Columns are now enlarged if needed when setting a value

python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/capidmscolumn_bool.pxd

@@ -3,5 +3,5 @@ from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
 
 cdef extern from "obidmscolumn_bool.h" nogil:
 
-    int obi_column_set_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
+    int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
-    obibool_t obi_column_get_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+    obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

python/obitools3/obidms/obidmscolumn/obidmscolumn_bool/capidmscolumn_bool.pyx

@@ -6,7 +6,7 @@ from .capidmscolumn_bool cimport *
 cdef class OBIDMS_column_bool(OBIDMS_column) :
 
     def get_item(self, line_nb, element_name):
-        return obi_column_get_bool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
+        return obi_column_get_obibool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
         
 
 cdef class OBIDMS_column_bool_read(OBIDMS_column_bool) :     
@@ -22,7 +22,7 @@ cdef class OBIDMS_column_bool_read(OBIDMS_column_bool) :
 cdef class OBIDMS_column_bool_writable(OBIDMS_column_bool) :     
   
     def set_item(self, line_nb, element_name, value):
-        return obi_column_set_bool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
+        return obi_column_set_obibool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
 
     def close(self):
         if obi_truncate_and_close_column(self.pointer) < 0 :

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

@@ -3,5 +3,5 @@ from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
 
 cdef extern from "obidmscolumn_char.h" nogil:
 
-    int obi_column_set_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t* value)
+    int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t* value)
-    obichar_t* obi_column_get_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+    obichar_t* obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)

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

@@ -6,7 +6,7 @@ from .capidmscolumn_char cimport *
 cdef class OBIDMS_column_char(OBIDMS_column) :
 
     def get_item(self, line_nb, element_name):
-        return (obi_column_get_char_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))).decode(encoding='utf-8')[:1]
+        return (obi_column_get_obichar_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))).decode(encoding='utf-8')[:1]
 
 
 cdef class OBIDMS_column_char_read(OBIDMS_column_char) :     
@@ -22,7 +22,7 @@ cdef class OBIDMS_column_char_read(OBIDMS_column_char) :
 cdef class OBIDMS_column_char_writable(OBIDMS_column_char) :     
 
     def set_item(self, line_nb, element_name, value):
-        return obi_column_set_char_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value.encode('utf-8'))
+        return obi_column_set_obichar_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value.encode('utf-8'))
 
     def close(self):
         if obi_truncate_and_close_column(self.pointer) < 0 :

python/obitools3/obidms/obidmscolumn/obidmscolumn_float/capidmscolumn_float.pxd

@@ -3,5 +3,5 @@ from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
 
 cdef extern from "obidmscolumn_float.h" nogil:
 
-    int obi_column_set_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
+    int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
-    obifloat_t obi_column_get_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+    obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

python/obitools3/obidms/obidmscolumn/obidmscolumn_float/capidmscolumn_float.pyx

@@ -6,7 +6,7 @@ from .capidmscolumn_float cimport *
 cdef class OBIDMS_column_float(OBIDMS_column) :
 
     def get_item(self, line_nb, element_name):
-        return obi_column_get_float_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
+        return obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
 
 
 cdef class OBIDMS_column_float_read(OBIDMS_column_float) :     
@@ -22,7 +22,7 @@ cdef class OBIDMS_column_float_read(OBIDMS_column_float) :
 cdef class OBIDMS_column_float_writable(OBIDMS_column_float) :     
 
     def set_item(self, line_nb, element_name, value):
-        return obi_column_set_float_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
+        return obi_column_set_obifloat_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
 
     def close(self):
         if obi_truncate_and_close_column(self.pointer) < 0 :

python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.pxd

@@ -3,5 +3,5 @@ from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
 
 cdef extern from "obidmscolumn_idx.h" nogil:
 
-    int obi_column_set_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
+    int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
-    obiidx_t obi_column_get_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+    obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

python/obitools3/obidms/obidmscolumn/obidmscolumn_idx/capidmscolumn_idx.pyx

@@ -6,7 +6,7 @@ from .capidmscolumn_idx cimport *
 cdef class OBIDMS_column_idx(OBIDMS_column) :
     
     def get_item(self, line_nb, element_name):
-        return obi_column_get_idx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
+        return obi_column_get_obiidx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
 
     
 cdef class OBIDMS_column_idx_read(OBIDMS_column_idx) :     
@@ -22,7 +22,7 @@ cdef class OBIDMS_column_idx_read(OBIDMS_column_idx) :
 cdef class OBIDMS_column_idx_writable(OBIDMS_column_idx) :     
 
     def set_item(self, line_nb, element_name, value):
-        return obi_column_set_idx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
+        return obi_column_set_obiidx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
 
     def close(self):
         if obi_truncate_and_close_column(self.pointer) < 0 :

python/obitools3/obidms/obidmscolumn/obidmscolumn_int/capidmscolumn_int.pxd

@@ -3,5 +3,5 @@ from obitools3.obidms.obidmscolumn.capidmscolumn cimport *
 
 cdef extern from "obidmscolumn_int.h" nogil:
 
-    int obi_column_set_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
+    int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
-    obiint_t obi_column_get_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+    obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);

python/obitools3/obidms/obidmscolumn/obidmscolumn_int/capidmscolumn_int.pyx

@@ -6,7 +6,7 @@ from .capidmscolumn_int cimport *
 cdef class OBIDMS_column_int(OBIDMS_column) :
 
     def get_item(self, line_nb, element_name):
-        return obi_column_get_int_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
+        return obi_column_get_obiint_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
   
   
 cdef class OBIDMS_column_int_read(OBIDMS_column_int) :     
@@ -22,7 +22,7 @@ cdef class OBIDMS_column_int_read(OBIDMS_column_int) :
 cdef class OBIDMS_column_int_writable(OBIDMS_column_int) :     
 
     def set_item(self, line_nb, element_name, value):
-        return obi_column_set_int_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
+        return obi_column_set_obiint_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'), value)
 
     def close(self):
         if obi_truncate_and_close_column(self.pointer) < 0 :

src/obidmscolumn.c

@@ -600,7 +600,6 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 	int						column_dir_file_descriptor;
 	size_t 					header_size;
 	size_t 					data_size;
-	size_t					i, nb_elements;
 
 	new_column = NULL;
 
@@ -732,41 +731,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 	strncpy(header->name, column_name, OBIDMS_MAX_COLNAME);
 
 	// Fill the data with NA values
-	nb_elements = nb_lines*nb_elements_per_line;
+	obi_ini_to_NA_values (new_column, 0, nb_lines);
-	switch (type) {
-	case OBI_VOID:  // TODO;
-					break;
-
-	case OBI_INT:   for (i=0;i<nb_elements;i++)
-					{
-						*(((obiint_t*) (new_column->data)) + i) = OBIInt_NA;
-					}
-					break;
-
-	case OBI_FLOAT: for (i=0;i<nb_elements;i++)
-					{
-						*(((obifloat_t*) (new_column->data)) + i) = OBIFloat_NA;
-					}
-					break;
-
-	case OBI_BOOL:  for (i=0;i<nb_elements;i++)
-					{
-						*(((obibool_t*) (new_column->data)) + i) = OBIBool_NA;
-					}
-					break;
-
-	case OBI_CHAR:  for (i=0;i<nb_elements;i++)
-					{
-						*(((obichar_t*) (new_column->data)) + i) = OBIChar_NA;
-					}
-					break;
-
-	case OBI_IDX:   for (i=0;i<nb_elements;i++)
-					{
-						*(((obiidx_t*) (new_column->data)) + i) = OBIIdx_NA;
-					}
-					break;
-	}
 
 	free(column_file_name);
 	close(column_file_descriptor);
@@ -1006,7 +971,7 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column)
 	}
 
 	// Open the column file
-	column_file_descriptor = openat(column_dir_file_descriptor, column_file_name, O_RDWR | O_CREAT);
+	column_file_descriptor = openat(column_dir_file_descriptor, column_file_name, O_RDWR);
 	if (column_file_descriptor < 0)
 	{
 		obi_set_errno(OBICOL_UNKNOWN_ERROR);
@@ -1066,6 +1031,139 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column)
 }
 
 
+int obi_enlarge_column(OBIDMS_column_p column)
+{
+	size_t file_size;
+	size_t old_data_size;
+	size_t new_data_size;
+	size_t header_size;
+	size_t old_line_count;
+	size_t new_line_count;
+	int column_dir_file_descriptor;
+	int column_file_descriptor;
+	char* column_file_name;
+
+	// Get the file descriptor associated to the column directory
+	column_dir_file_descriptor = dirfd((column->column_directory)->directory);
+	if (column_dir_file_descriptor < 0)
+	{
+		obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
+		obidebug(1, "\nError getting the file descriptor for a column directory");
+		return -1;
+	}
+
+	// Get the column file name
+	column_file_name = build_column_file_name((column->header)->name, (column->header)->version);
+	if (column_file_name == NULL)
+	{
+		return -1;
+	}
+
+	// Open the column file
+	column_file_descriptor = openat(column_dir_file_descriptor, column_file_name, O_RDWR | O_CREAT);
+	if (column_file_descriptor < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError getting the file descriptor of a column file");
+		free(column_file_name);
+		return -1;
+	}
+
+	// Calculate the new file size
+	old_line_count = (column->header)->line_count;
+	new_line_count = old_line_count * GROWTH_FACTOR;
+	if (new_line_count > MAXIMUM_LINE_COUNT)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError enlarging a column file: new line count greater than the maximum allowed");
+		free(column_file_name);
+		close(column_file_descriptor);
+		return -1;
+	}
+	old_data_size = (column->header)->line_count * (column->header)->nb_elements_per_line * sizeof((column->header)->data_type);
+	new_data_size = old_data_size * GROWTH_FACTOR;
+	header_size = (column->header)->header_size;
+	file_size = header_size + new_data_size;
+
+	// Unmap the data
+	if (munmap(column->data, old_data_size) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError munmapping the data of a column before enlarging");
+		free(column_file_name);
+		close(column_file_descriptor);
+		return -1;
+	}
+
+	// Unmap the header
+	if (munmap(column->header, header_size) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError munmapping the header of a column before enlarging");
+		free(column_file_name);
+		close(column_file_descriptor);
+		return -1;
+	}
+
+	// Enlarge the file
+	if (ftruncate(column_file_descriptor, file_size) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError enlarging a column file");
+		free(column_file_name);
+		close(column_file_descriptor);
+		return -1;
+	}
+
+	// Remap the header (TODO not sure if necessary??)
+	column->header 			 = mmap(NULL,
+			                  	  	header_size,
+									PROT_READ | PROT_WRITE,
+									MAP_SHARED,
+			                  	  	column_file_descriptor,
+			                  	  	0
+			                 	 	);
+
+	if (column->header == MAP_FAILED)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError mmapping the header of a column after enlarging file");
+		close(column_file_descriptor);
+		free(column_file_name);
+		return -1;
+	}
+
+	// Remap the data
+	column->data   			 = mmap(NULL,
+			                 	 	new_data_size,
+			                 	 	PROT_READ | PROT_WRITE,
+			                 	 	MAP_SHARED,
+			                 	 	column_file_descriptor,
+									(column->header)->header_size
+			                		);
+
+	if (column->data == MAP_FAILED)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError re-mmapping the data of a column after enlarging the file");
+		free(column_file_name);
+		close(column_file_descriptor);
+		return -1;
+	}
+
+	// Set new line count
+	(column->header)->line_count = new_line_count;
+
+	// Initialize new data lines to NA
+	obi_ini_to_NA_values(column, old_line_count, new_line_count - old_line_count);
+
+	free(column_file_name);
+	close(column_file_descriptor);
+
+	return 0;
+}
+
+
 int obi_truncate_and_close_column(OBIDMS_column_p column)
 {
 	if (obi_truncate_column_to_lines_used(column) < 0)
@@ -1077,6 +1175,50 @@ int obi_truncate_and_close_column(OBIDMS_column_p column)
 }
 
 
+void obi_ini_to_NA_values(OBIDMS_column_p column, size_t start, size_t nb_lines)
+{
+	size_t i, end, nb_elements;
+
+	nb_elements = nb_lines*((column->header)->nb_elements_per_line);
+	end = start + nb_elements;
+
+	switch ((column->header)->data_type) {
+	case OBI_VOID:  // TODO;
+					break;
+
+	case OBI_INT:   for (i=start;i<end;i++)
+					{
+						*(((obiint_t*) (column->data)) + i) = OBIInt_NA;
+					}
+					break;
+
+	case OBI_FLOAT: for (i=start;i<end;i++)
+					{
+						*(((obifloat_t*) (column->data)) + i) = OBIFloat_NA;
+					}
+					break;
+
+	case OBI_BOOL:  for (i=start;i<end;i++)
+					{
+						*(((obibool_t*) (column->data)) + i) = OBIBool_NA;
+					}
+					break;
+
+	case OBI_CHAR:  for (i=start;i<end;i++)
+					{
+						*(((obichar_t*) (column->data)) + i) = OBIChar_NA;
+					}
+					break;
+
+	case OBI_IDX:   for (i=start;i<end;i++)
+					{
+						*(((obiidx_t*) (column->data)) + i) = OBIIdx_NA;
+					}
+					break;
+	}
+}
+
+
 void obi_column_make_unwritable(OBIDMS_column_p column)
 {
 	column->writable = false;

src/obidmscolumn.h

@@ -27,6 +27,8 @@
 
 #define ELEMENTS_NAMES_MAX (2048)
 #define INITIAL_LINE_COUNT (1000)
+#define GROWTH_FACTOR (2)
+#define MAXIMUM_LINE_COUNT (1000000)
 
 
 typedef int32_t obiversion_t; 	/**< Used to store the column version number
@@ -205,6 +207,20 @@ int obi_close_column(OBIDMS_column_p column);
 int obi_truncate_column_to_lines_used(OBIDMS_column_p column);
 
 
+/**
+ * @brief Enlarges a column file.
+ *
+ * @param column a pointer on an OBIDMS column
+ *
+ * @return 0 if the operation was successfully completed
+ * @return -1 if an error occurred
+ *
+ * @since August 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_enlarge_column(OBIDMS_column_p column);
+
+
 /**
  * @brief Truncates a column file to the number of lines used and closes it.
  *
@@ -219,6 +235,19 @@ int obi_truncate_column_to_lines_used(OBIDMS_column_p column);
 int obi_truncate_and_close_column(OBIDMS_column_p column);
 
 
+/*
+ * @brief Sets the data in a column to the NA value of the data type.
+ *
+ * @param column a pointer on an OBIDMS column
+ * @param start the first line number of the block that should be set
+ * @param nb_lines the number of lines that should be set
+ *
+ * @since August 2015
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+void obi_ini_to_NA_values(OBIDMS_column_p column, size_t start, size_t nb_lines);
+
+
 /**
  * @brief Sets the 'writable' header attribute of an OBIDMS column to False.
  *

src/obidmscolumn_bool.c

@@ -28,23 +28,47 @@
  *
  **********************************************************************/
 
-int obi_column_set_bool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value)
+int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value)
 {
+	// Check that the line number is not greater than the maximum allowed
+	if (line_nb >= MAXIMUM_LINE_COUNT)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
+    	return -1;
+	}
+
+	// Check if the file needs to be enlarged
+	while ((line_nb+1) > (column->header)->line_count)
+	{
+		// Enlarge the file
+		if (obi_enlarge_column(column) < 0)
+	    	return -1;
+	}
+
 	// Update lines used
 	if ((line_nb+1) > (column->header)->lines_used)
 		(column->header)->lines_used = line_nb+1;
+
+	// Set the value
 	*(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
+
 	return 0;
 }
 
 
-obibool_t obi_column_get_bool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
 {
+	if ((line_nb+1) > (column->header)->line_count)
+	{
+		obidebug(1, "\nError trying to get a value that is beyond the current line count");
+		return -1; // TODO return NA value?
+	}
 	return *(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
 
 
-int obi_column_set_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value)
+int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value)
 {
 	size_t element_idx;
 
@@ -66,13 +90,13 @@ int obi_column_set_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, ch
 			return -1;
     }
 
-	obi_column_set_bool_with_elt_idx(column, line_nb, element_idx, value);
+	obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
 
 	return 0;
 }
 
 
-obibool_t obi_column_get_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
 {
 	size_t element_idx;
 
@@ -94,5 +118,6 @@ obibool_t obi_column_get_bool_with_elt_name(OBIDMS_column_p column, size_t line_
 			return -1;
     }
 
-	return obi_column_get_bool_with_elt_idx(column, line_nb, element_idx);
+	return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
 }
+

src/obidmscolumn_bool.h

@@ -37,7 +37,7 @@
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_bool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value);
+int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obibool_t value);
 
 
 /**
@@ -54,7 +54,7 @@ int obi_column_set_bool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, siz
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obibool_t obi_column_get_bool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
 
 
 /**
@@ -78,7 +78,7 @@ obibool_t obi_column_get_bool_with_elt_idx(OBIDMS_column_p column, size_t line_n
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
+int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obibool_t value);
 
 
 /**
@@ -97,5 +97,5 @@ int obi_column_set_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, ch
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obibool_t obi_column_get_bool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
 

src/obidmscolumn_char.c

@@ -28,23 +28,47 @@
  *
  **********************************************************************/
 
-int obi_column_set_char_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value)
+int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t value)
 {
+	// Check that the line number is not greater than the maximum allowed
+	if (line_nb >= MAXIMUM_LINE_COUNT)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
+    	return -1;
+	}
+
+	// Check if the file needs to be enlarged
+	while ((line_nb+1) > (column->header)->line_count)
+	{
+		// Enlarge the file
+		if (obi_enlarge_column(column) < 0)
+	    	return -1;
+	}
+
 	// Update lines used
 	if ((line_nb+1) > (column->header)->lines_used)
 		(column->header)->lines_used = line_nb+1;
-	*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value[0];
+
+	// Set the value
+	*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
+
 	return 0;
 }
 
 
-obichar_t* obi_column_get_char_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+obichar_t obi_column_get_obichar_with_elt_idx(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;
+	if ((line_nb+1) > (column->header)->line_count)
+	{
+		obidebug(1, "\nError trying to get a value that is beyond the current line count");
+		return '\0'; // TODO return NA value?
+	}
+	return *(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
 
 
-int obi_column_set_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t* value)
+int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t value)
 {
 	size_t element_idx;
 
@@ -66,13 +90,13 @@ int obi_column_set_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, ch
 			return -1;
     }
 
-	obi_column_set_char_with_elt_idx(column, line_nb, element_idx, value);
+	obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
 
 	return 0;
 }
 
 
-obichar_t* obi_column_get_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
 {
 	size_t element_idx;
 
@@ -84,15 +108,16 @@ obichar_t* obi_column_get_char_with_elt_name(OBIDMS_column_p column, size_t line
 		{
 			obi_set_errno(OBICOL_UNKNOWN_ERROR);
 			obidebug(1, "\nAn element name must be specified");
-        	return NULL;
+        	return '\0';	// TODO
 		}
 	}
     else
     {
 		element_idx = obi_column_get_element_index_from_name(column, element_name);
 		if (element_idx == -1)
-			return NULL;
+			return '\0';	// TODO
     }
 
-	return obi_column_get_char_with_elt_idx(column, line_nb, element_idx);
+	return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
 }
+

src/obidmscolumn_char.h

@@ -37,7 +37,7 @@
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_char_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value);
+int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obichar_t* value);
 
 
 /**
@@ -54,7 +54,7 @@ int obi_column_set_char_with_elt_idx(OBIDMS_column_p column, size_t line_nb, siz
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obichar_t* obi_column_get_char_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obichar_t* obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
 
 
 /**
@@ -78,7 +78,7 @@ obichar_t* obi_column_get_char_with_elt_idx(OBIDMS_column_p column, size_t line_
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t* value);
+int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obichar_t* value);
 
 
 /**
@@ -97,5 +97,5 @@ int obi_column_set_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, ch
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obichar_t* obi_column_get_char_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obichar_t* obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
 

src/obidmscolumn_float.c

@@ -28,23 +28,47 @@
  *
  **********************************************************************/
 
-int obi_column_set_float_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value)
+int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value)
 {
+	// Check that the line number is not greater than the maximum allowed
+	if (line_nb >= MAXIMUM_LINE_COUNT)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
+    	return -1;
+	}
+
+	// Check if the file needs to be enlarged
+	while ((line_nb+1) > (column->header)->line_count)
+	{
+		// Enlarge the file
+		if (obi_enlarge_column(column) < 0)
+	    	return -1;
+	}
+
 	// Update lines used
 	if ((line_nb+1) > (column->header)->lines_used)
 		(column->header)->lines_used = line_nb+1;
+
+	// Set the value
 	*(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
+
 	return 0;
 }
 
 
-obifloat_t obi_column_get_float_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
 {
+	if ((line_nb+1) > (column->header)->line_count)
+	{
+		obidebug(1, "\nError trying to get a value that is beyond the current line count");
+		return -1; // TODO return NA value?
+	}
 	return *(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
 
 
-int obi_column_set_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value)
+int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value)
 {
 	size_t element_idx;
 
@@ -66,13 +90,13 @@ int obi_column_set_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, c
 			return -1;
     }
 
-	obi_column_set_float_with_elt_idx(column, line_nb, element_idx, value);
+	obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
 
 	return 0;
 }
 
 
-obifloat_t obi_column_get_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
 {
 	size_t element_idx;
 
@@ -94,5 +118,6 @@ obifloat_t obi_column_get_float_with_elt_name(OBIDMS_column_p column, size_t lin
 			return -1;
     }
 
-	return obi_column_get_float_with_elt_idx(column, line_nb, element_idx);
+	return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
 }
+

src/obidmscolumn_float.h

@@ -37,7 +37,7 @@
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_float_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value);
+int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obifloat_t value);
 
 
 /**
@@ -54,7 +54,7 @@ int obi_column_set_float_with_elt_idx(OBIDMS_column_p column, size_t line_nb, si
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obifloat_t obi_column_get_float_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
 
 
 /**
@@ -78,7 +78,7 @@ obifloat_t obi_column_get_float_with_elt_idx(OBIDMS_column_p column, size_t line
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
+int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obifloat_t value);
 
 
 /**
@@ -97,5 +97,5 @@ int obi_column_set_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, c
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obifloat_t obi_column_get_float_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
 

src/obidmscolumn_idx.c

@@ -28,23 +28,47 @@
  *
  **********************************************************************/
 
-int obi_column_set_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value)
+int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value)
 {
+	// Check that the line number is not greater than the maximum allowed
+	if (line_nb >= MAXIMUM_LINE_COUNT)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
+    	return -1;
+	}
+
+	// Check if the file needs to be enlarged
+	while ((line_nb+1) > (column->header)->line_count)
+	{
+		// Enlarge the file
+		if (obi_enlarge_column(column) < 0)
+	    	return -1;
+	}
+
 	// Update lines used
 	if ((line_nb+1) > (column->header)->lines_used)
 		(column->header)->lines_used = line_nb+1;
+
+	// Set the value
 	*(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
+
 	return 0;
 }
 
 
-obiidx_t obi_column_get_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
 {
+	if ((line_nb+1) > (column->header)->line_count)
+	{
+		obidebug(1, "\nError trying to get a value that is beyond the current line count");
+		return -1; // TODO return NA value?
+	}
 	return *(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
 
 
-int obi_column_set_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value)
+int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value)
 {
 	size_t element_idx;
 
@@ -66,13 +90,13 @@ int obi_column_set_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, cha
 			return -1;
     }
 
-	obi_column_set_idx_with_elt_idx(column, line_nb, element_idx, value);
+	obi_column_set_obiidx_with_elt_idx(column, line_nb, element_idx, value);
 
 	return 0;
 }
 
 
-obiidx_t obi_column_get_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
 {
 	size_t element_idx;
 
@@ -94,5 +118,6 @@ obiidx_t obi_column_get_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb
 			return -1;
     }
 
-	return obi_column_get_idx_with_elt_idx(column, line_nb, element_idx);
+	return obi_column_get_obiidx_with_elt_idx(column, line_nb, element_idx);
 }
+

src/obidmscolumn_idx.h

@@ -37,7 +37,7 @@
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value);
+int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiidx_t value);
 
 
 /**
@@ -54,7 +54,7 @@ int obi_column_set_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obiidx_t obi_column_get_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obiidx_t obi_column_get_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
 
 
 /**
@@ -78,7 +78,7 @@ obiidx_t obi_column_get_idx_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
+int obi_column_set_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiidx_t value);
 
 
 /**
@@ -97,5 +97,5 @@ int obi_column_set_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, cha
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obiidx_t obi_column_get_idx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obiidx_t obi_column_get_obiidx_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
 

src/obidmscolumn_int.c

@@ -28,23 +28,47 @@
  *
  **********************************************************************/
 
-int obi_column_set_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value)
+int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value)
 {
+	// Check that the line number is not greater than the maximum allowed
+	if (line_nb >= MAXIMUM_LINE_COUNT)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
+    	return -1;
+	}
+
+	// Check if the file needs to be enlarged
+	while ((line_nb+1) > (column->header)->line_count)
+	{
+		// Enlarge the file
+		if (obi_enlarge_column(column) < 0)
+	    	return -1;
+	}
+
 	// Update lines used
 	if ((line_nb+1) > (column->header)->lines_used)
 		(column->header)->lines_used = line_nb+1;
+
+	// Set the value
 	*(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
+
 	return 0;
 }
 
 
-obiint_t obi_column_get_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
+obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
 {
+	if ((line_nb+1) > (column->header)->line_count)
+	{
+		obidebug(1, "\nError trying to get a value that is beyond the current line count");
+		return -1; // TODO return NA value?
+	}
 	return *(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
 
 
-int obi_column_set_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value)
+int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value)
 {
 	size_t element_idx;
 
@@ -66,13 +90,13 @@ int obi_column_set_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, cha
 			return -1;
     }
 
-	obi_column_set_int_with_elt_idx(column, line_nb, element_idx, value);
+	obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
 
 	return 0;
 }
 
 
-obiint_t obi_column_get_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
+obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name)
 {
 	size_t element_idx;
 
@@ -94,6 +118,6 @@ obiint_t obi_column_get_int_with_elt_name(OBIDMS_column_p column, size_t line_nb
 			return -1;
     }
 
-	return obi_column_get_int_with_elt_idx(column, line_nb, element_idx);
+	return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
 }
 

src/obidmscolumn_int.h

@@ -37,7 +37,7 @@
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value);
+int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx, obiint_t value);
 
 
 /**
@@ -54,7 +54,7 @@ int obi_column_set_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size
  * @since July 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obiint_t obi_column_get_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
+obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx);
 
 
 /**
@@ -78,7 +78,7 @@ obiint_t obi_column_get_int_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-int obi_column_set_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
+int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name, obiint_t value);
 
 
 /**
@@ -97,5 +97,5 @@ int obi_column_set_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, cha
  * @since August 2015
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-obiint_t obi_column_get_int_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);
+obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, size_t line_nb, char* element_name);