AVLs: made some functions public and changed some rights to be able to

import AVLs from a DMS to another

src/obiavl.c

@@ -41,23 +41,6 @@
  **************************************************************************/
 
 
-/**
- * @brief Internal function building the complete AVL name for an AVL with an associated index (for AVL groups).
- *
- * @warning The returned pointer has to be freed by the caller.
- *
- * @param avl_name The base name of the AVL tree.
- * @param avl_idx The index associated with that AVL.
- *
- * @returns A pointer to the complete name of the AVL.
- * @retval NULL if an error occurred.
- *
- * @since April 2016
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-static char* build_avl_name_with_idx(const char* avl_name, int avl_idx);
-
-
 /**
  * @brief Internal function building the full path of an AVL directory containing an AVL or an AVL group.
  *
@@ -107,42 +90,6 @@ static char* build_avl_file_name(const char* avl_name);
 static char* build_avl_data_file_name(const char* avl_name);
 
 
-/**
- * @brief Internal function building the full path of an AVL tree file.
- *
- * @warning The returned pointer has to be freed by the caller.
- *
- * @param dms A pointer to the OBIDMS to which the AVL tree belongs.
- * @param avl_name The name of the AVL tree.
- * @param avl_idx The index of the AVL if it's part of an AVL group, or -1 if not.
- *
- * @returns A pointer to the full path of the file where the AVL tree is stored.
- * @retval NULL if an error occurred.
- *
- * @since May 2016
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-static char* get_full_path_of_avl_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx);
-
-
-/**
- * @brief Internal function building the file name for an AVL data file.
- *
- * @warning The returned pointer has to be freed by the caller.
- *
- * @param dms A pointer to the OBIDMS to which the AVL tree belongs.
- * @param avl_name The name of the AVL tree.
- * @param avl_idx The index of the AVL if it's part of an AVL group, or -1 if not.
- *
- * @returns A pointer to the full path of the file where the data referred to by the AVL tree is stored.
- * @retval NULL if an error occurred.
- *
- * @since May 2016
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-static char* get_full_path_of_avl_data_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx);
-
-
 /**
  * @brief Internal function returning the size of an AVL tree header on this platform,
  *        including the size of the bloom filter associated with the AVL tree.
@@ -501,36 +448,6 @@ void avl_print(OBIDMS_avl_p avl);
  *
  ************************************************************************/
 
-static char* build_avl_name_with_idx(const char* avl_name, int avl_idx)
-{
-	char* avl_name_with_idx;
-	int   avl_idx_length;
-
-	if (avl_idx < 0)
-	{
-		obi_set_errno(OBI_AVL_ERROR);
-		obidebug(1, "\nError building an AVL tree name with index: index < 0");
-		return NULL;
-	}
-
-	avl_idx_length = avl_idx == 0 ? 1 : (int)(log10(avl_idx)+1);
-	avl_name_with_idx = malloc((strlen(avl_name) + avl_idx_length + 2)*sizeof(char));
-	if (avl_name_with_idx == NULL)
-	{
-		obi_set_errno(OBI_MALLOC_ERROR);
-		obidebug(1, "\nError allocating memory for an AVL name");
-		return NULL;
-	}
-	if (sprintf(avl_name_with_idx, "%s_%u", avl_name, avl_idx) < 0)
-	{
-		obi_set_errno(OBI_AVL_ERROR);
-		obidebug(1, "\nError building an AVL tree name with index");
-		return NULL;
-	}
-
-	return avl_name_with_idx;
-}
-
 
 char* get_full_path_of_avl_dir(OBIDMS_p dms, const char* avl_name)
 {
@@ -604,102 +521,6 @@ static char* build_avl_data_file_name(const char* avl_name)
 }
 
 
-static char* get_full_path_of_avl_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx)
-{
-	char* complete_avl_name;
-	char* full_path;
-	char* avl_file_name;
-
-	if (avl_idx >= 0)
-	{
-		complete_avl_name = build_avl_name_with_idx(avl_name, avl_idx);
-		if (complete_avl_name == NULL)
-			return NULL;
-	}
-	else
-	{
-		complete_avl_name = (char*) malloc((strlen(avl_name)+1)*sizeof(char));
-		if (complete_avl_name == NULL)
-		{
-    		obi_set_errno(OBI_MALLOC_ERROR);
-    		obidebug(1, "\nError allocating memory for an AVL name");
-			return NULL;
-		}
-		strcpy(complete_avl_name, avl_name);
-	}
-
-	avl_file_name = build_avl_file_name(complete_avl_name);
-	if (avl_file_name == NULL)
-	{
-		free(complete_avl_name);
-		return NULL;
-	}
-
-	full_path = get_full_path_of_avl_dir(dms, avl_name);
-	if (full_path == NULL)
-	{
-		free(complete_avl_name);
-		free(avl_file_name);
-		return NULL;
-	}
-
-	strcat(full_path, "/");
-	strcat(full_path, avl_file_name);
-
-	free(complete_avl_name);
-
-	return full_path;
-}
-
-
-static char* get_full_path_of_avl_data_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx)
-{
-	char* complete_avl_name;
-	char* full_path;
-	char* avl_data_file_name;
-
-	if (avl_idx >= 0)
-	{
-		complete_avl_name = build_avl_name_with_idx(avl_name, avl_idx);
-		if (complete_avl_name == NULL)
-			return NULL;
-	}
-	else
-	{
-		complete_avl_name = (char*) malloc((strlen(avl_name)+1)*sizeof(char));
-		if (complete_avl_name == NULL)
-		{
-    		obi_set_errno(OBI_MALLOC_ERROR);
-    		obidebug(1, "\nError allocating memory for an AVL name");
-			return NULL;
-		}
-		strcpy(complete_avl_name, avl_name);
-	}
-
-	avl_data_file_name = build_avl_data_file_name(complete_avl_name);
-	if (avl_data_file_name == NULL)
-	{
-		free(complete_avl_name);
-		return NULL;
-	}
-
-	full_path = get_full_path_of_avl_dir(dms, avl_name);
-	if (full_path == NULL)
-	{
-		free(complete_avl_name);
-		free(avl_data_file_name);
-		return NULL;
-	}
-
-	strcat(full_path, "/");
-	strcat(full_path, avl_data_file_name);
-
-	free(complete_avl_name);
-
-	return full_path;
-}
-
-
 size_t get_avl_header_size()
 {
 	size_t header_size;
@@ -1103,13 +924,13 @@ int add_new_avl_in_group(OBIDMS_avl_group_p avl_group)
 
 int add_existing_avl_in_group(OBIDMS_avl_group_p avl_group_dest, OBIDMS_avl_group_p avl_group_source, int avl_idx)
 {
-	if (link(get_full_path_of_avl_file_name(avl_group_source->dms, avl_group_source->name, avl_idx), get_full_path_of_avl_file_name(avl_group_dest->dms, avl_group_dest->name, avl_idx)) < 0)
+	if (link(obi_get_full_path_of_avl_file_name(avl_group_source->dms, avl_group_source->name, avl_idx), obi_get_full_path_of_avl_file_name(avl_group_dest->dms, avl_group_dest->name, avl_idx)) < 0)
 	{
 		obi_set_errno(OBI_AVL_ERROR);
 		obidebug(1, "\nError creating a hard link to an existing AVL tree file");
 		return -1;
 	}
-	if (link(get_full_path_of_avl_data_file_name(avl_group_source->dms, avl_group_source->name, avl_idx), get_full_path_of_avl_data_file_name(avl_group_dest->dms, avl_group_dest->name, avl_idx)) < 0)
+	if (link(obi_get_full_path_of_avl_data_file_name(avl_group_source->dms, avl_group_source->name, avl_idx), obi_get_full_path_of_avl_data_file_name(avl_group_dest->dms, avl_group_dest->name, avl_idx)) < 0)
 	{
 		obi_set_errno(OBI_AVL_ERROR);
 		obidebug(1, "\nError creating a hard link to an existing AVL data file");
@@ -1400,6 +1221,134 @@ void avl_print(OBIDMS_avl_p avl)
  *
  **********************************************************************/
 
+
+char* obi_build_avl_name_with_idx(const char* avl_name, int avl_idx)
+{
+	char* avl_name_with_idx;
+	int   avl_idx_length;
+
+	if (avl_idx < 0)
+	{
+		obi_set_errno(OBI_AVL_ERROR);
+		obidebug(1, "\nError building an AVL tree name with index: index < 0");
+		return NULL;
+	}
+
+	avl_idx_length = avl_idx == 0 ? 1 : (int)(log10(avl_idx)+1);
+	avl_name_with_idx = malloc((strlen(avl_name) + avl_idx_length + 2)*sizeof(char));
+	if (avl_name_with_idx == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for an AVL name");
+		return NULL;
+	}
+	if (sprintf(avl_name_with_idx, "%s_%u", avl_name, avl_idx) < 0)
+	{
+		obi_set_errno(OBI_AVL_ERROR);
+		obidebug(1, "\nError building an AVL tree name with index");
+		return NULL;
+	}
+
+	return avl_name_with_idx;
+}
+
+
+char* obi_get_full_path_of_avl_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx)
+{
+	char* complete_avl_name;
+	char* full_path;
+	char* avl_file_name;
+
+	if (avl_idx >= 0)
+	{
+		complete_avl_name = obi_build_avl_name_with_idx(avl_name, avl_idx);
+		if (complete_avl_name == NULL)
+			return NULL;
+	}
+	else
+	{
+		complete_avl_name = (char*) malloc((strlen(avl_name)+1)*sizeof(char));
+		if (complete_avl_name == NULL)
+		{
+    		obi_set_errno(OBI_MALLOC_ERROR);
+    		obidebug(1, "\nError allocating memory for an AVL name");
+			return NULL;
+		}
+		strcpy(complete_avl_name, avl_name);
+	}
+
+	avl_file_name = build_avl_file_name(complete_avl_name);
+	if (avl_file_name == NULL)
+	{
+		free(complete_avl_name);
+		return NULL;
+	}
+
+	full_path = get_full_path_of_avl_dir(dms, avl_name);
+	if (full_path == NULL)
+	{
+		free(complete_avl_name);
+		free(avl_file_name);
+		return NULL;
+	}
+
+	strcat(full_path, "/");
+	strcat(full_path, avl_file_name);
+
+	free(complete_avl_name);
+
+	return full_path;
+}
+
+
+char* obi_get_full_path_of_avl_data_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx)
+{
+	char* complete_avl_name;
+	char* full_path;
+	char* avl_data_file_name;
+
+	if (avl_idx >= 0)
+	{
+		complete_avl_name = obi_build_avl_name_with_idx(avl_name, avl_idx);
+		if (complete_avl_name == NULL)
+			return NULL;
+	}
+	else
+	{
+		complete_avl_name = (char*) malloc((strlen(avl_name)+1)*sizeof(char));
+		if (complete_avl_name == NULL)
+		{
+    		obi_set_errno(OBI_MALLOC_ERROR);
+    		obidebug(1, "\nError allocating memory for an AVL name");
+			return NULL;
+		}
+		strcpy(complete_avl_name, avl_name);
+	}
+
+	avl_data_file_name = build_avl_data_file_name(complete_avl_name);
+	if (avl_data_file_name == NULL)
+	{
+		free(complete_avl_name);
+		return NULL;
+	}
+
+	full_path = get_full_path_of_avl_dir(dms, avl_name);
+	if (full_path == NULL)
+	{
+		free(complete_avl_name);
+		free(avl_data_file_name);
+		return NULL;
+	}
+
+	strcat(full_path, "/");
+	strcat(full_path, avl_data_file_name);
+
+	free(complete_avl_name);
+
+	return full_path;
+}
+
+
 int obi_avl_exists(OBIDMS_p dms, const char* avl_name)
 {
 	struct stat buffer;
@@ -1443,7 +1392,7 @@ OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
 	// Get complete name of AVL if index
 	if (avl_idx >= 0)
 	{
-		complete_avl_name = build_avl_name_with_idx(avl_name, avl_idx);
+		complete_avl_name = obi_build_avl_name_with_idx(avl_name, avl_idx);
 		if (complete_avl_name == NULL)
 			return NULL;
 	}
@@ -1740,7 +1689,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
 	// Get complete name of AVL if index
 	if (avl_idx >= 0)
 	{
-		complete_avl_name = build_avl_name_with_idx(avl_name, avl_idx);
+		complete_avl_name = obi_build_avl_name_with_idx(avl_name, avl_idx);
 		if (complete_avl_name == NULL)
 			return NULL;
 	}
@@ -1794,7 +1743,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
 		return NULL;
 
 		// Open file
-	avl_data_file_descriptor = openat(avl_dir_file_descriptor, avl_data_file_name, O_RDONLY, 0777);
+	avl_data_file_descriptor = openat(avl_dir_file_descriptor, avl_data_file_name, O_RDWR, 0777);
 	if (avl_data_file_descriptor < 0)
 	{
 		obi_set_errno(OBI_AVL_ERROR);
@@ -1832,7 +1781,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
 		// Fill the avl data structure
 	avl_data->header = mmap(NULL,
 			                header_size,
-			                PROT_READ,
+							PROT_READ | PROT_WRITE,
 			                MAP_SHARED,
 			                avl_data_file_descriptor,
 			                0
@@ -1881,7 +1830,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
 	}
 
 		// Open file
-	avl_file_descriptor = openat(avl_dir_file_descriptor, avl_file_name, O_RDONLY, 0777);
+	avl_file_descriptor = openat(avl_dir_file_descriptor, avl_file_name, O_RDWR, 0777);
 	if (avl_file_descriptor < 0)
 	{
 		obi_set_errno(OBI_AVL_ERROR);
@@ -1921,7 +1870,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
 		// Fill the avl structure
 	avl->header = mmap(NULL,
 			           header_size,
-			           PROT_READ,
+					   PROT_READ | PROT_WRITE,
 			           MAP_SHARED,
 			           avl_file_descriptor,
 			           0

src/obiavl.h

@@ -169,6 +169,60 @@ typedef struct OBIDMS_avl_group {
 } OBIDMS_avl_group_t, *OBIDMS_avl_group_p;
 
 
+
+/**
+ * @brief Function building the complete AVL name for an AVL with an associated index (for AVL groups).
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param avl_name The base name of the AVL tree.
+ * @param avl_idx The index associated with that AVL.
+ *
+ * @returns A pointer to the complete name of the AVL.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_build_avl_name_with_idx(const char* avl_name, int avl_idx);
+
+
+/**
+ * @brief Function building the full path of an AVL tree file.
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param dms A pointer to the OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ * @param avl_idx The index of the AVL if it's part of an AVL group, or -1 if not.
+ *
+ * @returns A pointer to the full path of the file where the AVL tree is stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since May 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_get_full_path_of_avl_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx);
+
+
+/**
+ * @brief Function building the file name for an AVL data file.
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param dms A pointer to the OBIDMS to which the AVL tree belongs.
+ * @param avl_name The name of the AVL tree.
+ * @param avl_idx The index of the AVL if it's part of an AVL group, or -1 if not.
+ *
+ * @returns A pointer to the full path of the file where the data referred to by the AVL tree is stored.
+ * @retval NULL if an error occurred.
+ *
+ * @since May 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* obi_get_full_path_of_avl_data_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx);
+
+
 /**
  * @brief Checks if an AVL tree or AVL tree group already exists or not.
  *