Added the handling of errors with the functions to get a value in a

column

python/obitools3/obidms/capidms.pxd

@@ -1,6 +1,9 @@
 cdef extern from *:
     ctypedef char* const_char_p "const char*"
 
+cdef extern from "obierrno.h" nogil:
+    extern int obi_errno
+
 cdef extern from "obidms.h" nogil:
     struct OBIDMS_t:
         pass

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

@@ -6,8 +6,11 @@ from .capidmscolumn_bool cimport *
 cdef class OBIDMS_column_bool(OBIDMS_column) :
 
     def get_item(self, line_nb, element_name):
-        return obi_column_get_obibool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
+        value = obi_column_get_obibool_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
-        
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        return value
+    
 
 cdef class OBIDMS_column_bool_read(OBIDMS_column_bool) :     
 

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

@@ -6,7 +6,10 @@ from .capidmscolumn_char cimport *
 cdef class OBIDMS_column_char(OBIDMS_column) :
 
     def get_item(self, line_nb, element_name):
-        return (obi_column_get_obichar_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))).decode(encoding='utf-8')[:1]
+        value = (obi_column_get_obichar_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))).decode(encoding='utf-8')[:1]
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        return value
 
 
 cdef class OBIDMS_column_char_read(OBIDMS_column_char) :     

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

@@ -6,7 +6,10 @@ from .capidmscolumn_float cimport *
 cdef class OBIDMS_column_float(OBIDMS_column) :
 
     def get_item(self, line_nb, element_name):
-        return obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
+        value = obi_column_get_obifloat_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        return value
 
 
 cdef class OBIDMS_column_float_read(OBIDMS_column_float) :     

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

@@ -6,7 +6,10 @@ from .capidmscolumn_idx cimport *
 cdef class OBIDMS_column_idx(OBIDMS_column) :
     
     def get_item(self, line_nb, element_name):
-        return obi_column_get_obiidx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
+        value = obi_column_get_obiidx_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        return value
 
     
 cdef class OBIDMS_column_idx_read(OBIDMS_column_idx) :     

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

@@ -6,8 +6,11 @@ from .capidmscolumn_int cimport *
 cdef class OBIDMS_column_int(OBIDMS_column) :
 
     def get_item(self, line_nb, element_name):
-        return obi_column_get_obiint_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
+        value = obi_column_get_obiint_with_elt_name(self.pointer, line_nb, element_name.encode('utf-8'))
-  
+        if obi_errno > 0 :
+            raise IndexError(line_nb, element_name)
+        return value
+
   
 cdef class OBIDMS_column_int_read(OBIDMS_column_int) :     
 

src/obidmscolumn.c

@@ -603,7 +603,18 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 
 	new_column = NULL;
 
-	// TODO check that informations are not NULL/invalid?
+	// Check that the informations given are not NULL/invalid/greater than the allowed sizes
+	if (dms == NULL)
+	{
+		obidebug(1, "\nCan't create column because of invalid DMS");
+		return NULL;
+	}
+	if (column_name == NULL)
+	{
+		obidebug(1, "\nCan't create column because of empty column name");
+		return NULL;
+	}
+	//if (type < 1)
 
 	// Get the column directory structure associated to the column
 	column_directory = obi_column_directory(dms, column_name);
@@ -731,7 +742,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
 	strncpy(header->name, column_name, OBIDMS_MAX_COLNAME);
 
 	// Fill the data with NA values
-	obi_ini_to_NA_values (new_column, 0, nb_lines);
+	obi_ini_to_NA_values(new_column, 0, nb_lines);
 
 	free(column_file_name);
 	close(column_file_descriptor);
@@ -1146,7 +1157,7 @@ int obi_enlarge_column(OBIDMS_column_p column)
 			                 	 	PROT_READ | PROT_WRITE,
 			                 	 	MAP_SHARED,
 			                 	 	column_file_descriptor,
-									(column->header)->header_size
+									header_size
 			                		);
 
 	if (column->data == MAP_FAILED)

src/obidmscolumn_bool.c

@@ -59,10 +59,11 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
 
 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)
+	if ((line_nb+1) > (column->header)->lines_used)
 	{
-		obidebug(1, "\nError trying to get a value that is beyond the current line count");
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		return -1; // TODO return NA value?
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		return OBIBool_NA;
 	}
 	return *(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
@@ -108,14 +109,14 @@ obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, size_t li
 		{
 			obi_set_errno(OBICOL_UNKNOWN_ERROR);
 			obidebug(1, "\nAn element name must be specified");
-        	return -1;
+        	return OBIBool_NA;
 		}
 	}
     else
     {
 		element_idx = obi_column_get_element_index_from_name(column, element_name);
 		if (element_idx == -1)
-			return -1;
+			return OBIBool_NA;
     }
 
 	return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);

src/obidmscolumn_char.c

@@ -59,10 +59,11 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
 
 obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, size_t line_nb, size_t element_idx)
 {
-	if ((line_nb+1) > (column->header)->line_count)
+	if ((line_nb+1) > (column->header)->lines_used)
 	{
-		obidebug(1, "\nError trying to get a value that is beyond the current line count");
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		return '\0'; // TODO return NA value?
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		return OBIChar_NA;
 	}
 	return *(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
@@ -108,14 +109,14 @@ obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, size_t li
 		{
 			obi_set_errno(OBICOL_UNKNOWN_ERROR);
 			obidebug(1, "\nAn element name must be specified");
-        	return '\0';	// TODO
+        	return OBIChar_NA;
 		}
 	}
     else
     {
 		element_idx = obi_column_get_element_index_from_name(column, element_name);
 		if (element_idx == -1)
-			return '\0';	// TODO
+			return OBIChar_NA;
     }
 
 	return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);

src/obidmscolumn_float.c

@@ -59,10 +59,11 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, size_t line_nb,
 
 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)
+	if ((line_nb+1) > (column->header)->lines_used)
 	{
-		obidebug(1, "\nError trying to get a value that is beyond the current line count");
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		return -1; // TODO return NA value?
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		return OBIFloat_NA;
 	}
 	return *(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
@@ -108,14 +109,14 @@ obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, size_t
 		{
 			obi_set_errno(OBICOL_UNKNOWN_ERROR);
 			obidebug(1, "\nAn element name must be specified");
-        	return -1;
+        	return OBIFloat_NA;
 		}
 	}
     else
     {
 		element_idx = obi_column_get_element_index_from_name(column, element_name);
 		if (element_idx == -1)
-			return -1;
+			return OBIFloat_NA;
     }
 
 	return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);

src/obidmscolumn_idx.c

@@ -59,10 +59,11 @@ int obi_column_set_obiidx_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
 
 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)
+	if ((line_nb+1) > (column->header)->lines_used)
 	{
-		obidebug(1, "\nError trying to get a value that is beyond the current line count");
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		return -1; // TODO return NA value?
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		return OBIIdx_NA;
 	}
 	return *(((obiidx_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
@@ -108,14 +109,14 @@ obiidx_t obi_column_get_obiidx_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 -1;
+        	return OBIIdx_NA;
 		}
 	}
     else
     {
 		element_idx = obi_column_get_element_index_from_name(column, element_name);
 		if (element_idx == -1)
-			return -1;
+			return OBIIdx_NA;
     }
 
 	return obi_column_get_obiidx_with_elt_idx(column, line_nb, element_idx);

src/obidmscolumn_int.c

@@ -59,10 +59,11 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, size_t line_nb, s
 
 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)
+	if ((line_nb+1) > (column->header)->lines_used)
 	{
-		obidebug(1, "\nError trying to get a value that is beyond the current line count");
+		obi_set_errno(OBICOL_UNKNOWN_ERROR);
-		return -1; // TODO return NA value?
+		obidebug(1, "\nError trying to get a value that is beyond the current number of lines used");
+		return OBIInt_NA;
 	}
 	return *(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
 }
@@ -108,14 +109,14 @@ obiint_t obi_column_get_obiint_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 -1;
+        	return OBIInt_NA;
 		}
 	}
     else
     {
 		element_idx = obi_column_get_element_index_from_name(column, element_name);
 		if (element_idx == -1)
-			return -1;
+			return OBIInt_NA;
     }
 
 	return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);