Views: implemented handling of JSON formatted comments

src/obiview.c

@@ -38,6 +38,7 @@
 #include "linked_list.h"
 #include "utils.h"
 #include "obiblob.h"
+#include "libjson/json_utils.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -122,24 +123,6 @@ static size_t get_platform_view_file_size();
 static int enlarge_view_file(Obiview_p view, size_t new_size);
 
 
-/**
- * @brief Internal function writing new comments in a view file.
- *
- * The new comments are concatenated to the pre-existing ones.
- * The view file is enlarged if necessary.
- *
- * @param view A pointer on the view.
- * @param comments The new comments that should be added.
- *
- * @retval 0 if the operation was successfully completed.
- * @retval -1 if an error occurred.
- *
- * @since August 2016
- * @author Celine Mercier (celine.mercier@metabarcoding.org)
- */
-static int write_comments_to_view_file(Obiview_p view, const char* comments);
-
-
 /**
  * @brief Internal function creating a file containing all the informations on a view.
  *
@@ -490,14 +473,15 @@ static char* view_check_one_predicate(Obiview_p view, char* (*predicate_function
  * @brief Internal function checking all the predicates associated with a view.
  *
  * @param view The view.
+ * @param write Whether the verified predicates should be written in the view comments.
  *
- * @returns A character string describing all the predicates separated by line breaks.
+ * @retval 0 if the operation was successfully completed.
- * @retval NULL if at least one of the predicates is false or if there was an error.
+ * @retval -1 if at least one of the predicates is false or if there was an error.
  *
  * @since July 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-static char* view_check_all_predicates(Obiview_p view);
+static int view_check_all_predicates(Obiview_p view, bool write);
 
 
 /************************************************************************
@@ -694,30 +678,6 @@ static int enlarge_view_file(Obiview_p view, size_t new_size)
 }
 
 
-static int write_comments_to_view_file(Obiview_p view, const char* comments)
-{
-	size_t new_size;
-
-	if (comments == NULL)
-		return 0;	// TODO or error? discuss
-
-	new_size = (view->infos)->used_size + strlen(comments);
-
-	// Check if the file has to be enlarged
-	if (new_size >= (view->infos)->file_size)
-	{
-		if (enlarge_view_file(view, new_size) < 0)
-			return -1;
-	}
-
-	strcat((view->infos)->comments, comments);
-
-	(view->infos)->used_size = new_size;
-
-	return 0;
-}
-
-
 static int create_obiview_file(OBIDMS_p dms, const char* view_name)
 {
 	char* 				file_name;
@@ -1067,7 +1027,6 @@ static int rename_finished_view(Obiview_p view)
 
 static int finish_view(Obiview_p view)
 {
-	char*           predicates;
 	int             i;
 	OBIDMS_column_p column;
 
@@ -1100,16 +1059,11 @@ static int finish_view(Obiview_p view)
 	}
 
 	// Check predicates
-	predicates = view_check_all_predicates(view);
+	if (view_check_all_predicates(view, true) < 0)
-	if (predicates == NULL)
 	{
-		obidebug(1, "\nView predicates not respected");
+		obidebug(1, "\nView predicates not respected, view rollbacked");
-		return -1;	// TODO reverse view (delete files)
+		obi_rollback_view(view);  // TODO discuss, maybe never call from C layer
-	}
+		return -1;
-	else
-	{
-		write_comments_to_view_file(view, predicates);
-		free(predicates);
 	}
 
 	if (save_view(view) < 0)
@@ -1419,9 +1373,9 @@ static char* view_check_qual_match_seqs(Obiview_p view)
 					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))
+						if ((size_t)qual_len != strlen(seq))
 						{
-							obidebug(1, "\nError checking the predicate for view %s: The sequences and sequence quality arrays match. \n%d, %s, %d", (view->infos)->name, j, seq, qual_len);
+							obidebug(1, "\nError checking the predicate for view %s: The sequences and sequence quality arrays match.", (view->infos)->name);
 							return NULL;
 						}
 					}
@@ -1471,78 +1425,37 @@ static char* view_check_one_predicate(Obiview_p view, char* (*predicate_function
 }
 
 
-static char* view_check_all_predicates(Obiview_p view)
+static int view_check_all_predicates(Obiview_p view, bool write)
 {
-	int    i, j;
+	int    i;
-	size_t size_to_allocate;
 	char*  predicate = NULL;
-	char*  all_predicates_string = NULL;
-	char** all_predicates = NULL;
-
-	if (view->nb_predicates == 0)
-	{
-		all_predicates_string = (char*) malloc(1*sizeof(char));
-		strcpy(all_predicates_string, "");
-		return all_predicates_string;
-	}
-
-	size_to_allocate = 0;
-
-	// Allocate memory for predicate array
-	all_predicates = (char**) malloc((view->nb_predicates) * sizeof(char*));
-	if (all_predicates == NULL)
-	{
-		obi_set_errno(OBI_MALLOC_ERROR);
-		obidebug(1, "\nError allocating memory for predicate array.");
-		return NULL;
-	}
 
 	for (i=0; i < view->nb_predicates; i++)
 	{
-		// Initialize predicate in predicate array
+		// Check predicate
-		all_predicates[i] = NULL;
-		// Check the predicate
 		predicate = view_check_one_predicate(view, (view->predicate_functions)[i]);
 		if (predicate == NULL)
 		{
-			// TODO discuss
+			// TODO discuss what to do
-			for (j=0; j<=i; j++)
+			return -1;
-				free(all_predicates[j]);
-			free(all_predicates);
-			return NULL;
 		}
 		else
 		{
-			all_predicates[i] = predicate;
+			if ((write) && (predicate[0]!='\0'))
-			size_to_allocate = size_to_allocate + strlen(predicate) + 1;	// +1 for '\n'
+			{
+				// Add predicate in comments
+				if (obi_view_add_comment(view, PREDICATE_KEY, predicate) < 0)
+				{
+					obi_set_errno(OBIVIEW_ERROR);
+					obidebug(1, "\nError adding a verified predicate (%s) in the comments of a view.", predicate);
+					free(predicate);
+					return -1;
+				}
+			}
+			free(predicate);
 		}
 	}
-
+	return 0;
-	size_to_allocate += 1;	// +1 for '\0'
-
-	all_predicates_string = (char*) malloc(size_to_allocate * sizeof(char));
-	if (all_predicates_string == NULL)
-	{
-		obi_set_errno(OBI_MALLOC_ERROR);
-		obidebug(1, "\nError allocating memory for predicate character string.");
-		return NULL;
-	}
-
-	// Build the character string with all the predicates
-	strcpy(all_predicates_string, all_predicates[0]);
-	for (i=1; i < view->nb_predicates; i++)
-	{
-		if (strlen(all_predicates_string))	// First predicate not empty
-			strcat(all_predicates_string, "\n");
-		strcat(all_predicates_string, all_predicates[i]);
-	}
-
-	// Free everything
-	for (i=0; i < view->nb_predicates; i++)
-		free(all_predicates[i]);
-	free(all_predicates);
-
-	return all_predicates_string;
 }
 
 
@@ -1561,8 +1474,8 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 	Obiview_p 		view;
 	int 			i;
 	index_t 		line_nb;
-	char*           clone_comment;
 	OBIDMS_column_p column;
+	int             comments_ok;
 
 	// Check that the DMS is a valid pointer
 	if (dms == NULL)
@@ -1708,27 +1621,6 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 		// Fill informations
 		strcpy((view->infos)->view_type, (view_to_clone->infos)->view_type);
 		strcpy((view->infos)->created_from, (view_to_clone->infos)->name);
-
-		// Write comment specifying the name of the cloned view
-		clone_comment = (char*) malloc((strlen((view_to_clone->infos)->name) + 15)*sizeof(char));
-		if (clone_comment == NULL)
-		{
-			obi_set_errno(OBI_MALLOC_ERROR);
-			obidebug(1, "\nError allocating memory for a view comment");
-			return NULL;
-		}
-		if (sprintf(clone_comment, "Cloned from %s.\n", (view_to_clone->infos)->name) < 0)
-		{
-			obi_set_errno(OBIVIEW_ERROR);
-			obidebug(1, "\nError building a view comment");
-			return NULL;
-		}
-		if (write_comments_to_view_file(view, clone_comment) < 0)
-		{
-			obidebug(1, "\nError writing comments when creating a view");
-			close_view(view);
-			return NULL;
-		}
 	}
 
 	// Else, fill empty view structure
@@ -1759,13 +1651,29 @@ Obiview_p obi_new_view(OBIDMS_p dms, const char* view_name, Obiview_p view_to_cl
 	(view->predicate_functions)[0] = view_check_qual_match_seqs;
 
 	// Write comments
-	if (write_comments_to_view_file(view, comments) < 0)
+	// Comments must be a json string, even empty
+	if ((strcmp(comments, "") == 0) || (comments == NULL))
+		comments_ok = obi_view_write_comments(view, "{}");
+	else
+		comments_ok = obi_view_write_comments(view, comments);
+	if (comments_ok < 0)
 	{
 		obidebug(1, "\nError writing comments when creating a view");
 		close_view(view);
 		return NULL;
 	}
 
+	// Add the comment specifying the name of the cloned view if there is one
+	if (view_to_clone != NULL)
+	{
+		if (obi_view_add_comment(view, "Cloned from", (view_to_clone->infos)->name) < 0)
+		{
+			obidebug(1, "\nError adding comment about cloned view when creating a view");
+			close_view(view);
+			return NULL;
+		}
+	}
+
 	// Store reference for line selection
 	if (view->line_selection == NULL)
 	{
@@ -2524,6 +2432,69 @@ int obi_view_create_column_alias(Obiview_p view, const char* current_name, const
 }
 
 
+int obi_view_write_comments(Obiview_p view, const char* comments)
+{
+	size_t new_size;
+
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to write comments in a read-only view");
+		return -1;
+	}
+
+	if (comments == NULL)
+		return 0;	// TODO or error? discuss
+
+	new_size = sizeof(Obiview_infos_t) + strlen(comments) + 1;
+
+	// Check if the file has to be enlarged
+	if (new_size >= (view->infos)->file_size)
+	{
+		if (enlarge_view_file(view, new_size) < 0)
+			return -1;
+	}
+
+	strcpy((view->infos)->comments, comments);
+
+	(view->infos)->used_size = new_size;
+
+	return 0;
+}
+
+
+int obi_view_add_comment(Obiview_p view, const char* key, const char* value)
+{
+	char* new_comments = NULL;
+
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to add a comment to a read-only view");
+		return -1;
+	}
+
+	new_comments = obi_add_comment((view->infos)->comments, key, value);
+	if (new_comments == NULL)
+	{
+		obidebug(1, "\nError adding a comment to a view, key: %s, value: %s", key, value);
+		return -1;
+	}
+
+	if (obi_view_write_comments(view, new_comments) < 0)
+	{
+		obidebug(1, "\nError adding a comment to a view, key: %s, value: %s", key, value);
+		return -1;
+	}
+
+	free(new_comments);
+
+	return 0;
+}
+
+
 int obi_save_and_close_view(Obiview_p view)
 {
 	// Finish and save the view if it is not read-only

src/obiview.h

@@ -59,6 +59,8 @@
                                 	             */
 #define ID_PREFIX "seq"						    /**< The default prefix of sequence identifiers in automatic ID columns.
                                 	 	  	  	 */
+#define PREDICATE_KEY "predicates"		        /**< The key used in the json-formatted view comments to store predicates.
+                                	 	  	  	 */
 
 
 /**
@@ -484,6 +486,44 @@ OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const ch
 int obi_view_create_column_alias(Obiview_p view, const char* current_name, const char* alias);
 
 
+/**
+ * @brief Internal function writing new comments in a view file.
+ *
+ * The new comments replace the pre-existing ones.
+ * The view file is enlarged if necessary.
+ *
+ * @param view A pointer on the view.
+ * @param comments The new comments that should be written.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since August 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_view_write_comments(Obiview_p view, const char* comments);
+
+
+/**
+ * @brief Adds comments to a view file.
+ *
+ * This reads the comments in the JSON format and adds the key value pair.
+ * If the key already exists, the value format is turned into an array and the new value is appended
+ * if it is not already in the array.
+ *
+ * @param column A pointer on an OBIDMS column.
+ * @param key The key.
+ * @param value The value associated with the key.
+ *
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since August 2018
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_view_add_comment(Obiview_p view, const char* key, const char* value);
+
+
 /**
  * @brief Closes an opened view, and saves it if it is not read-only (meaning it is not already saved in the view file).
  *