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Comments in column headers are now working.

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This commit is contained in:
Celine Mercier
2015-11-10 10:56:45 +01:00
parent f6ec8ba963
commit c4b7e579cf
7 changed files with 33 additions and 19 deletions
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6
python/obitools3/obidms/_obidms.pxd
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@ -24,7 +24,8 @@ cdef class OBIDMS:
index_t nb_lines=*, index_t nb_lines=*,
index_t nb_elements_per_line=*, index_t nb_elements_per_line=*,
list elements_names=*, list elements_names=*,
str array_name=*) str array_name=*,
str comments=*)
cdef class OBIDMS_column: cdef class OBIDMS_column:
@ -34,7 +35,7 @@ cdef class OBIDMS_column:
cdef str data_type # TODO keep as OBIType_t? both? cdef str data_type # TODO keep as OBIType_t? both?
cdef str dms_name cdef str dms_name
cdef str column_name cdef str column_name
cdef index_t nb_elements_per_line cdef index_t nb_elements_per_line
cdef list elements_names cdef list elements_names
# cpdef object get_item(self, index_t line_nb, str element_name) TODO can't declare because not the same in all subclasses # cpdef object get_item(self, index_t line_nb, str element_name) TODO can't declare because not the same in all subclasses
@ -43,5 +44,6 @@ cdef class OBIDMS_column:
cpdef str get_data_type(self) cpdef str get_data_type(self)
cpdef index_t get_nb_lines_used(self) cpdef index_t get_nb_lines_used(self)
cpdef str get_creation_date(self) cpdef str get_creation_date(self)
cpdef str get_comments(self)
cpdef close(self) cpdef close(self)

15
python/obitools3/obidms/_obidms.pyx
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@ -120,7 +120,8 @@ cdef class OBIDMS :
index_t nb_lines=0, index_t nb_lines=0,
index_t nb_elements_per_line=0, index_t nb_elements_per_line=0,
list elements_names=None, list elements_names=None,
str array_name="default_obiarray"): str array_name="default_obiarray",
str comments=""):
# Declarations # Declarations
cdef OBIDMS_column column cdef OBIDMS_column column
@ -221,7 +222,8 @@ cdef class OBIDMS :
create, clone, clone_data, create, clone, clone_data,
version_number, data_type, version_number, data_type,
nb_lines, nb_elements_per_line, nb_lines, nb_elements_per_line,
elements_names, array_name) elements_names, array_name,
comments)
return column return column
@ -240,13 +242,15 @@ cdef class OBIDMS_column :
index_t nb_lines, index_t nb_lines,
index_t nb_elements_per_line, index_t nb_elements_per_line,
list elements_names, list elements_names,
str array_name): str array_name,
str comments):
# Declarations # Declarations
cdef bytes column_name_b cdef bytes column_name_b
cdef bytes dms_name_b cdef bytes dms_name_b
cdef bytes array_name_b cdef bytes array_name_b
cdef bytes elements_names_b cdef bytes elements_names_b
cdef bytes comments_b
# Fill structure # Fill structure
self.dms = dms self.dms = dms
@ -259,6 +263,7 @@ cdef class OBIDMS_column :
column_name_b = str2bytes(column_name) column_name_b = str2bytes(column_name)
dms_name_b = str2bytes(self.dms.dms_name) dms_name_b = str2bytes(self.dms.dms_name)
array_name_b = str2bytes(array_name) array_name_b = str2bytes(array_name)
comments_b = str2bytes(comments)
# Create, clone or open column # Create, clone or open column
if create : if create :
@ -268,7 +273,7 @@ cdef class OBIDMS_column :
elements_names_b = str2bytes(";".join(elements_names)) elements_names_b = str2bytes(";".join(elements_names))
self.pointer = obi_create_column(self.dms.pointer, column_name_b, type, self.pointer = obi_create_column(self.dms.pointer, column_name_b, type,
nb_lines, nb_elements_per_line, nb_lines, nb_elements_per_line,
elements_names_b, array_name_b) elements_names_b, array_name_b, comments_b)
else : else :
if clone : if clone :
self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, clone_data) self.pointer = obi_clone_column(self.dms.pointer, column_name_b, version_number, clone_data)
@ -327,6 +332,8 @@ cdef class OBIDMS_column :
cpdef str get_creation_date(self): cpdef str get_creation_date(self):
return bytes2str(obi_column_format_date(self.pointer.header.creation_date)) return bytes2str(obi_column_format_date(self.pointer.header.creation_date))
cpdef str get_comments(self):
return bytes2str(self.pointer.header.comments)
cpdef close(self): cpdef close(self):
raise NotImplementedError raise NotImplementedError

3
python/obitools3/obidms/capi/obidmscolumn.pxd
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@ -43,7 +43,8 @@ cdef extern from "obidmscolumn.h" nogil:
index_t nb_lines, index_t nb_lines,
index_t nb_elements_per_line, index_t nb_elements_per_line,
const_char_p elements_names, const_char_p elements_names,
const_char_p array_name) const_char_p array_name,
const_char_p comments)
OBIDMS_column_p obi_open_column(OBIDMS_p dms, OBIDMS_column_p obi_open_column(OBIDMS_p dms,
const_char_p column_name, const_char_p column_name,

2
src/obiarray.h
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@ -25,7 +25,7 @@
#include "obitypes.h" #include "obitypes.h"
#define ARRAY_MAX_NAME (2048) /**< The maximum length of an array name. #define ARRAY_MAX_NAME (1024) /**< The maximum length of an array name.
*/ */
#define ARRAY_GROWTH_FACTOR (2) /**< The growth factor when an array is enlarged. #define ARRAY_GROWTH_FACTOR (2) /**< The growth factor when an array is enlarged.
*/ */

13
src/obidmscolumn.c
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@ -495,7 +495,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
index_t nb_lines, index_t nb_lines,
index_t nb_elements_per_line, index_t nb_elements_per_line,
const char* elements_names, const char* elements_names,
const char* array_name) const char* array_name,
const char* comments)
{ {
OBIDMS_column_p new_column; OBIDMS_column_p new_column;
OBIDMS_column_directory_p column_directory; OBIDMS_column_directory_p column_directory;
@ -682,12 +683,14 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
header->creation_date = time(NULL); header->creation_date = time(NULL);
header->version = version_number; header->version = version_number;
header->cloned_from = -1; header->cloned_from = -1;
header->comments[0] = 0x0; // TODO
obi_column_set_elements_names(new_column, elements_names); obi_column_set_elements_names(new_column, elements_names);
strncpy(header->name, column_name, OBIDMS_COLUMN_MAX_NAME); strncpy(header->name, column_name, OBIDMS_COLUMN_MAX_NAME);
if (comments != NULL)
strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
// If the data type is OBI_IDX, the associated obi_array is opened or created // If the data type is OBI_IDX, the associated obi_array is opened or created
if (data_type == 5) if (data_type == 5)
{ {
@ -880,7 +883,8 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
nb_lines, nb_lines,
nb_elements_per_line, nb_elements_per_line,
(column_to_clone->header)->elements_names, (column_to_clone->header)->elements_names,
(column_to_clone->header)->array_name); (column_to_clone->header)->array_name,
(column_to_clone->header)->comments);
if (new_column == NULL) if (new_column == NULL)
{ {
@ -893,7 +897,6 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
} }
(new_column->header)->cloned_from = version_number; (new_column->header)->cloned_from = version_number;
//memcpy((new_column->header)->comments, (column_to_clone->header)->comments, obi_get_platform_header_size() - //??(column_to_clone->header)->comments); // TODO
if (clone_data) if (clone_data)
{ {
@ -1284,7 +1287,7 @@ int obi_unmap_header(OBIDMS_column_header_p header)
} }
// TODO to be rewritten in an optimized and safe way // 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; char* elements_names;

11
src/obidmscolumn.h
View File

@ -36,9 +36,10 @@
*/ */
#define MAXIMUM_LINE_COUNT (1000000) /**< The maximum line count for the data of a column. //TODO #define MAXIMUM_LINE_COUNT (1000000) /**< The maximum line count for the data of a column. //TODO
*/ */
#define FORMATTED_TIME_LENGTH (1024) /**< The length allocated for the character string containing a formatted date #define FORMATTED_TIME_LENGTH (1024) /**< The length allocated for the character string containing a formatted date.
*/
#define COMMENTS_MAX_LENGTH (2048) /**< The maximum length for comments.
*/ */
typedef int32_t obiversion_t; /**< Used to store the column version number typedef int32_t obiversion_t; /**< Used to store the column version number
*/ */
@ -75,8 +76,7 @@ typedef struct OBIDMS_column_header {
*/ */
char array_name[ARRAY_MAX_NAME+1]; /**< If there is one, the obi_array name as a NULL terminated string. char array_name[ARRAY_MAX_NAME+1]; /**< If there is one, the obi_array name as a NULL terminated string.
*/ */
char comments[1]; /**< Comments stored as a classical zero end C string. char comments[COMMENTS_MAX_LENGTH+1]; /**< Comments stored as a classical zero end C string.
* The size of the comment is only limited by the header size.
*/ */
} OBIDMS_column_header_t, *OBIDMS_column_header_p; } OBIDMS_column_header_t, *OBIDMS_column_header_p;
@ -182,7 +182,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
index_t nb_lines, index_t nb_lines,
index_t nb_elements_per_line, index_t nb_elements_per_line,
const char* elements_names, const char* elements_names,
const char* array_name); const char* array_name,
const char* comments);
/** /**

2
src/obidmscolumndir.h
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@ -21,7 +21,7 @@
#include "obidms.h" #include "obidms.h"
#define OBIDMS_COLUMN_MAX_NAME (2048) /**< The maximum length of an OBIDMS column name. #define OBIDMS_COLUMN_MAX_NAME (1024) /**< The maximum length of an OBIDMS column name.
*/ */