obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

Major update : views

Browse Source
This commit is contained in:
Celine Mercier
2016-02-18 10:38:51 +01:00
parent cfaf069095
commit a8f03248a8
46 changed files with 3207 additions and 1070 deletions
Download Patch File Download Diff File Expand all files Collapse all files

167
src/obidmscolumn.c
View File

@ -515,8 +515,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
index_t nb_elements_per_line,
const char* elements_names,
const char* avl_name,
const char* comments,
bool referring)
const char* comments
)
{
OBIDMS_column_p new_column;
OBIDMS_column_directory_p column_directory;
@ -531,8 +531,6 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
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;
@ -547,7 +545,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
obidebug(1, "\nCan't create column because of empty column name");
return NULL;
}
if ((data_type < 1) || (data_type > 6))
if ((data_type < 1) || (data_type > 7))
{
obidebug(1, "\nCan't create column because of invalid data type");
return NULL;
@ -559,21 +557,14 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
}
returned_data_type = data_type;
if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || referring)
if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
// 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(stored_data_type, stored_nb_elements_per_line);
minimum_line_count = get_line_count_per_page(stored_data_type, 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);
@ -583,12 +574,12 @@ 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) && (returned_nb_elements_per_line > 1))
if ((elements_names == NULL) && (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) && (returned_nb_elements_per_line > 1))
else if ((elements_names != NULL) && (nb_elements_per_line > 1))
{
char* token;
index_t n = 0;
@ -605,7 +596,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
return NULL;
}
}
else if ((returned_nb_elements_per_line == 1) && (strcmp(elements_names, column_name) != 0))
else if ((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;
@ -622,7 +613,7 @@ 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(stored_data_type, nb_lines, stored_nb_elements_per_line);
data_size = obi_array_sizeof(stored_data_type, nb_lines, nb_elements_per_line);
file_size = header_size + data_size;
// Get the latest version number
@ -708,22 +699,19 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
return NULL;
}
new_column->writable = true;
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->stored_nb_elements_per_line = stored_nb_elements_per_line;
header->returned_nb_elements_per_line = returned_nb_elements_per_line;
header->nb_elements_per_line = 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);
@ -780,7 +768,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
column_directory = obi_open_column_directory(dms, column_name);
if (column_directory == NULL)
{
obidebug(1, "\nError opening a column directory structure");
//obidebug(1, "\nError opening a column directory structure");
return NULL;
}
@ -818,7 +806,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
if (column_file_descriptor < 0)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError opening column file");
//obidebug(1, "\nError opening column file");
free(column_file_name);
return NULL;
}
@ -854,7 +842,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
MAP_PRIVATE,
column_file_descriptor,
0
);
);
if (column->header == MAP_FAILED)
{
@ -872,7 +860,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
MAP_PRIVATE,
column_file_descriptor,
header_size
);
);
if (column->data == MAP_FAILED)
{
@ -884,7 +872,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
return NULL;
}
column->writable = false;
column->writable = false;
// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is opened
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
@ -901,18 +889,6 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
column->avl = avl;
}
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);
// Add in the list of opened columns and set column counter to 1
@ -925,9 +901,9 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
OBIDMS_column_p line_selection,
const char* column_name,
obiversion_t version_number,
bool referring,
bool clone_data)
{
OBIDMS_column_p column_to_clone;
@ -935,6 +911,10 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
index_t nb_lines;
index_t nb_elements_per_line;
OBIType_t data_type;
size_t line_size;
index_t i, index;
obidebug(1, "\nline_selection == NULL = %d\n", (line_selection == NULL));
column_to_clone = obi_open_column(dms, column_name, version_number);
if (column_to_clone == NULL)
@ -944,25 +924,11 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
return NULL;
}
// A referring column can't be cloned
if ((column_to_clone->header)->referring)
{
obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError: can't clone a referring column");
return NULL;
}
data_type = (column_to_clone->header)->returned_data_type;
nb_elements_per_line = (column_to_clone->header)->returned_nb_elements_per_line;
nb_elements_per_line = (column_to_clone->header)->nb_elements_per_line;
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)
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
@ -974,8 +940,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
nb_elements_per_line,
(column_to_clone->header)->elements_names,
(column_to_clone->header)->avl_name,
(column_to_clone->header)->comments,
referring);
(column_to_clone->header)->comments
);
if (new_column == NULL)
{
@ -989,24 +955,29 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
(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)
if (clone_data && (line_selection == NULL))
{
memcpy(new_column->data, column_to_clone->data, (column_to_clone->header)->data_size);
(new_column->header)->lines_used = (column_to_clone->header)->lines_used;
}
else if (clone_data && (line_selection != NULL))
{
obidebug(1, "\nCloning data from line selection\n");
line_size = obi_sizeof((new_column->header)->stored_data_type) * (new_column->header)->nb_elements_per_line;
fprintf(stderr, "\nline size = %ld\n", line_size);
for (i=0; i<((line_selection->header)->lines_used); i++)
{
index = *(((index_t*) (line_selection->data)) + i);
fprintf(stderr, "\nindex = %lld, i = %lld\n", index, i);
memcpy((new_column->data)+(i*line_size), (column_to_clone->data)+(index*line_size), line_size);
fprintf(stderr, "\nmemcpied\n");
}
(new_column->header)->lines_used = (line_selection->header)->lines_used;
obidebug(1, "\nCloned data from line selection\n");
}
// 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)
// Close column_to_clone
if (obi_close_column(column_to_clone) < 0)
{
obidebug(1, "\nError closing a column that has been cloned");
// TODO return NULL or not?
@ -1049,9 +1020,6 @@ int obi_close_column(OBIDMS_column_p column)
}
}
if ((column->header)->referring)
obi_close_column(column->referred_column);
// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is closed
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
{
@ -1095,8 +1063,8 @@ 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)->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)));
multiple = ceil((double) (ONE_IF_ZERO((column->header)->lines_used) * (column->header)->nb_elements_per_line * obi_sizeof((column->header)->stored_data_type)) / (double) getpagesize());
new_line_count = floor((((int) multiple) * getpagesize()) / ((column->header)->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)
@ -1131,7 +1099,7 @@ 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)->stored_data_type, new_line_count, (column->header)->stored_nb_elements_per_line);
data_size = obi_array_sizeof((column->header)->stored_data_type, new_line_count, (column->header)->nb_elements_per_line);
file_size = (column->header)->header_size + data_size;
if (ftruncate(column_file_descriptor, file_size) < 0)
{
@ -1262,8 +1230,11 @@ int obi_enlarge_column(OBIDMS_column_p column)
int obi_truncate_and_close_column(OBIDMS_column_p column)
{
if (obi_truncate_column_to_lines_used(column) < 0)
return -1;
if (column->writable) // TODO discuss
{
if (obi_truncate_column_to_lines_used(column) < 0)
return -1;
}
if (obi_close_column(column) < 0)
return -1;
@ -1277,8 +1248,8 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
{
index_t i, start, end, nb_elements;
nb_elements = nb_lines*((column->header)->stored_nb_elements_per_line);
start = first_line_nb*((column->header)->stored_nb_elements_per_line);
nb_elements = nb_lines*((column->header)->nb_elements_per_line);
start = first_line_nb*((column->header)->nb_elements_per_line);
end = start + nb_elements;
switch ((column->header)->stored_data_type) {
@ -1476,35 +1447,3 @@ char* obi_column_format_date(time_t date)
return formatted_time;
}
// TODO put in separate file ?
// 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;
}