Files and functions for columns with the data type OBIChar_t, working

but using char* (needs to be changed)

python/obitools3/obidms/obidmscolumn/capidmscolumn.pyx

@@ -4,7 +4,7 @@ from .capidmscolumn cimport *
 from obitools3.obidms.obidmscolumn.obidmscolumn_int.capidmscolumn_int import OBIDMS_column_int
 from obitools3.obidms.obidmscolumn.obidmscolumn_float.capidmscolumn_float import OBIDMS_column_float
 from obitools3.obidms.obidmscolumn.obidmscolumn_bool.capidmscolumn_bool import OBIDMS_column_bool
-#from obitools3.obidms.obidmscolumn.obidmscolumn_char.capidmscolumn_char import OBIDMS_column_char
+from obitools3.obidms.obidmscolumn.obidmscolumn_char.capidmscolumn_char import OBIDMS_column_char
 from obitools3.obidms.obidmscolumn.obidmscolumn_idx.capidmscolumn_idx import OBIDMS_column_idx
 
 
@@ -112,12 +112,12 @@ cdef class OBIDMS_column:
                                        nb_elements, nb_elements_per_line, 
                                        elements_names)
 
-#        elif type == 4 :
-#            column = OBIDMS_column_char(dms_name, column_name, 
-#                                       create, clone, clone_data, 
-#                                       version_number, type, 
-#                                       nb_elements, nb_elements_per_line, 
-#                                       elements_names)
+        elif type == 4 :
+            column = OBIDMS_column_char(dms_name, column_name, 
+                                       create, clone, clone_data, 
+                                       version_number, type, 
+                                       nb_elements, nb_elements_per_line, 
+                                       elements_names)
 
         elif type == 5 :
             column = OBIDMS_column_idx(dms_name, column_name, 

python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.cfiles

+../../../../../src/obidmscolumn_char.c
+../../../../../src/obidmscolumn_char.h
+../../../../../src/obidmscolumn.h
+../../../../../src/obidmscolumn.c
+../../../../../src/obidmscolumndir.h
+../../../../../src/obidmscolumndir.c
+../../../../../src/obidms.h
+../../../../../src/obidms.c
+../../../../../src/obierrno.h
+../../../../../src/obierrno.c
+../../../../../src/obilittlebigman.h
+../../../../../src/obilittlebigman.c
+../../../../../src/obitypes.h
+../../../../../src/obitypes.c
+../../../../../src/private_at_functions.h
+../../../../../src/private_at_functions.c

python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.pxd

+from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
+
+
+cdef extern from "obidmscolumn_char.h" nogil:
+
+    int obi_column_set_char(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value)
+    obichar_t* obi_column_get_char(OBIDMS_column_p column, size_t line_nb, size_t element_idx)

python/obitools3/obidms/obidmscolumn/obidmscolumn_char/capidmscolumn_char.pyx

+#cython: language_level=3
+
+from .capidmscolumn_char cimport *
+
+
+cdef class OBIDMS_column_char(OBIDMS_column) :
+  
+    def set_item(self, line_nb, element_name, value):
+        if element_name != "" :
+            element_idx = self.get_element_index_from_name(element_name)
+        else :
+            if obi_column_get_nb_elements_per_line(self.pointer) == 1 :
+                element_idx = 0
+            else : 
+                print("An element name must be specified")
+                return -1
+        return obi_column_set_char(self.pointer, line_nb, element_idx, value)
+     
+    def get_item(self, line_nb, element_name):
+        if element_name != "" :
+            element_idx = self.get_element_index_from_name(element_name)
+        else :
+            if obi_column_get_nb_elements_per_line(self.pointer) == 1 :
+                element_idx = 0
+            else : 
+                print("An element name must be specified")
+                return -1
+        return (obi_column_get_char(self.pointer, line_nb, element_idx)).decode(encoding='UTF-8')[:1]    #not ideal...
+        
+    
\ No newline at end of file

src/obidmscolumn_char.c

+/****************************************************************************
+ * OBIDMS_column_char functions                                              *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_char.c
+ * @author Celine Mercier
+ * @date August 10th 2015
+ * @brief Functions handling OBIColumns containing data with the OBIType OBI_CHAR.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidmscolumn.h"
+#include "obitypes.h"
+#include "obierrno.h"
+#include "obidebug.h"
+
+
+/**********************************************************************
+ *
+ * D E F I N I T I O N   O F   T H E   P U B L I C   F U N C T I O N S
+ *
+ **********************************************************************/
+
+int obi_column_set_char(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value)
+{
+	// when/where check if can write?
+	*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value[0];
+	return 0;
+}
+
+
+obichar_t* obi_column_get_char(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+{
+	return ((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx;
+}
+

src/obidmscolumn_char.h

+/****************************************************************************
+ * OBIDMS_column_char header file                                            *
+ ****************************************************************************/
+
+/**
+ * @file obidsmcolumn_char.h
+ * @author Celine Mercier
+ * @date August 10th 2015
+ * @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_CHAR.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "obidmscolumn.h"
+#include "obitypes.h"
+
+
+/**
+ * @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR.
+ *
+ * @param column a pointer as returned by obi_create_column()
+ * @warning Pointers returned by obi_open_column() don't allow writing.
+ *
+ * @param line_nb the number of the line where the value should be set
+ *
+ * @param element_idx the index of the element that should be set in the line
+ *
+ * @param value the value that should be set
+ *
+ * @return an integer value indicating the success of the operation.
+ *
+ * @retvalue 0 on success
+ * @retvalue -1 on failure and the `obi_errno` variable is set.
+ *
+ * @since August 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_column_set_char(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value);
+
+
+/**
+ * @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR.
+ *
+ * @param column a pointer as returned by obi_create_column()
+ *
+ * @param line_nb the number of the line where the value should be recovered
+ *
+ * @param element_idx the index of the element that should be recovered in the line
+ *
+ * @return the recovered value
+ *
+ * @since August 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+obichar_t* obi_column_get_char(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+
+