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The elements names when a column contains several elements per line are

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now formatted with '\0' as separator and handled in a more optimized way
This commit is contained in:
Celine Mercier
2017-01-31 16:48:06 +01:00
parent 651c1d7845
commit e50da64ea1
6 changed files with 411 additions and 152 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
python/obitools3/commands/test.pyx
View File

@ -97,8 +97,7 @@ def test_set_and_get(config, infos):
return return
idx = random_int(config) idx = random_int(config)
value = infos['random_generator'][data_type](config) value = infos['random_generator'][data_type](config)
if col.nb_elements_per_line > 1 :
if len(element_names) > 1 :
elt = random.choice(element_names) elt = random.choice(element_names)
col[idx][elt] = value col[idx][elt] = value
assert col[idx][elt] == value, "Set value != gotten value "+str(col[idx][elt])+" != "+str(value) assert col[idx][elt] == value, "Set value != gotten value "+str(col[idx][elt])+" != "+str(value)
@ -187,6 +186,7 @@ def create_random_column(config, infos) :
elements_names = [] elements_names = []
for i in range(nb_elements_per_line) : for i in range(nb_elements_per_line) :
elements_names.append(random_unique_element_name(config, infos)) elements_names.append(random_unique_element_name(config, infos))
elements_names = random.choice([None, elements_names])
name = random_unique_name(infos) name = random_unique_name(infos)
infos['view'].add_column(name, infos['view'].add_column(name,
alias=alias, alias=alias,
@ -358,7 +358,9 @@ def run(config):
config['test']['elt_name_max_len'] = int((COL_COMMENTS_MAX_LEN - config['test']['maxelts']) / config['test']['maxelts']) config['test']['elt_name_max_len'] = int((COL_COMMENTS_MAX_LEN - config['test']['maxelts']) / config['test']['maxelts'])
print("Initializing the DMS and the first view...") print("Initializing the DMS and the first view...")
shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
ini_dms_and_first_view(config, infos) ini_dms_and_first_view(config, infos)
print_test(config, repr(infos['view'])) print_test(config, repr(infos['view']))

14
python/obitools3/obidms/_obidms.pyx
View File

@ -7,7 +7,8 @@ from .capi.obidms cimport obi_dms, \
from .capi.obidmscolumn cimport obi_close_column, \ from .capi.obidmscolumn cimport obi_close_column, \
OBIDMS_column_p, \ OBIDMS_column_p, \
OBIDMS_column_header_p OBIDMS_column_header_p, \
obi_get_elements_names
from .capi.obiutils cimport obi_format_date from .capi.obiutils cimport obi_format_date
@ -75,7 +76,7 @@ from .capi.obiview cimport Obiview_p, \
DEFINITION_COLUMN, \ DEFINITION_COLUMN, \
QUALITY_COLUMN QUALITY_COLUMN
from libc.stdlib cimport malloc from libc.stdlib cimport malloc, free
cdef class OBIDMS_column : cdef class OBIDMS_column :
@ -138,7 +139,12 @@ cdef class OBIDMS_column :
# elements_names property getter # elements_names property getter
@property @property
def elements_names(self): def elements_names(self):
return (bytes2str(((self._pointer)[0].header).elements_names)).split(';') cdef char* elts_names_b
cdef str elts_names
elts_names_b = obi_get_elements_names((self._pointer)[0])
elts_names = bytes2str(elts_names_b)
free(<char*>elts_names_b)
return elts_names.split(';')
# nb_elements_per_line property getter # nb_elements_per_line property getter
@property @property
@ -376,7 +382,7 @@ cdef class OBIView :
elements_names_b = str2bytes("") elements_names_b = str2bytes("")
else : else :
elements_names_b = str2bytes(';'.join(elements_names)) elements_names_b = str2bytes(';'.join(elements_names))
if type : # TODO make C function that does that if type : # TODO make C function that does that
if type == 'OBI_INT' : if type == 'OBI_INT' :
data_type = OBI_INT data_type = OBI_INT

29
python/obitools3/obidms/capi/obidmscolumn.pxd
View File

@ -47,31 +47,8 @@ cdef extern from "obidmscolumn.h" nogil:
bint writable bint writable
ctypedef OBIDMS_column_t* OBIDMS_column_p ctypedef OBIDMS_column_t* OBIDMS_column_p
OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const_char_p column_name,
OBIType_t type,
index_t nb_lines,
index_t nb_elements_per_line,
const_char_p elements_names,
const_char_p indexer_name,
const_char_p associated_colum_name,
obiversion_t associated_colum_version,
const_char_p comments)
OBIDMS_column_p obi_open_column(OBIDMS_p dms,
const_char_p column_name,
obiversion_t version_number)
int obi_close_column(OBIDMS_column_p column) int obi_close_column(OBIDMS_column_p column)
OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
OBIDMS_column_p line_selection,
const_char_p column_name,
obiversion_t version_number,
bint clone_data)
int obi_close_column(OBIDMS_column_p column)
obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms,
const_char_p column_name) const_char_p column_name)
@ -81,9 +58,9 @@ cdef extern from "obidmscolumn.h" nogil:
obiversion_t version_number) obiversion_t version_number)
int obi_close_header(OBIDMS_column_header_p header) int obi_close_header(OBIDMS_column_header_p header)
int obi_select(OBIDMS_column_p line_selection_column, index_t line_to_grep) char* obi_get_elements_names(OBIDMS_column_p column)
cdef extern from "obidmscolumn_int.h" nogil: cdef extern from "obidmscolumn_int.h" nogil:

376
src/obidmscolumn.c
View File

@ -119,7 +119,7 @@ static obiversion_t create_version_file(OBIDMS_column_directory_p column_directo
/** /**
* @brief Internal function building the default elements names of the lines of a * @brief Internal function building the default elements names of the lines of a
* column (i.e. "0;1;2;...;n"). * column, with ';' as separator (i.e. "0;1;2;...;n\0").
* *
* @warning The returned pointer has to be freed by the caller. * @warning The returned pointer has to be freed by the caller.
* *
@ -134,12 +134,61 @@ static obiversion_t create_version_file(OBIDMS_column_directory_p column_directo
static char* build_default_elements_names(index_t nb_elements_per_line); static char* build_default_elements_names(index_t nb_elements_per_line);
/**
* @brief Internal function formatting the elements names of the lines of a
* column with '\0' as separator (e.g. "0\01\02\0...\0n\0").
*
* @param elements_names The character string formatted with ';' as separator (e.g. "0;1;2;...;n\0").
* @param elts_names_length A pointer on an integer where the function will store the length of the character string.
*
* @since January 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static void format_elements_names(char* elements_names, int* elts_names_length);
/**
* @brief Internal function comparing two element names using their sorted index, using data stored in the column header.
*
* @param n1_sort_idx A pointer on the sorted index of the first name.
* @param n2_sort_idx A pointer on the sorted index of the second name.
* @param h A pointer on the column header.
*
* @returns A value < 0 if name1 < name2,
* a value > 0 if name1 > name2,
* and 0 if name1 == name2.
*
* @since January 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static int cmp_elements_names_with_idx(const void* n1_sort_idx, const void* n2_sort_idx, const void* h);
/**
* @brief Internal function comparing two element names using a pointer on the first name and the sorted index of the second name,
* using data stored in the column header.
*
* @param name1 A pointer on the first name.
* @param n2_sort_idx A pointer on the sorted index of the second name.
* @param h A pointer on the column header.
*
* @returns A value < 0 if name1 < name2,
* a value > 0 if name1 > name2,
* and 0 if name1 == name2.
*
* @since January 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static int cmp_elements_names_with_name_and_idx(const void* name1, const void* n2_sort_idx, const void* h);
/** /**
* @brief Internal function setting the elements names of the lines of a * @brief Internal function setting the elements names of the lines of a
* column in the header of the OBIDMS column structure. * column in the header of the OBIDMS column structure.
* *
* @param column A pointer as returned by obi_create_column(). * @param column A pointer as returned by obi_create_column().
* @param elements_names The names of the elements with ';' as separator. * @param elements_names The names of the elements as formatted by format_elements_names().
* @param elts_names_length The length of elements_names.
* *
* @retval 0 if the operation was successfully completed. * @retval 0 if the operation was successfully completed.
* @retval -1 if an error occurred. * @retval -1 if an error occurred.
@ -147,7 +196,35 @@ static char* build_default_elements_names(index_t nb_elements_per_line);
* @since July 2015 * @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)
*/ */
static int obi_column_set_elements_names(OBIDMS_column_p column, char* elements_names); static int set_elements_names(OBIDMS_column_p column, char* elements_names, int elts_names_length);
/**
* @brief Internal function counting the number of elements names in a character array.
*
* @param elements_names A pointer on the character string corresponding to the elements names,
* formatted with ';' or with '\0' as separator.
* @param elt_names_formatted Whether the separator is ';' (false), or '\0' (true, as formatted by format_elements_names()).
*
* @returns The number of elements names in the character array.
*
* @since January 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static index_t check_elt_names_count(const char* elements_names, bool elt_names_formatted);
/**
* @brief Internal function computing the length of a character array containing elements names as formatted by format_elements_names().
*
* @param elements_names A pointer on the character string corresponding to the elements names as formatted by format_elements_names().
*
* @returns The length of a character array.
*
* @since January 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
static int get_formatted_elt_names_length(const char* elements_names);
/** /**
@ -198,6 +275,7 @@ static char* build_column_file_name(const char* column_name, obiversion_t versio
} }
static char* build_version_file_name(const char* column_name) static char* build_version_file_name(const char* column_name)
{ {
char* file_name; char* file_name;
@ -222,6 +300,7 @@ static char* build_version_file_name(const char* column_name)
} }
static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_directory, bool block) static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_directory, bool block)
{ {
off_t loc_size; off_t loc_size;
@ -346,6 +425,7 @@ static obiversion_t obi_get_new_version_number(OBIDMS_column_directory_p column_
} }
static obiversion_t create_version_file(OBIDMS_column_directory_p column_directory) static obiversion_t create_version_file(OBIDMS_column_directory_p column_directory)
{ {
off_t loc_size; off_t loc_size;
@ -437,10 +517,12 @@ static obiversion_t create_version_file(OBIDMS_column_directory_p column_directo
} }
static char* build_default_elements_names(index_t nb_elements_per_line) static char* build_default_elements_names(index_t nb_elements_per_line)
{ {
char* elements_names; char* elements_names;
int i; int i;
int len;
elements_names = (char*) malloc(ELEMENTS_NAMES_MAX * sizeof(char)); elements_names = (char*) malloc(ELEMENTS_NAMES_MAX * sizeof(char));
if (elements_names == NULL) if (elements_names == NULL)
@ -457,31 +539,169 @@ static char* build_default_elements_names(index_t nb_elements_per_line)
return NULL; return NULL;
} }
for (i= 0; i < nb_elements_per_line; i++) len = 0;
sprintf(elements_names, "%d", i); for (i = 0; i < nb_elements_per_line; i++)
len += sprintf(elements_names+len, "%d;", i);
// Terminal character // Terminal character
elements_names[strlen(elements_names)] = '\0'; elements_names[len-1] = '\0'; // -1 to delete last ';'
len--;
return elements_names; return elements_names;
} }
int obi_column_set_elements_names(OBIDMS_column_p column, char* elements_names)
static void format_elements_names(char* elements_names, int* elts_names_length)
{ {
if (strlen(elements_names) > ELEMENTS_NAMES_MAX) int i;
*elts_names_length = strlen(elements_names);
// Replace the ';' with '\0'
for (i=0; i < *elts_names_length; i++)
{
if (elements_names[i] == ';')
elements_names[i] = '\0';
}
}
static int cmp_elements_names_with_idx(const void* n1_sort_idx, const void* n2_sort_idx, const void* h)
{
char* name1=NULL;
char* name2=NULL;
int name1_idx;
int name2_idx;
int name1_sort_idx = *((int*)n1_sort_idx);
int name2_sort_idx = *((int*)n2_sort_idx);
OBIDMS_column_header_p header = (OBIDMS_column_header_p) h;
name1_idx = (header->elements_names_idx)[name1_sort_idx];
name1 = (header->elements_names)+name1_idx;
name2_idx = (header->elements_names_idx)[name2_sort_idx];
name2 = (header->elements_names)+name2_idx;
return strcmp(name1, name2);
}
static int cmp_elements_names_with_name_and_idx(const void* name1, const void* n2_sort_idx, const void* h)
{
char* name2=NULL;
int name2_idx;
int name2_sort_idx = *((int*)n2_sort_idx);
OBIDMS_column_header_p header = (OBIDMS_column_header_p) h;
name2_idx = (header->elements_names_idx)[name2_sort_idx];
name2 = (header->elements_names)+name2_idx;
return strcmp(name1, name2);
}
static int set_elements_names(OBIDMS_column_p column, char* elements_names, int elts_names_length)
{
int i, j;
// Check that the elements names are not too long
if (elts_names_length+2 > ELEMENTS_NAMES_MAX)
{ {
obi_set_errno(OBICOL_UNKNOWN_ERROR); obi_set_errno(OBICOL_UNKNOWN_ERROR);
obidebug(1, "\nError: element names too long (max: %d)", ELEMENTS_NAMES_MAX); obidebug(1, "\nError: element names too long (max: %d)", ELEMENTS_NAMES_MAX);
return -1; return -1;
} }
strcpy((column->header)->elements_names, elements_names); // Copy the elements names in the header
memcpy((column->header)->elements_names, elements_names, elts_names_length*sizeof(char));
// Terminal characters
(column->header)->elements_names[elts_names_length] = '\0';
(column->header)->elements_names[elts_names_length + 1] = '\0';
// Store the length of the character array containing the elements names
(column->header)->elements_names_length = elts_names_length;
// Build the elements names index
i = 0;
j = 0;
// Index the first element name
((column->header)->elements_names_idx)[j] = i;
((column->header)->sorted_elements_idx)[j] = j;
i++;
j++;
while (i < elts_names_length)
{
if (elements_names[i] == '\0')
{ // Index new element name
((column->header)->elements_names_idx)[j] = i+1;
((column->header)->sorted_elements_idx)[j] = j;
j++;
}
i++;
}
// Build the sorted index
qsort_user_data((column->header)->sorted_elements_idx, j, sizeof(int), column->header, cmp_elements_names_with_idx);
return 0; return 0;
} }
index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line)
static index_t check_elt_names_count(const char* elements_names, bool elt_names_formatted)
{
char sep;
int i = 0;
bool stop = false;
index_t count = 0;
if (elt_names_formatted)
sep = FORMATTED_ELT_NAMES_SEPARATOR;
else
sep = NOT_FORMATTED_ELT_NAMES_SEPARATOR;
while (! stop)
{
if ((elt_names_formatted && (elements_names[i] == '\0') && (elements_names[i+1] == '\0')) ||
((! elt_names_formatted) && (elements_names[i] == '\0')))
stop = true;
if ((elements_names[i] == sep) || (elements_names[i] == '\0'))
count++;
i++;
}
return count;
}
static int get_formatted_elt_names_length(const char* elements_names)
{
int i = 0;
bool stop = false;
while (! stop)
{
if ((elements_names[i] == '\0') && (elements_names[i+1] == '\0'))
stop = true;
else
i++;
}
return i;
}
static index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_line)
{ {
return getpagesize() / (obi_sizeof(data_type) * nb_elements_per_line); return getpagesize() / (obi_sizeof(data_type) * nb_elements_per_line);
} }
@ -493,6 +713,7 @@ index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_per_lin
* *
**********************************************************************/ **********************************************************************/
obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_directory) obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_directory)
{ {
off_t loc_size; off_t loc_size;
@ -557,6 +778,7 @@ obiversion_t obi_get_latest_version_number(OBIDMS_column_directory_p column_dire
} }
obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name) obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* column_name)
{ {
OBIDMS_column_directory_p column_directory; OBIDMS_column_directory_p column_directory;
@ -582,6 +804,7 @@ obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms, const char* c
} }
size_t obi_get_platform_header_size() size_t obi_get_platform_header_size()
{ {
size_t header_size; size_t header_size;
@ -607,7 +830,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const char* indexer_name, const char* indexer_name,
const char* associated_column_name, const char* associated_column_name,
obiversion_t associated_column_version, obiversion_t associated_column_version,
const char* comments const char* comments,
bool elt_names_formatted
) )
{ {
OBIDMS_column_p new_column; OBIDMS_column_p new_column;
@ -623,6 +847,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
OBIType_t returned_data_type; OBIType_t returned_data_type;
OBIType_t stored_data_type; OBIType_t stored_data_type;
char* final_indexer_name; char* final_indexer_name;
char* built_elements_names = NULL;
int elts_names_length;
new_column = NULL; new_column = NULL;
@ -695,31 +921,29 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
else if (nb_lines < minimum_line_count) else if (nb_lines < minimum_line_count)
nb_lines = minimum_line_count; nb_lines = minimum_line_count;
// Check and build if needed the element names // Check, format, and build if needed the element names
if ((elements_names == NULL) || (strcmp(elements_names, "") == 0)) // Build the default element names: str of the element index if ((elements_names == NULL) || (*elements_names == '\0')) // Build the default element names: str of the element index
{ {
elements_names = build_default_elements_names(nb_elements_per_line); built_elements_names = build_default_elements_names(nb_elements_per_line);
if (elements_names == NULL) if (built_elements_names == NULL)
return NULL; return NULL;
elements_names = built_elements_names;
} }
else if (((elements_names == NULL) || (strcmp(elements_names, "") != 0)) && (nb_elements_per_line > 1)) else
{ // The number of elements names should be equal to the number of elements per line { // The number of elements names should be equal to the number of elements per line
char* token; if (check_elt_names_count(elements_names, elt_names_formatted) != nb_elements_per_line)
index_t n = 0;
token = strdup(elements_names);
token = strtok(token, ";");
while (token != NULL)
{ {
token = strtok(NULL, ";"); obidebug(1, "\nCan't create column because the number of elements names given is not equal to the number of elements per line:"
n++; "\n%lld elements per line\nelements names:%s\n", nb_elements_per_line, elements_names);
}
if (n != nb_elements_per_line)
{
obidebug(1, "\nCan't create column because the number of elements names given is not equal to the number of elements per line");
return NULL; return NULL;
} }
} }
// TODO what if 1 element and name specified? doc
// Format the elements names string
if (! elt_names_formatted)
format_elements_names(elements_names, &elts_names_length);
else
elts_names_length = get_formatted_elt_names_length(elements_names);
// Calculate the size needed // Calculate the size needed
header_size = obi_get_platform_header_size(); header_size = obi_get_platform_header_size();
@ -816,11 +1040,11 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
header->version = version_number; header->version = version_number;
header->cloned_from = -1; header->cloned_from = -1;
obi_column_set_elements_names(new_column, elements_names); set_elements_names(new_column, elements_names, elts_names_length);
// Free the element names if they were built // Free the element names if they were built
if ((elements_names == NULL) || (strcmp(elements_names, "") == 0)) if (built_elements_names != NULL)
free(elements_names); free(built_elements_names);
strncpy(header->name, column_name, OBIDMS_COLUMN_MAX_NAME); strncpy(header->name, column_name, OBIDMS_COLUMN_MAX_NAME);
@ -886,6 +1110,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
} }
OBIDMS_column_p obi_open_column(OBIDMS_p dms, OBIDMS_column_p obi_open_column(OBIDMS_p dms,
const char* column_name, const char* column_name,
obiversion_t version_number) obiversion_t version_number)
@ -1043,6 +1268,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
} }
OBIDMS_column_p obi_clone_column(OBIDMS_p dms, OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
OBIDMS_column_p line_selection, OBIDMS_column_p line_selection,
const char* column_name, const char* column_name,
@ -1083,7 +1309,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
(column_to_clone->header)->indexer_name, (column_to_clone->header)->indexer_name,
((column_to_clone->header)->associated_column).column_name, ((column_to_clone->header)->associated_column).column_name,
((column_to_clone->header)->associated_column).version, ((column_to_clone->header)->associated_column).version,
(column_to_clone->header)->comments (column_to_clone->header)->comments,
true
); );
if (new_column == NULL) if (new_column == NULL)
@ -1097,6 +1324,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
return NULL; return NULL;
} }
(new_column->header)->cloned_from = (column_to_clone->header)->version; (new_column->header)->cloned_from = (column_to_clone->header)->version;
if (clone_data && (line_selection == NULL)) if (clone_data && (line_selection == NULL))
@ -1137,6 +1366,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
} }
int obi_close_column(OBIDMS_column_p column) int obi_close_column(OBIDMS_column_p column)
{ {
int ret_val = 0; int ret_val = 0;
@ -1185,6 +1415,7 @@ int obi_close_column(OBIDMS_column_p column)
} }
int obi_clone_column_indexer(OBIDMS_column_p column) int obi_clone_column_indexer(OBIDMS_column_p column)
{ {
char* new_indexer_name; char* new_indexer_name;
@ -1208,6 +1439,7 @@ int obi_clone_column_indexer(OBIDMS_column_p column)
} }
int obi_truncate_column(OBIDMS_column_p column) // TODO is it necessary to unmap/remap? int obi_truncate_column(OBIDMS_column_p column) // TODO is it necessary to unmap/remap?
{ {
size_t file_size; size_t file_size;
@ -1309,6 +1541,7 @@ int obi_truncate_column(OBIDMS_column_p column) // TODO is it necessary to unmap
} }
int obi_enlarge_column(OBIDMS_column_p column) int obi_enlarge_column(OBIDMS_column_p column)
{ {
size_t file_size; size_t file_size;
@ -1363,7 +1596,7 @@ int obi_enlarge_column(OBIDMS_column_p column)
header_size = (column->header)->header_size; header_size = (column->header)->header_size;
file_size = header_size + new_data_size; file_size = header_size + new_data_size;
// Enlarge the file // TODO isn't it possible that this makes the file "move"? // Enlarge the file
if (ftruncate(column_file_descriptor, file_size) < 0) if (ftruncate(column_file_descriptor, file_size) < 0)
{ {
obi_set_errno(OBICOL_UNKNOWN_ERROR); obi_set_errno(OBICOL_UNKNOWN_ERROR);
@ -1414,6 +1647,7 @@ int obi_enlarge_column(OBIDMS_column_p column)
} }
void obi_ini_to_NA_values(OBIDMS_column_p column, void obi_ini_to_NA_values(OBIDMS_column_p column,
index_t first_line_nb, index_t first_line_nb,
index_t nb_lines) index_t nb_lines)
@ -1479,6 +1713,7 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
} }
OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name, obiversion_t version_number) OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char* column_name, obiversion_t version_number)
{ {
OBIDMS_column_header_p header; OBIDMS_column_header_p header;
@ -1562,6 +1797,7 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
} }
int obi_close_header(OBIDMS_column_header_p header) int obi_close_header(OBIDMS_column_header_p header)
{ {
if (munmap(header, header->header_size) < 0) if (munmap(header, header->header_size) < 0)
@ -1574,47 +1810,56 @@ int obi_close_header(OBIDMS_column_header_p header)
} }
// TODO to be rewritten in an optimized and safe way if possible
index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name) index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name)
{ {
char* elements_names; int* elt_names_idx;
char* name;
index_t element_index;
elements_names = strdup((column->header)->elements_names); elt_names_idx = bsearch_user_data(element_name, (column->header)->sorted_elements_idx, (column->header)->nb_elements_per_line, sizeof(int), column->header, cmp_elements_names_with_name_and_idx);
if (elements_names == NULL)
{
obidebug(1, "\nError strdup-ing the elements names");
return OBIIdx_NA;
}
element_index = 0; if (elt_names_idx != NULL)
return (index_t)(*elt_names_idx);
name = strtok(elements_names, ";"); // TODO not thread safe, see strtok_r maybe obi_set_errno(OBICOL_UNKNOWN_ERROR);
if (strcmp(element_name, name) == 0) obidebug(1, "\nError: could not find element name %s", element_name);
{
free(elements_names);
return element_index;
}
element_index++;
while (name != NULL)
{
name = strtok(NULL, ";"); // TODO not thread safe, see strtok_r maybe
if (strcmp(element_name, name) == 0)
{
free(elements_names);
return element_index;
}
element_index++;
}
obidebug(1, "\nCan't find an element name");
free(elements_names);
return OBIIdx_NA; return OBIIdx_NA;
} }
// TODO doc, returns elements names with ; as separator (discuss maybe char**)
char* obi_get_elements_names(OBIDMS_column_p column)
{
char* elements_names;
int i, j;
int elt_idx;
int len;
elements_names = (char*) malloc(ELEMENTS_NAMES_MAX * sizeof(char));
if (elements_names == NULL)
{
obi_set_errno(OBI_MALLOC_ERROR);
obidebug(1, "\nError allocating memory for elements names");
return NULL;
}
j = 0;
for (i=0; i < (column->header)->nb_elements_per_line; i++)
{
elt_idx = ((column->header)->elements_names_idx)[i];
len = strlen(((column->header)->elements_names)+elt_idx);
memcpy(elements_names+j, ((column->header)->elements_names)+elt_idx, len*sizeof(char));
j = j + len;
elements_names[j] = ';';
j++;
}
elements_names[j - 1] = '\0';
return elements_names;
}
int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb) int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb)
{ {
// Check if the column is read-only // Check if the column is read-only
@ -1649,6 +1894,7 @@ int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb)
} }
int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb) int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)
{ {
if ((line_nb+1) > ((column->header)->line_count)) if ((line_nb+1) > ((column->header)->line_count))

128
src/obidmscolumn.h
View File

@ -28,17 +28,21 @@
#include "obiblob_indexer.h" #include "obiblob_indexer.h"
#define ELEMENTS_NAMES_MAX (2048) /**< The maximum length of the list of elements names. // TODO Discuss #define ELEMENTS_NAMES_MAX (2048) /**< The maximum length of the list of elements names. // TODO Discuss
*/ */
#define NB_ELTS_MAX_IF_DEFAULT_NAME (539) /**< The maximum number of elements per line if the default element names #define NB_ELTS_MAX_IF_DEFAULT_NAME (539) /**< The maximum number of elements per line if the default element names
* are used ("0;1;2;...;n"), considering ELEMENTS_NAMES_MAX. * are used ("0\01\02\0...\0n"), considering ELEMENTS_NAMES_MAX.
*/ */
#define COLUMN_GROWTH_FACTOR (2) /**< The growth factor when a column is enlarged. #define COLUMN_GROWTH_FACTOR (2) /**< The growth factor when a column is enlarged.
*/ */
#define MAXIMUM_LINE_COUNT (1000000000) /**< The maximum line count for the data of a column. //TODO #define MAXIMUM_LINE_COUNT (1000000000) /**< The maximum line count for the data of a column. //TODO
*/ */
#define COMMENTS_MAX_LENGTH (2048) /**< The maximum length for comments. #define COMMENTS_MAX_LENGTH (2048) /**< The maximum length for comments.
*/ */
#define FORMATTED_ELT_NAMES_SEPARATOR '\0' /**< The maximum length for comments.
*/
#define NOT_FORMATTED_ELT_NAMES_SEPARATOR ';' /**< The maximum length for comments.
*/
/** /**
@ -56,42 +60,48 @@ typedef struct Column_reference {
* @brief OBIDMS column header structure. * @brief OBIDMS column header structure.
*/ */
typedef struct OBIDMS_column_header { typedef struct OBIDMS_column_header {
size_t header_size; /**< Size of the header in bytes. size_t header_size; /**< Size of the header in bytes.
*/ */
size_t data_size; /**< Size of the data in bytes. size_t data_size; /**< Size of the data in bytes.
*/ */
index_t line_count; /**< Number of lines of data allocated. index_t line_count; /**< Number of lines of data allocated.
*/ */
index_t lines_used; /**< Number of lines of data used. index_t lines_used; /**< Number of lines of data used.
*/ */
index_t nb_elements_per_line; /**< Number of elements per line. index_t nb_elements_per_line; /**< Number of elements per line.
*/ */
char elements_names[ELEMENTS_NAMES_MAX+1]; /**< Names of the line elements with ';' as separator char elements_names[ELEMENTS_NAMES_MAX+1]; /**< Names of the line elements with '\0' as separator
* (no terminal ';'). * and '\0\0' as terminal flag.
* (default are the indices: "0;1;2;...;n"). * (default are the indices: "0\01\02\0...\0n\0\0").
*/ */
OBIType_t returned_data_type; /**< Type of the data that is returned when getting an int elements_names_length; /**< Length of the character array where the elements names are stored.
* element from the column. */
*/ int elements_names_idx[NB_ELTS_MAX_IF_DEFAULT_NAME]; /**< Index for the start of each element name in elements_names.
OBIType_t stored_data_type; /**< Type of the data that is actually stored in the data */
* part of the column. int sorted_elements_idx[NB_ELTS_MAX_IF_DEFAULT_NAME]; /**< Index for the sorted element names in elements_names_idx.
*/ */
time_t creation_date; /**< Date of creation of the file. OBIType_t returned_data_type; /**< Type of the data that is returned when getting an
*/ * element from the column.
obiversion_t version; /**< Version of the column. */
*/ OBIType_t stored_data_type; /**< Type of the data that is actually stored in the data
obiversion_t cloned_from; /**< Version of the column from which this column * part of the column.
* was cloned from (-1 if it was not created by cloning */
* another column). time_t creation_date; /**< Date of creation of the file.
*/ */
char name[OBIDMS_COLUMN_MAX_NAME+1]; /**< The column name as a NULL terminated string. obiversion_t version; /**< Version of the column.
*/ */
char indexer_name[INDEXER_MAX_NAME+1]; /**< If there is one, the indexer name as a NULL terminated string. obiversion_t cloned_from; /**< Version of the column from which this column
*/ * was cloned from (-1 if it was not created by cloning
Column_reference_t associated_column; /**< If there is one, the reference to the associated column. * another column).
*/ */
char comments[COMMENTS_MAX_LENGTH+1]; /**< Comments stored as a classical zero end C string. char name[OBIDMS_COLUMN_MAX_NAME+1]; /**< The column name as a NULL terminated string.
*/ */
char indexer_name[INDEXER_MAX_NAME+1]; /**< If there is one, the indexer name as a NULL terminated string.
*/
Column_reference_t associated_column; /**< If there is one, the reference to the associated column.
*/
char comments[COMMENTS_MAX_LENGTH+1]; /**< Comments stored as a classical zero end C string.
*/
} OBIDMS_column_header_t, *OBIDMS_column_header_p; } OBIDMS_column_header_t, *OBIDMS_column_header_p;
@ -184,12 +194,13 @@ size_t obi_get_platform_header_size();
* @param nb_lines The number of lines to be stored. * @param nb_lines The number of lines to be stored.
* @param nb_elements_per_line The number of elements per line. // TODO talk about default values * @param nb_elements_per_line The number of elements per line. // TODO talk about default values
* @param elements_names The names of the elements with ';' as separator (no terminal ';'), * @param elements_names The names of the elements with ';' as separator (no terminal ';'),
* NULL or "" if the default names are to be used ("0;1;2;...;n"). * NULL or "" if the default names are to be used ("0\01\02\0...\0n").
* @param indexer_name The name of the indexer if there is one associated with the column. * @param indexer_name The name of the indexer if there is one associated with the column.
* If NULL or "", the indexer name is set as the column 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. * @param associated_column_name The name of the associated column if there is one.
* @param associated_column_version The version of the associated column if there is one. * @param associated_column_version The version of the associated column if there is one.
* @param comments Optional comments associated with the column. * @param comments Optional comments associated with the column.
* @param elt_names_formatted Whether the separator for the elements names is ';' (false), or '\0' (true, as formatted by format_elements_names()).
* *
* @returns A pointer on the newly created column structure. * @returns A pointer on the newly created column structure.
* @retval NULL if an error occurred. * @retval NULL if an error occurred.
@ -206,7 +217,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
const char* indexer_name, const char* indexer_name,
const char* associated_column_name, const char* associated_column_name,
obiversion_t associated_column_version, obiversion_t associated_column_version,
const char* comments const char* comments,
bool elt_names_formatted
); );
@ -353,7 +365,7 @@ int obi_close_header(OBIDMS_column_header_p header);
* @param element_name The name of the element. * @param element_name The name of the element.
* *
* @returns The index of the element in a line of the column. * @returns The index of the element in a line of the column.
* @retval OBIIdx_NA if an error occurred. // TODO not sure if this is "clean". * @retval OBIIdx_NA if an error occurred.
* *
* @since July 2015 * @since July 2015
* @author Celine Mercier (celine.mercier@metabarcoding.org) * @author Celine Mercier (celine.mercier@metabarcoding.org)
@ -361,6 +373,22 @@ int obi_close_header(OBIDMS_column_header_p header);
index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name); index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const char* element_name);
/**
* @brief Recovers the elements names of the lines of a column, with ';' as separator (i.e. "0;1;2;...;n\0").
*
* @warning The returned pointer has to be freed by the caller.
*
* @param column A pointer on an OBIDMS column.
*
* @returns A pointer on a character array where the elements names are stored.
* @retval NULL if an error occurred.
*
* @since January 2017
* @author Celine Mercier (celine.mercier@metabarcoding.org)
*/
char* obi_get_elements_names(OBIDMS_column_p column);
/** /**
* @brief Prepares a column to set a value. * @brief Prepares a column to set a value.
* *

8
src/obiview.c
View File

@ -445,8 +445,8 @@ static char* build_obiview_file_name(const char* view_name)
bool view_exists(OBIDMS_p dms, const char* view_name) bool view_exists(OBIDMS_p dms, const char* view_name)
{ {
struct dirent* dp; struct dirent* dp;
char* file_name; char* file_name;
// Create file name // Create file name
file_name = build_obiview_file_name(view_name); file_name = build_obiview_file_name(view_name);
@ -1236,7 +1236,7 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
// If there is a new line selection, build it by combining it with the one from the view to clone if there is one // If there is a new line selection, build it by combining it with the one from the view to clone if there is one
else if (line_selection != NULL) else if (line_selection != NULL)
{ {
view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, NULL, NULL, NULL, -1, NULL); view->line_selection = obi_create_column(view->dms, LINES_COLUMN_NAME, OBI_IDX, 0, 1, NULL, NULL, NULL, -1, NULL, false);
if ((view->line_selection) == NULL) if ((view->line_selection) == NULL)
{ {
obidebug(1, "\nError creating a column corresponding to a line selection"); obidebug(1, "\nError creating a column corresponding to a line selection");
@ -1792,7 +1792,7 @@ int obi_view_add_column(Obiview_p view,
// Open or create the column // Open or create the column
if (create) if (create)
{ // Create column { // Create column
column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, associated_column_name, associated_column_version, comments); column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, associated_column_name, associated_column_version, comments, false);
if (column == NULL) if (column == NULL)
{ {
obidebug(1, "\nError creating a column to add to a view"); obidebug(1, "\nError creating a column to add to a view");