Major update: new type of columns containing indices referring to lines
in other columns
This commit is contained in:
Celine Mercier
@ -515,7 +515,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
index_t nb_elements_per_line,
|
||||
const char* elements_names,
|
||||
const char* array_name,
|
||||
const char* comments)
|
||||
const char* comments,
|
||||
bool referring)
|
||||
{
|
||||
OBIDMS_column_p new_column;
|
||||
OBIDMS_column_directory_p column_directory;
|
||||
@ -528,6 +529,10 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
size_t header_size;
|
||||
size_t data_size;
|
||||
index_t minimum_line_count;
|
||||
OBIType_t returned_data_type;
|
||||
OBIType_t stored_data_type;
|
||||
index_t returned_nb_elements_per_line;
|
||||
index_t stored_nb_elements_per_line;
|
||||
|
||||
new_column = NULL;
|
||||
|
||||
@ -547,15 +552,28 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
obidebug(1, "\nCan't create column because of invalid data type");
|
||||
return NULL;
|
||||
}
|
||||
if (((data_type == 5) || (data_type == 6)) && (array_name == NULL))
|
||||
if (((data_type == OBI_STR) || (data_type == OBI_SEQ)) && (array_name == NULL))
|
||||
{
|
||||
obidebug(1, "\nCan't create column because of empty array name");
|
||||
return NULL;
|
||||
}
|
||||
|
||||
returned_data_type = data_type;
|
||||
if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || referring)
|
||||
// stored data is indices referring to data stored elsewhere
|
||||
stored_data_type = OBI_IDX;
|
||||
else
|
||||
stored_data_type = returned_data_type;
|
||||
|
||||
returned_nb_elements_per_line = nb_elements_per_line;
|
||||
if (referring)
|
||||
// stored data is indices referring to lines in another column
|
||||
stored_nb_elements_per_line = 1;
|
||||
else
|
||||
stored_nb_elements_per_line = returned_nb_elements_per_line;
|
||||
|
||||
// The initial line count should be between the minimum (corresponding to the page size) and the maximum allowed
|
||||
minimum_line_count = get_line_count_per_page(data_type, nb_elements_per_line);
|
||||
minimum_line_count = get_line_count_per_page(stored_data_type, stored_nb_elements_per_line);
|
||||
if (nb_lines > MAXIMUM_LINE_COUNT)
|
||||
{
|
||||
obidebug(1, "\nCan't create column because of line count greater than the maximum allowed (%d)", MAXIMUM_LINE_COUNT);
|
||||
@ -565,12 +583,12 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
nb_lines = minimum_line_count;
|
||||
|
||||
// The number of elements names should be equal to the number of elements per line
|
||||
if ((elements_names == NULL) && (nb_elements_per_line > 1))
|
||||
if ((elements_names == NULL) && (returned_nb_elements_per_line > 1))
|
||||
{
|
||||
obidebug(1, "\nCan't create column because no elements names were given for a number of elements per line greater than 1");
|
||||
return NULL;
|
||||
}
|
||||
else if ((elements_names != NULL) && (nb_elements_per_line > 1))
|
||||
else if ((elements_names != NULL) && (returned_nb_elements_per_line > 1))
|
||||
{
|
||||
char* token;
|
||||
index_t n = 0;
|
||||
@ -587,7 +605,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
return NULL;
|
||||
}
|
||||
}
|
||||
else if ((nb_elements_per_line == 1) && (strcmp(elements_names, column_name) != 0))
|
||||
else if ((returned_nb_elements_per_line == 1) && (strcmp(elements_names, column_name) != 0))
|
||||
{
|
||||
obidebug(1, "\nCan't create column because the element name does not match the column name");
|
||||
return NULL;
|
||||
@ -604,7 +622,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
|
||||
// Calculate the size needed
|
||||
header_size = obi_get_platform_header_size();
|
||||
data_size = obi_array_sizeof(data_type, nb_lines, nb_elements_per_line);
|
||||
data_size = obi_array_sizeof(stored_data_type, nb_lines, stored_nb_elements_per_line);
|
||||
file_size = header_size + data_size;
|
||||
|
||||
// Get the latest version number
|
||||
@ -692,16 +710,20 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
|
||||
new_column->writable = true;
|
||||
|
||||
header = new_column->header;
|
||||
header->header_size = header_size;
|
||||
header->data_size = data_size;
|
||||
header->line_count = nb_lines;
|
||||
header->lines_used = 0;
|
||||
header->nb_elements_per_line = nb_elements_per_line;
|
||||
header->data_type = data_type;
|
||||
header->creation_date = time(NULL);
|
||||
header->version = version_number;
|
||||
header->cloned_from = -1;
|
||||
header = new_column->header;
|
||||
header->header_size = header_size;
|
||||
header->data_size = data_size;
|
||||
header->line_count = nb_lines;
|
||||
header->lines_used = 0;
|
||||
header->stored_nb_elements_per_line = stored_nb_elements_per_line;
|
||||
header->returned_nb_elements_per_line = returned_nb_elements_per_line;
|
||||
header->stored_data_type = stored_data_type;
|
||||
header->returned_data_type = returned_data_type;
|
||||
header->creation_date = time(NULL);
|
||||
header->version = version_number;
|
||||
header->cloned_from = -1;
|
||||
header->referring = referring;
|
||||
header->referred_column_version = -1;
|
||||
|
||||
obi_column_set_elements_names(new_column, elements_names);
|
||||
|
||||
@ -710,8 +732,9 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
if (comments != NULL)
|
||||
strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
|
||||
|
||||
// If the data type is OBI_STR or OBI_SEQ, the associated obi_array is opened or created
|
||||
if ((data_type == 5) || (data_type == 6))
|
||||
// If the data type is OBI_STR or OBI_SEQ, and the column is not referring another,
|
||||
// the associated obi_array is opened or created
|
||||
if ((stored_data_type == OBI_STR) || (stored_data_type == OBI_SEQ))
|
||||
{
|
||||
array = obi_array(dms, array_name);
|
||||
if (array == NULL)
|
||||
@ -847,8 +870,9 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
||||
|
||||
column->writable = false;
|
||||
|
||||
// If the data type is OBI_STR or OBI_SEQ, the associated obi_array is opened or created
|
||||
if (((column->header)->data_type == 5) || ((column->header)->data_type == 6))
|
||||
// If the data type is OBI_STR or OBI_SEQ, and the column is not referring,
|
||||
// the associated obi_array is opened
|
||||
if (((column->header)->stored_data_type == OBI_STR) || ((column->header)->stored_data_type == OBI_SEQ))
|
||||
{
|
||||
array = obi_array(dms, (column->header)->array_name);
|
||||
if (array == NULL)
|
||||
@ -862,16 +886,29 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
||||
column->array = array;
|
||||
}
|
||||
|
||||
if ((column->header)->referring)
|
||||
{
|
||||
column->referred_column = obi_open_column(dms, column_name, (column->header)->referred_column_version);
|
||||
if (column->referred_column == NULL)
|
||||
{
|
||||
obidebug(1, "\nError opening a referred column");
|
||||
obi_close_column(column);
|
||||
close(column_file_descriptor);
|
||||
return NULL;
|
||||
}
|
||||
}
|
||||
|
||||
close(column_file_descriptor);
|
||||
|
||||
return column;
|
||||
}
|
||||
|
||||
|
||||
OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
||||
const char* column_name,
|
||||
obiversion_t version_number,
|
||||
bool clone_data)
|
||||
OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
||||
const char* column_name,
|
||||
obiversion_t version_number,
|
||||
bool referring,
|
||||
bool clone_data)
|
||||
{
|
||||
OBIDMS_column_p column_to_clone;
|
||||
OBIDMS_column_p new_column;
|
||||
@ -887,11 +924,17 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
||||
return NULL;
|
||||
}
|
||||
|
||||
data_type = (column_to_clone->header)->data_type;
|
||||
data_type = (column_to_clone->header)->returned_data_type;
|
||||
|
||||
nb_elements_per_line = (column_to_clone->header)->nb_elements_per_line;
|
||||
nb_elements_per_line = (column_to_clone->header)->returned_nb_elements_per_line;
|
||||
|
||||
if (clone_data)
|
||||
if (clone_data && referring)
|
||||
{
|
||||
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||
obidebug(1, "\nError: can't clone the data when creating a referring column");
|
||||
return NULL;
|
||||
}
|
||||
else if (clone_data)
|
||||
nb_lines = (column_to_clone->header)->line_count;
|
||||
else
|
||||
nb_lines = get_line_count_per_page(data_type, nb_elements_per_line); // minimum line count corresponding to one memory page
|
||||
@ -903,7 +946,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
||||
nb_elements_per_line,
|
||||
(column_to_clone->header)->elements_names,
|
||||
(column_to_clone->header)->array_name,
|
||||
(column_to_clone->header)->comments);
|
||||
(column_to_clone->header)->comments,
|
||||
referring);
|
||||
|
||||
if (new_column == NULL)
|
||||
{
|
||||
@ -915,7 +959,15 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
||||
obidebug(1, "\nError deleting a bad cloned file");
|
||||
}
|
||||
|
||||
(new_column->header)->cloned_from = version_number;
|
||||
(new_column->header)->cloned_from = (column_to_clone->header)->version;
|
||||
|
||||
if (referring)
|
||||
{
|
||||
if ((column_to_clone->header)->referring)
|
||||
(new_column->header)->referred_column_version = (column_to_clone->header)->referred_column_version;
|
||||
else
|
||||
(new_column->header)->referred_column_version = (column_to_clone->header)->version;
|
||||
}
|
||||
|
||||
if (clone_data)
|
||||
{
|
||||
@ -923,8 +975,10 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
||||
(new_column->header)->lines_used = (column_to_clone->header)->lines_used;
|
||||
}
|
||||
|
||||
// close column_to_clone
|
||||
if (obi_close_column(column_to_clone) < 0)
|
||||
// close column_to_clone or store the pointer if it's referred
|
||||
if (referring)
|
||||
new_column->referred_column = column_to_clone;
|
||||
else if (obi_close_column(column_to_clone) < 0)
|
||||
{
|
||||
obidebug(1, "\nError closing a column that has been cloned");
|
||||
// TODO return NULL or not?
|
||||
@ -936,6 +990,9 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
||||
|
||||
int obi_close_column(OBIDMS_column_p column)
|
||||
{
|
||||
if ((column->header)->referring)
|
||||
obi_close_column(column->referred_column);
|
||||
|
||||
// Munmap data
|
||||
if (munmap(column->data, (column->header)->data_size) < 0)
|
||||
{
|
||||
@ -952,7 +1009,7 @@ int obi_close_column(OBIDMS_column_p column)
|
||||
return -1;
|
||||
}
|
||||
|
||||
obi_close_column_directory(column->column_directory); // TODO or not
|
||||
//obi_close_column_directory(column->column_directory); // TODO or not
|
||||
|
||||
free(column);
|
||||
|
||||
@ -970,8 +1027,8 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column) // TODO is it nece
|
||||
char* column_file_name;
|
||||
|
||||
// Compute the new line count = the number of lines used rounded to the nearest greater multiple of page size greater than 0
|
||||
multiple = ceil((double) (ONE_IF_ZERO((column->header)->lines_used) * (column->header)->nb_elements_per_line * obi_sizeof((column->header)->data_type)) / (double) getpagesize());
|
||||
new_line_count = floor((((int) multiple) * getpagesize()) / ((column->header)->nb_elements_per_line * obi_sizeof((column->header)->data_type)));
|
||||
multiple = ceil((double) (ONE_IF_ZERO((column->header)->lines_used) * (column->header)->stored_nb_elements_per_line * obi_sizeof((column->header)->stored_data_type)) / (double) getpagesize());
|
||||
new_line_count = floor((((int) multiple) * getpagesize()) / ((column->header)->stored_nb_elements_per_line * obi_sizeof((column->header)->stored_data_type)));
|
||||
|
||||
// Check that it is actually greater than the current number of lines allocated in the file, otherwise no need to truncate
|
||||
if ((column->header)->line_count == new_line_count)
|
||||
@ -1006,7 +1063,7 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column) // TODO is it nece
|
||||
}
|
||||
|
||||
// Truncate the column file
|
||||
data_size = obi_array_sizeof((column->header)->data_type, new_line_count, (column->header)->nb_elements_per_line);
|
||||
data_size = obi_array_sizeof((column->header)->stored_data_type, new_line_count, (column->header)->stored_nb_elements_per_line);
|
||||
file_size = (column->header)->header_size + data_size;
|
||||
if (ftruncate(column_file_descriptor, file_size) < 0)
|
||||
{
|
||||
@ -1152,11 +1209,11 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
|
||||
{
|
||||
index_t i, start, end, nb_elements;
|
||||
|
||||
nb_elements = nb_lines*((column->header)->nb_elements_per_line);
|
||||
start = first_line_nb*((column->header)->nb_elements_per_line);
|
||||
nb_elements = nb_lines*((column->header)->stored_nb_elements_per_line);
|
||||
start = first_line_nb*((column->header)->stored_nb_elements_per_line);
|
||||
end = start + nb_elements;
|
||||
|
||||
switch ((column->header)->data_type) {
|
||||
switch ((column->header)->stored_data_type) {
|
||||
case OBI_VOID: // TODO;
|
||||
break;
|
||||
|
||||
@ -1184,8 +1241,9 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
|
||||
}
|
||||
break;
|
||||
|
||||
case OBI_STR:
|
||||
case OBI_SEQ: for (i=start;i<end;i++)
|
||||
case OBI_STR: // fallthrough
|
||||
case OBI_SEQ: // fallthrough
|
||||
case OBI_IDX: for (i=start;i<end;i++)
|
||||
{
|
||||
*(((index_t*) (column->data)) + i) = OBIIdx_NA;
|
||||
}
|
||||
@ -1350,3 +1408,35 @@ char* obi_column_format_date(time_t date)
|
||||
return formatted_time;
|
||||
}
|
||||
|
||||
|
||||
// TODO put in separate file and needs to lock the dependency with the referred column but...
|
||||
// warning for the dependency and for the fact that it's always added at the next line (or not cuz might not be a good idea?)
|
||||
int obi_grep_line(OBIDMS_column_p referring_column, index_t line_to_grep)
|
||||
{
|
||||
// Check that the column is referring another
|
||||
if (!((referring_column->header)->referring))
|
||||
{
|
||||
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||
obidebug(1, "\nError: Grepping a line can only be done with a referring column");
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Check if the file needs to be enlarged
|
||||
if ((referring_column->header)->lines_used == (referring_column->header)->line_count)
|
||||
{
|
||||
// Enlarge the file
|
||||
if (obi_enlarge_column(referring_column) < 0)
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Set the value
|
||||
*(((index_t*) (referring_column->data)) + (referring_column->header)->lines_used) = line_to_grep;
|
||||
|
||||
// Update lines used
|
||||
((referring_column->header)->lines_used)++;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user