Functions to truncate and/or close a column

python/obitools3/obidms/obidmscolumn/capidmscolumn.pxd

@@ -34,6 +34,7 @@ cdef extern from "obidmscolumn.h" nogil:
     int obi_close_column(OBIDMS_column_p column)
     OBIType_t obi_column_get_data_type_from_name(OBIDMS_p dms, const char* column_name)
     OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversion_t version_number, bint clone_data)
+    int obi_truncate_and_close_column(OBIDMS_column_p column)
 
 
 cdef class OBIDMS_column:

python/obitools3/obidms/obidmscolumn/capidmscolumn.pyx

@@ -66,10 +66,6 @@ cdef class OBIDMS_column:
     def get_data_type(self):
         return self.data_type
         
-#    def __del__(self):
-#        if obi_close_column(self.pointer) != 0 :
-#            raise Exception("Problem closing a column")
-    
     @staticmethod
     def open(dms_name, column_name, 
              create=False, clone=False, clone_data=True,

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

@@ -14,10 +14,19 @@ cdef class OBIDMS_column_bool_read(OBIDMS_column_bool) :
     def set_item(self, line_nb, element_name, value):
         raise Exception('Column is read-only')
     
+    def close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+                        
         
 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)
 
+    def close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+                        
+    
     

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

@@ -8,16 +8,25 @@ 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]
 
+
 cdef class OBIDMS_column_char_read(OBIDMS_column_char) :     
 
     def set_item(self, line_nb, element_name, value):
         raise Exception('Column is read-only')
 
+    def close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+                        
         
 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'))
 
+    def close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+     
         
     

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

@@ -8,15 +8,24 @@ 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'))
 
+
 cdef class OBIDMS_column_float_read(OBIDMS_column_float) :     
 
     def set_item(self, line_nb, element_name, value):
         raise Exception('Column is read-only')
 
+    def close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+                        
         
 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)
 
+    def close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+     
     

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

@@ -8,14 +8,23 @@ 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'))
 
+    
 cdef class OBIDMS_column_idx_read(OBIDMS_column_idx) :     
 
     def set_item(self, line_nb, element_name, value):
         raise Exception('Column is read-only')
 
+    def close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+                        
         
 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)
 
+    def close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+     

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

@@ -14,9 +14,17 @@ cdef class OBIDMS_column_int_read(OBIDMS_column_int) :
     def set_item(self, line_nb, element_name, value):
         raise Exception('Column is read-only')
 
+    def close(self):
+        if obi_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+                   
         
 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)
 
+    def close(self):
+        if obi_truncate_and_close_column(self.pointer) < 0 :
+            raise Exception("Problem closing a column")
+ 

src/obidmscolumn.c

@@ -948,15 +948,130 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversi
 		(new_column->header)->lines_used = nb_lines;
 	}
 
+	// close column_to_clone TODO
+
 	return new_column;
 }
 
 
 int obi_close_column(OBIDMS_column_p column)
 {
-	//munmap? TODO
+	size_t data_size;
-	//truncate to lines used TODO
+
+	// Munmap data
+	data_size = (column->header)->line_count * (column->header)->nb_elements_per_line * sizeof((column->header)->data_type);
+	if (munmap(column->data, data_size) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError munmapping column data");
+		return -1;
+	}
+
+	// Munmap header
+	if (munmap(column->header, (column->header)->header_size) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError munmapping a column header");
+		return -1;
+	}
+
 	free(column);
+
+	return 0;
+}
+
+
+int obi_truncate_column_to_lines_used(OBIDMS_column_p column)
+{
+	size_t file_size;
+	size_t data_size;
+	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);
+		free(column_file_name);
+		return -1;
+	}
+
+	// Unmap the data before truncating the file
+	data_size = (column->header)->line_count * (column->header)->nb_elements_per_line * sizeof((column->header)->data_type);
+	if (munmap(column->data, data_size) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError munmapping the data of a column before truncating");
+		free(column_file_name);
+		close(column_file_descriptor);
+		return -1;
+	}
+
+	// Truncate the column file at the number of lines used
+	data_size = (column->header)->lines_used * (column->header)->nb_elements_per_line * sizeof((column->header)->data_type);
+	file_size = (column->header)->header_size + data_size;
+	if (ftruncate(column_file_descriptor, file_size) < 0)
+	{
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
+		obidebug(1, "\nError truncating a column file at the number of lines used");
+		free(column_file_name);
+		close(column_file_descriptor);
+		return -1;
+	}
+
+	// Remap the data
+	column->data   			 = mmap(NULL,
+			                 	 	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 truncating");
+		free(column_file_name);
+		close(column_file_descriptor);
+		return -1;
+	}
+
+	// Set line_count to lines_used
+	(column->header)->line_count = (column->header)->lines_used;
+
+	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)
+		return -1;
+	if (obi_close_column(column) < 0)
+		return -1;
+
 	return 0;
 }
 

src/obidmscolumn.h

@@ -191,6 +191,34 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms, const char* column_name, obiversi
 int obi_close_column(OBIDMS_column_p column);
 
 
+/**
+ * @brief Truncates a column file to the number of lines used.
+ *
+ * @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_truncate_column_to_lines_used(OBIDMS_column_p column);
+
+
+/**
+ * @brief Truncates a column file to the number of lines used and closes it.
+ *
+ * @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_truncate_and_close_column(OBIDMS_column_p column);
+
+
 /**
  * @brief Sets the 'writable' header attribute of an OBIDMS column to False.
  *