A first version of predicate functions that are checked when a new view

is saved and closed

src/obiview.c

@@ -129,7 +129,7 @@ OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name);
 
 
 /**
- * Internal function preparing to set a value in a column, in the context of a view.
+ * @brief Internal function preparing to set a value in a column, in the context of a view.
  *
  * The function checks that the view is not read-only, clones the column or all columns if needed,
  * and updates the line count if needed.
@@ -148,7 +148,7 @@ int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, i
 
 
 /**
- * Internal function preparing to get a value from a column, in the context of a view.
+ * @brief Internal function preparing to get a value from a column, in the context of a view.
  *
  * The function checks that the line index is not beyond the current line count of the view,
  * and modifies it if there is a line selection associated with the view.
@@ -165,6 +165,116 @@ int prepare_to_set_value_in_column(Obiview_p view, OBIDMS_column_p* column_pp, i
 int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p);
 
 
+/****** PREDICATE FUNCTIONS *******/
+
+/**
+ * @brief Internal function checking if a view has a NUC_SEQUENCE_COLUMN column.
+ *
+ * The function checks that the view has a column with the name attributed to obligatory
+ * nucleotide sequence columns.
+ *
+ * @param view The view.
+ *
+ * @returns A boolean value indicating whether the view has a NUC_SEQUENCE_COLUMN column.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+bool view_has_nuc_sequence_column(Obiview_p view);
+
+
+/**
+ * @brief Internal function checking if a view has a QUALITY_COLUMN column.
+ *
+ * The function checks that the view has a column with the name attributed to obligatory
+ * quality columns.
+ *
+ * @param view The view.
+ *
+ * @returns A boolean value indicating whether the view has a QUALITY_COLUMN column.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+bool view_has_quality_column(Obiview_p view);
+
+
+/**
+ * @brief Internal function checking if a view has a ID_COLUMN column.
+ *
+ * The function checks that the view has a column with the name attributed to obligatory
+ * id columns.
+ *
+ * @param view The view.
+ *
+ * @returns A boolean value indicating whether the view has a ID_COLUMN column.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+bool view_has_id_column(Obiview_p view);
+
+
+/**
+ * @brief Internal function checking if a view has a DEFINITION_COLUMN column.
+ *
+ * The function checks that the view has a column with the name attributed to obligatory
+ * definition columns.
+ *
+ * @param view The view.
+ *
+ * @returns A boolean value indicating whether the view has a DEFINITION_COLUMN column.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+bool view_has_definition_column(Obiview_p view);
+
+
+/**
+ * @brief Internal function checking that the quality column of a view and the sequence column associated to it
+ * 		  correspond properly:
+ * 		  	- when a line is defined for either column, it must also be defined for the other column
+ * 		  	- when a line is defined, the lengths of the sequence and of the quality must be equal
+ *
+ * @param view The view.
+ *
+ * @returns A boolean value indicating whether the sequence and quality columns correspond properly.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+bool view_check_quality_matches_seq_column(Obiview_p view);
+
+
+/**
+ * @brief Internal function checking one predicate function on a view.
+ *
+ * @param view The view.
+ * @param predicate_function The predicate function to use.
+ *
+ * @returns The boolean value returned by the predicate function.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+bool view_check_one_predicate(Obiview_p view, bool (*predicate_function)(Obiview_p view));
+
+
+/**
+ * @brief Internal function checking all the predicates associated with a view.
+ *
+ * @param view The view.
+ *
+ * @retval 0 if all the predicates are OK.
+ * @retval -1 if at least one predicate was found to be false.
+ *
+ * @since July 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int view_check_all_predicates(Obiview_p view);
+
+
 /************************************************************************
  *
  * D E F I N I T I O N   O F   T H E   P R I V A T E   F U N C T I O N S
@@ -229,11 +339,11 @@ int create_obiview_file(OBIDMS_p dms, const char* view_name)
 	{
 		obi_set_errno(OBIVIEW_ERROR);
 		obidebug(1, "\nError creating an obiview file");
-//		free(file_name);  TODO
+//		free(file_name);
 		return -1;
 	}
 
-	//free(file_name); TODO
+	//free(file_name);
 
 	// Truncate file to the right size
 	file_size = get_platform_view_file_size();
@@ -419,6 +529,111 @@ int prepare_to_get_value_from_column(Obiview_p view, index_t* line_nb_p)
 }
 
 
+
+/****** PREDICATE FUNCTIONS *******/
+
+bool view_has_nuc_sequence_column(Obiview_p view)
+{
+	if (obi_view_get_column(view, NUC_SEQUENCE_COLUMN) != NULL)
+		return true;
+	else
+		return false;
+}
+
+
+bool view_has_quality_column(Obiview_p view)
+{
+	if (obi_view_get_column(view, QUALITY_COLUMN) != NULL)
+		return true;
+	else
+		return false;
+}
+
+
+bool view_has_id_column(Obiview_p view)
+{
+	if (obi_view_get_column(view, ID_COLUMN) != NULL)
+		return true;
+	else
+		return false;
+}
+
+
+bool view_has_definition_column(Obiview_p view)
+{
+	if (obi_view_get_column(view, DEFINITION_COLUMN) != NULL)
+		return true;
+	else
+		return false;
+}
+
+
+bool view_check_quality_matches_seq_column(Obiview_p view)	// TODO Print error if there is one?
+{
+	index_t 		i, j;
+	index_t			nb_elements_per_line;
+	int	    		qual_len;
+	const uint8_t*	qual;
+	char* 			seq;
+	OBIDMS_column_p qual_column;
+	OBIDMS_column_p seq_column;
+
+	qual_column = obi_view_get_column(view, QUALITY_COLUMN);
+	if (qual_column == NULL)
+		return false;
+
+	seq_column = obi_view_get_column(view, NUC_SEQUENCE_COLUMN);	// TODO Get associated nuc column
+	if (seq_column == NULL)
+		return false;
+
+	nb_elements_per_line = (qual_column->header)->nb_elements_per_line;
+	// Check that the quality and the sequence columns have the same number of elements per line
+	if (nb_elements_per_line != (seq_column->header)->nb_elements_per_line)
+		return false;
+
+	for (i=0; i < (view->infos)->line_count; i++)
+	{
+		for (j=0; j < nb_elements_per_line; j++)
+		{
+			qual = obi_column_get_obiqual_int_with_elt_idx(qual_column, i, j, &qual_len);
+			seq = obi_column_get_obiseq_with_elt_idx(seq_column, i, j);
+			if ((qual != OBIQual_int_NA) && (seq != OBISeq_NA))
+			{
+				// Test that the lengths of the quality and the sequence are equal
+				if (qual_len != (int)strlen(seq))
+					return false;
+			}
+			// Test if one value is NA and not the other
+			else if (((qual == OBIQual_int_NA) && (seq != OBISeq_NA)) || ((qual != OBIQual_int_NA) && (seq == OBISeq_NA)))
+				return false;
+		}
+	}
+	return true;
+}
+
+
+bool view_check_one_predicate(Obiview_p view, bool (*predicate_function)(Obiview_p view))
+{
+	return predicate_function(view);
+}
+
+
+int view_check_all_predicates(Obiview_p view)
+{
+	int i;
+
+	for (i=0; i < view->nb_predicates; i++)
+	{
+		if (view_check_one_predicate(view, (view->predicate_functions)[i]) == false)
+			return -1;
+	}
+	return 0;
+}
+
+
+// TODO predicate function that goes through each line / each elements
+
+
 /**********************************************************************
  *
  * 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
@@ -581,6 +796,8 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 	strcpy((view->infos)->comments, comments);
 	(view->infos)->creation_date = time(NULL);
 	view->read_only = 0;
+	view->nb_predicates = 0;
+	view->predicate_functions = NULL;
 
 	// Store reference for line selection
 	if (view->line_selection == NULL)
@@ -665,6 +882,17 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 		}
 	}
 
+	// Add predicate functions of the view type
+	view->nb_predicates = 5;	// TODO macro?
+
+	view->predicate_functions = malloc((view->nb_predicates) * sizeof(bool (*) (bool)));
+
+	(view->predicate_functions)[0] = view_has_nuc_sequence_column;
+	(view->predicate_functions)[1] = view_has_quality_column;
+	(view->predicate_functions)[2] = view_has_id_column;
+	(view->predicate_functions)[3] = view_has_definition_column;
+	(view->predicate_functions)[4] = view_check_quality_matches_seq_column;
+
 	return view;
 }
 
@@ -704,11 +932,11 @@ Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name)
 	{
 		obi_set_errno(OBIVIEW_ERROR);
 		obidebug(1, "\nError opening an obiview file");
-//		free(file_name);   TODO
+//		free(file_name);
 		return NULL;
 	}
 
-	//free(file_name); TODO
+	//free(file_name);
 
 	// Map the view infos structure
 	file_size = get_platform_view_file_size();
@@ -750,11 +978,11 @@ int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos)
 		{
 			obi_set_errno(OBIVIEW_ERROR);
 			obidebug(1, "\nError opening an obiview file");
-	//		free(file_name);   TODO
+	//		free(file_name);
 			return -1;
 		}
 
-		//free(file_name); TODO
+		//free(file_name);
 
 		// Unmap the view infos structure
 		file_size = get_platform_view_file_size();
@@ -819,6 +1047,8 @@ Obiview_p obi_open_view(OBIDMS_p dms, const char* view_name)
 	view->dms = dms;
 	view->new_line_selection = NULL;
 	view->read_only = true;
+	view->nb_predicates = 0;
+	view->predicate_functions = NULL;
 
 	return view;
 }
@@ -1159,6 +1389,8 @@ int obi_save_and_close_view(Obiview_p view)
 {
 	if (!(view->read_only))
 	{
+		if (view_check_all_predicates(view) < 0)
+			return -1;	// TODO reverse view (delete files)
 		if (obi_save_view(view) < 0)
 			return -1;
 	}

src/obiview.h

@@ -99,24 +99,28 @@ typedef struct Obiview_infos {
  * @brief Structure for an opened view.
  */
 typedef struct Obiview {
-	Obiview_infos_p     infos;										/**< A pointer on the mapped view informations.
+	Obiview_infos_p     infos;											/**< A pointer on the mapped view informations.
-		 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+		 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	OBIDMS_p         	dms;    									/**< A pointer on the DMS to which the view belongs.
+	OBIDMS_p         	dms;    										/**< A pointer on the DMS to which the view belongs.
-	 	 	    													 */
+	 	 	    													 	 */
-	bool             	read_only;    								/**< Whether the view is read-only or can be modified.
+	bool             	read_only;    									/**< Whether the view is read-only or can be modified.
-																	 */
+																	 	 */
-	OBIDMS_column_p  	line_selection;    							/**< A pointer on the column containing the line selection
+	OBIDMS_column_p  	line_selection;    								/**< A pointer on the column containing the line selection
-																	 *   associated with the view if there is one.
+																	 	 *   associated with the view if there is one.
-																	 *   This line selection is read-only, and when a line from the view is read,
+																	 	 *   This line selection is read-only, and when a line from the view is read,
-																	 *   it is this line selection that is used.
+																	 	 *   it is this line selection that is used.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+																	 	 */
-	OBIDMS_column_p  	new_line_selection;    						/**< A pointer on the column containing the new line selection being built
+	OBIDMS_column_p  	new_line_selection;    							/**< A pointer on the column containing the new line selection being built
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   to associate with the view, if there is one.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   to associate with the view, if there is one.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   When a line is selected with obi_select_line() or obi_select_lines(),
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   When a line is selected with obi_select_line() or obi_select_lines(),
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   it is recorded in this line selection.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 *   it is recorded in this line selection.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
-	OBIDMS_column_p  	columns[MAX_NB_OPENED_COLUMNS];    			/**< Array of pointers on all the columns of the view.
+	OBIDMS_column_p  	columns[MAX_NB_OPENED_COLUMNS];    				/**< Array of pointers on all the columns of the view.
-	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	int					nb_predicates;    								/**< Number of predicates to test when closing the view.
+ 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
+	bool 				(**predicate_functions)(struct Obiview* view);  /**< Array of pointers on all predicate functions to test when closing the view.
+	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 } Obiview_t, *Obiview_p;