_rdm_two_e(trexio_t* file, const int64_t o
   - [ ] Error handling with errno
   - [ ] HDF5 back-end
   - [ ] JSON back-end
-  - [ ] File locking with flock
   - [ ] Caching of the struct saving last modification date in structs

src/trexio_hdf5.c

@@ -95,10 +95,10 @@ trexio_exit_code trexio_hdf5_init(trexio_t* file) {
     switch (file->mode) {
     case 'r': 
     case 'a': 
-      // reading non-existing file -> error
+      // reading or appending non-existing file -> error
       return TREXIO_FAILURE;
     case 'w': 
-      // appending or writing non-existing file -> create it
+      // writing non-existing file -> create it
       f->file_id = H5Fcreate(file->file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
       break;
     }  
@@ -107,10 +107,11 @@ trexio_exit_code trexio_hdf5_init(trexio_t* file) {
 
   /* Create or open groups in the hdf5 file assuming that they exist if file exists */    
   switch (file->mode) {
+    // the switch for 'r'/'a' is reached only if file exists
     case 'r':
     case 'a': 
       f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
-      //f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT);   
+      //f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT); 
       break;
     case 'w':
       f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
@@ -370,7 +371,7 @@ trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint6
 
     if (nucleus->num != 0) {
 	printf("%ld -> %ld %s \n", num, nucleus->num, 
-	       "This variable alreasy exists. Overwriting it is not supported");
+	       "This variable already exists. Overwriting it is not supported");
         trexio_hdf5_free_nucleus(nucleus);
     	return TREXIO_FAILURE;
     }

src/trexio_hdf5.org

@@ -186,10 +186,10 @@ trexio_exit_code trexio_hdf5_init(trexio_t* file) {
     switch (file->mode) {
     case 'r': 
     case 'a': 
-      // reading non-existing file -> error
+      // reading or appending non-existing file -> error
       return TREXIO_FAILURE;
     case 'w': 
-      // appending or writing non-existing file -> create it
+      // writing non-existing file -> create it
       f->file_id = H5Fcreate(file->file_name, H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
       break;
     }  
@@ -198,10 +198,11 @@ trexio_exit_code trexio_hdf5_init(trexio_t* file) {
 
  /* Create or open groups in the hdf5 file assuming that they exist if file exists */    
   switch (file->mode) {
+    // the switch for 'r'/'a' is reached only if file exists
     case 'r':
     case 'a': 
       f->nucleus_group = H5Gopen(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT);
-      //f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT);   
+      //f->electron_group = H5Gopen(f->file_id, ELECTRON_GROUP_NAME, H5P_DEFAULT); 
       break;
     case 'w':
       f->nucleus_group = H5Gcreate(f->file_id, NUCLEUS_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
@@ -521,7 +522,7 @@ trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint6
 
     if (nucleus->num != 0) {
 	printf("%ld -> %ld %s \n", num, nucleus->num, 
-	       "This variable alreasy exists. Overwriting it is not supported");
+	       "This variable already exists. Overwriting it is not supported");
         trexio_hdf5_free_nucleus(nucleus);
     	return TREXIO_FAILURE;
     }

src/trexio_text.c

@@ -38,7 +38,18 @@ trexio_exit_code trexio_text_init(trexio_t* file) {
   assert (f->lock_file > 0);
   free(file_name);
 
-  /* Lock the directory for the current process */
+  f->nucleus = NULL;
+  f->electron= NULL;
+  f->rdm     = NULL;
+  
+  return TREXIO_SUCCESS;
+}
+
+trexio_exit_code trexio_text_lock(trexio_t* file) {
+  if (file == NULL) return TREXIO_INVALID_ARG_1;
+
+  trexio_text_t* f = (trexio_text_t*) file;
+
   struct flock fl;
   
   fl.l_type   = F_WRLCK;
@@ -50,20 +61,12 @@ trexio_exit_code trexio_text_init(trexio_t* file) {
   int rc = fcntl(f->lock_file, F_SETLKW, &fl);
   if (rc == -1) return TREXIO_FAILURE;
 
-  trexio_text_t* f_child = (trexio_text_t*) file;
-
-  f_child->nucleus = NULL;
-  f_child->electron= NULL;
-  f_child->rdm     = NULL;
-  
   return TREXIO_SUCCESS;
 }
 
 trexio_exit_code trexio_text_finalize(trexio_t* file) {
   if (file  == NULL) return TREXIO_INVALID_ARG_1;
 
-  trexio_text_t* f = (trexio_text_t*) file;
-
   trexio_exit_code rc;
   rc = trexio_text_free_nucleus( (trexio_text_t*) file);
   assert (rc == TREXIO_SUCCESS);
@@ -71,7 +74,14 @@ trexio_exit_code trexio_text_finalize(trexio_t* file) {
   rc = trexio_text_free_rdm( (trexio_text_t*) file);
   assert (rc == TREXIO_SUCCESS);
   
-  /* Release lock */
+  return TREXIO_SUCCESS;
+}
+
+trexio_exit_code trexio_text_unlock(trexio_t* file) {
+  if (file  == NULL) return TREXIO_INVALID_ARG_1;
+
+  trexio_text_t* f = (trexio_text_t*) file;
+
   struct flock fl;
 
   fl.l_type   = F_WRLCK;

src/trexio_text.h

@@ -56,8 +56,12 @@ typedef struct trexio_text_s {
 
 trexio_exit_code trexio_text_init(trexio_t* file);
 
+trexio_exit_code trexio_text_lock(trexio_t* file);
+
 trexio_exit_code trexio_text_finalize(trexio_t* file);
 
+trexio_exit_code trexio_text_unlock(trexio_t* file);
+
 nucleus_t* trexio_text_read_nucleus(trexio_text_t* file);
 
 trexio_exit_code trexio_text_flush_nucleus(const trexio_text_t* file);

src/trexio_text.org

@@ -137,7 +137,25 @@ trexio_exit_code trexio_text_init(trexio_t* file) {
   assert (f->lock_file > 0);
   free(file_name);
 
- /* Lock the directory for the current process */
+  f->nucleus = NULL;
+  f->electron= NULL;
+  f->rdm     = NULL;
+  
+  return TREXIO_SUCCESS;
+}
+
+    #+end_src
+
+    #+begin_src c :tangle trexio_text.h
+trexio_exit_code trexio_text_lock(trexio_t* file);
+    #+end_src
+  
+    #+begin_src c :tangle trexio_text.c
+trexio_exit_code trexio_text_lock(trexio_t* file) {
+  if (file == NULL) return TREXIO_INVALID_ARG_1;
+
+  trexio_text_t* f = (trexio_text_t*) file;
+
   struct flock fl;
   
   fl.l_type   = F_WRLCK;
@@ -149,12 +167,6 @@ trexio_exit_code trexio_text_init(trexio_t* file) {
   int rc = fcntl(f->lock_file, F_SETLKW, &fl);
   if (rc == -1) return TREXIO_FAILURE;
 
-  trexio_text_t* f_child = (trexio_text_t*) file;
-
-  f_child->nucleus = NULL;
-  f_child->electron= NULL;
-  f_child->rdm     = NULL;
-  
   return TREXIO_SUCCESS;
 }
 
@@ -169,8 +181,6 @@ trexio_exit_code trexio_text_finalize(trexio_t* file);
 trexio_exit_code trexio_text_finalize(trexio_t* file) {
   if (file  == NULL) return TREXIO_INVALID_ARG_1;
 
-  trexio_text_t* f = (trexio_text_t*) file;
-
   trexio_exit_code rc;
   rc = trexio_text_free_nucleus( (trexio_text_t*) file);
   assert (rc == TREXIO_SUCCESS);
@@ -178,7 +188,20 @@ trexio_exit_code trexio_text_finalize(trexio_t* file) {
   rc = trexio_text_free_rdm( (trexio_text_t*) file);
   assert (rc == TREXIO_SUCCESS);
   
- /* Release lock */
+  return TREXIO_SUCCESS;
+}
+    #+end_src
+
+    #+begin_src c :tangle trexio_text.h
+trexio_exit_code trexio_text_unlock(trexio_t* file);
+    #+end_src
+    
+    #+begin_src c :tangle trexio_text.c
+trexio_exit_code trexio_text_unlock(trexio_t* file) {
+  if (file  == NULL) return TREXIO_INVALID_ARG_1;
+
+  trexio_text_t* f = (trexio_text_t*) file;
+
   struct flock fl;
 
   fl.l_type   = F_WRLCK;