Columns: implemented handling of JSON formatted comments

src/obidmscolumn.c

@@ -32,6 +32,7 @@
 #include "obilittlebigman.h"
 #include "obiblob_indexer.h"
 #include "utils.h"
+#include "libjson/json_utils.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -931,6 +932,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 	int 						column_file_descriptor;
 	size_t 						header_size;
 	size_t 						data_size;
+	int 						comments_ok;
 	index_t						minimum_line_count;
 	OBIType_t  					returned_data_type;
 	OBIType_t  					stored_data_type;
@@ -1146,8 +1148,19 @@ OBIDMS_column_p obi_create_column(OBIDMS_p     dms,
 
 	strncpy(header->name, column_name, OBIDMS_COLUMN_MAX_NAME);
 
-	if ((comments != NULL) && (*comments != '\0'))
+	// Comments must be a json string, even empty
-		strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
+	if ((strcmp(comments, "") == 0) || (comments == NULL))
+		comments_ok = obi_column_write_comments(new_column, "{}");
+	else
+		comments_ok = obi_column_write_comments(new_column, comments);
+	if (comments_ok < 0)
+	{
+		obidebug(1, "\nError writing comments in new column");
+		munmap(new_column->header, header_size);
+		close(column_file_descriptor);
+		free(new_column);
+		return NULL;
+	}
 
 	// Store the associated column reference if needed // TODO discuss cases
 	if (data_type == OBI_QUAL)
@@ -1750,6 +1763,46 @@ int obi_enlarge_column(OBIDMS_column_p column)
 }
 
 
+int obi_column_write_comments(OBIDMS_column_p column, const char* comments)
+{
+	if (comments == NULL)
+		return 0;	// TODO or error? or set to empty string? discuss
+
+	if (strlen(comments) > COMMENTS_MAX_LENGTH)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError: comments too long (maximum length: %d, length: %lu, comments: %s",
+				COMMENTS_MAX_LENGTH, strlen(comments), comments);
+		return -1;
+	}
+
+	strcpy((column->header)->comments, comments);
+
+	return 0;
+}
+
+
+int obi_column_add_comment(OBIDMS_column_p column, const char* key, const char* value)
+{
+	char* new_comments = NULL;
+
+	new_comments = obi_add_comment((column->header)->comments, key, value);
+	if (new_comments == NULL)
+	{
+		obidebug(1, "\nError adding a comment in a column, key: %s, value: %s", key, value);
+		return -1;
+	}
+
+	if (obi_column_write_comments(column, new_comments) < 0)
+	{
+		obidebug(1, "\nError adding a comment in a column, key: %s, value: %s", key, value);
+		return -1;
+	}
+
+	return 0;
+}
+
+
 void obi_set_column_to_value(OBIDMS_column_p column,
 						  	 index_t first_line_nb,
 							 index_t nb_lines,
@@ -2067,7 +2120,7 @@ int obi_clean_unfinished_columns(OBIDMS_p dms)
 	struct dirent*         dms_dirent;
 	struct dirent*  	   col_dirent;
 	DIR*           		   col_dir;
-	int		       		   i,j;
+	size_t	      		   i,j;
 	char*          		   column_file_path;
 	char*		   		   column_dir_path;
 	char*          		   col_name;

src/obidmscolumn.h

@@ -38,7 +38,7 @@
                                 	   	   	   	 */
 #define MAXIMUM_LINE_COUNT (1000000000)   		/**< The maximum line count for the data of a column (1E9). //TODO
                                 	       	   	 */
-#define COMMENTS_MAX_LENGTH (2048)        		/**< The maximum length for comments.
+#define COMMENTS_MAX_LENGTH (4096)        		/**< The maximum length for comments.
  	 	 	 	 	 	 	 	 	       	   	 */
 #define FORMATTED_ELT_NAMES_SEPARATOR '\0'		/**< The separator between elements names once formatted to be stored in columns.
  	 	 	 	 	 	 	 	 	       	   	 */
@@ -256,7 +256,7 @@ size_t obi_calculate_header_size(index_t nb_elements_per_line, int64_t elts_name
  *                     If NULL or "", the indexer name is set as the column name.
  * @param associated_column_name The name of the associated column if there is one (otherwise NULL or "").
  * @param associated_column_version The version of the associated column if there is one (otherwise -1).
- * @param comments Optional comments associated with the column (NULL or "" if no comments associated).
+ * @param comments Optional comments associated with the column in JSON format (NULL, "" or "{}" if no comments associated).
  *
  * @returns A pointer on the newly created column structure.
  * @retval NULL if an error occurred.
@@ -372,6 +372,43 @@ int obi_truncate_column(OBIDMS_column_p column);
 int obi_enlarge_column(OBIDMS_column_p column);
 
 
+/**
+ * @brief Writes comments to a column file.
+ *
+ * @warning This overwrites any other previous comments.
+ *
+ * @param column A pointer on an OBIDMS column.
+ * @param comments A character string containing the comments.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since August 2018
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_write_comments(OBIDMS_column_p column, const char* comments);
+
+
+/**
+ * @brief Adds comments to a column file.
+ *
+ * This reads the comments in the JSON format and adds the key value pair.
+ * If the key already exists, the value format is turned to array and the new value is appended
+ * if it is not already in the array.
+ *
+ * @param column A pointer on an OBIDMS column.
+ * @param key The key.
+ * @param value The value associated with the key.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since August 2018
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_add_comment(OBIDMS_column_p column, const char* key, const char* value);
+
+
 /*
  * @brief Sets the data in a column to the specified value.
  *