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Columns: implemented handling of JSON formatted comments

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This commit is contained in:
Celine Mercier
2018-10-07 18:54:51 +02:00
parent cef458f570
commit bc8c394061
2 changed files with 95 additions and 5 deletions
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59
src/obidmscolumn.c
View File

@ -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'))
strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
// Comments must be a json string, even empty
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;

41
src/obidmscolumn.h
View File

@ -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.
*