First version of automatic ID and COUNT columns, to discuss (for now,

columns created when NUC_SEQ views are closed if the columns don't
already exist)

src/obiview.c

@@ -1072,6 +1072,26 @@ static int finish_view(Obiview_p view)
 		return -1;
 	}
 
+	// Add count column if it's a NUC_SEQ_VIEW with no count column // TODO discuss
+	if ((!strcmp((view->infos)->view_type, VIEW_TYPE_NUC_SEQS)) && (!obi_view_column_exists(view, COUNT_COLUMN)))
+	{
+		if (obi_create_auto_count_column(view) < 0)
+		{
+			obidebug(1, "\nError creating an automatic count column when finishing a view");
+			return -1;
+		}
+	}
+
+	// Add id column if it's a NUC_SEQ_VIEW with no id column // TODO discuss
+	if ((!strcmp((view->infos)->view_type, VIEW_TYPE_NUC_SEQS)) && (!obi_view_column_exists(view, ID_COLUMN)))
+	{
+		if (obi_create_auto_id_column(view, NULL) < 0)
+		{
+			obidebug(1, "\nError creating an automatic id column when finishing a view");
+			return -1;
+		}
+	}
+
 	// Check predicates
 	predicates = view_check_all_predicates(view);
 	if (predicates == NULL)
@@ -1824,7 +1844,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
 			return NULL;
 		}
 		// Adding id column
-		if (obi_view_add_column(view, ID_COLUMN, -1, ID_COLUMN, OBI_STR, 0, 1, NULL, "", NULL, -1, "Ids", true) < 0)
+		if (obi_view_add_column(view, ID_COLUMN, -1, ID_COLUMN, OBI_STR, 0, 1, NULL, "", NULL, -1, "Sequence identifiers", true) < 0)
 		{
 			obidebug(1, "Error adding an obligatory column in a nucleotide sequences view");
 			return NULL;
@@ -2391,6 +2411,15 @@ OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name)
 }
 
 
+bool obi_view_column_exists(Obiview_p view, const char* column_name)
+{
+	if (obi_view_get_column(view, column_name) == NULL)
+		return false;
+	else
+		return true;
+}
+
+
 OBIDMS_column_p* obi_view_get_pointer_on_column_in_view(Obiview_p view, const char* column_name)
 {
 	return (OBIDMS_column_p*)(ht_get(view->column_dict, column_name));
@@ -2459,8 +2488,8 @@ int obi_save_and_close_view(Obiview_p view)
 
 int obi_create_auto_count_column(Obiview_p view)
 {
-	index_t  i;
+	index_t         i;
-	OBIDMS_p column;
+	OBIDMS_column_p column;
 
 	// Check that the view is not read-only
 	if (view->read_only)
@@ -2470,7 +2499,7 @@ int obi_create_auto_count_column(Obiview_p view)
 		return -1;
 	}
 
-	if (obi_view_add_column(view, COUNT_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, NULL, "Sequence counts", true) < 0)
+	if (obi_view_add_column(view, COUNT_COLUMN, -1, NULL, OBI_INT, 0, 1, NULL, NULL, NULL, -1, "Sequence counts", true) < 0)
 	{
 		obidebug(1, "Error adding an automatic count column in a view");
 		return -1;
@@ -2486,7 +2515,7 @@ int obi_create_auto_count_column(Obiview_p view)
 	// Fill the column with 1s
 	for (i=0; i < (view->infos)->line_count; i++)
 	{
-		if (obi_column_set_obiint_with_elt_idx(column, i, 0, 1) < 0)
+		if (obi_set_int_with_elt_idx_and_col_p_in_view(view, column, i, 0, 1) < 0)
 		{
 			obidebug(1, "Error adding an automatic count column in a view");
 			return -1;
@@ -2497,6 +2526,69 @@ int obi_create_auto_count_column(Obiview_p view)
 }
 
 
+int obi_create_auto_id_column(Obiview_p view, const char* prefix)
+{
+	index_t         i;
+	OBIDMS_column_p column;
+	char*           id;
+
+	// Check that the view is not read-only
+	if (view->read_only)
+	{
+		obi_set_errno(OBIVIEW_ERROR);
+		obidebug(1, "\nError trying to create an automatic count column in a read-only view");
+		return -1;
+	}
+
+	// Delete old ID column if it exists
+	if (obi_view_get_column(view, ID_COLUMN) != NULL)
+	{
+		if (obi_view_delete_column(view, ID_COLUMN) < 0)
+		{
+			obidebug(1, "Error deleting an ID column to replace it in a view");
+			return -1;
+		}
+	}
+
+	// Create the new ID column
+	if (obi_view_add_column(view, ID_COLUMN, -1, NULL, OBI_STR, 0, 1, NULL, NULL, NULL, -1, "Sequence identifiers", true) < 0)
+	{
+		obidebug(1, "Error adding an automatic ID column in a view");
+		return -1;
+	}
+
+	column = obi_view_get_column(view, ID_COLUMN);
+	if (column == NULL)
+	{
+		obidebug(1, "Error adding an automatic ID column in a view");
+		return -1;
+	}
+
+	// If prefix is NULL, use default prefix
+	if (prefix == NULL)
+		prefix = ID_PREFIX;
+
+	// Fill the column with automatic ids
+	for (i=0; i < (view->infos)->line_count; i++)
+	{
+		id = build_word_with_idx(prefix, i);
+		if (id == NULL)
+		{
+			obidebug(1, "Error building an id for an automatic ID column");
+			return -1;
+		}
+		if (obi_set_str_with_elt_idx_and_col_p_in_view(view, column, i, 0, id) < 0)
+		{
+			obidebug(1, "Error adding an automatic count column in a view");
+			return -1;
+		}
+		free(id);
+	}
+
+	return 0;
+}
+
+
 // TODO Move to another file?
 /*********** FOR BLOB COLUMNS ***********/
 

src/obiview.h

@@ -55,6 +55,8 @@
 #define COUNT_COLUMN "COUNT"				    /**< The name of the column containing the sequence counts
  	 	 	 	 	 	 	 	 	 	 	 	 *   in NUC_SEQS_VIEW views.
                                 	 	  	  	 */
+#define ID_PREFIX "seq"						    /**< The default prefix of sequence identifiers in automatic ID columns.
+                                	 	  	  	 */
 
 
 /**
@@ -409,6 +411,20 @@ int obi_view_delete_column(Obiview_p view, const char* column_name);
 OBIDMS_column_p obi_view_get_column(Obiview_p view, const char* column_name);
 
 
+/**
+ * @brief Checks if a column exists in a view.
+ *
+ * @param view A pointer on the view.
+ * @param column_name The name of the column in the view.
+ *
+ * @returns A boolean indicating whether or not the column exists in the view.
+ *
+ * @since July 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+bool obi_view_column_exists(Obiview_p view, const char* column_name);
+
+
 /**
  * @brief Gets the pointer on the pointer on a column from its name in a view.
  *
@@ -527,6 +543,25 @@ int obi_save_and_close_view(Obiview_p view);
 int obi_create_auto_count_column(Obiview_p view);
 
 
+/**
+ * @brief Creates an OBI_STR column with the line count of the view it belongs to, and sets all lines with automatic identifiers
+ *        with the form prefix_index.
+ *
+ * @warning The number of lines set corresponds to the line count of the view.
+ *
+ * @param view A pointer on the view.
+ * @param prefix The prefix of automatic ids. The ids have the form prefix_index. If NULL, the default ID_PREFIX is used.
+ *
+ * @returns A value indicating the success of the operation.
+ * @retval 0 if the operation was successfully completed.
+ * @retval -1 if an error occurred.
+ *
+ * @since July 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_create_auto_id_column(Obiview_p view, const char* prefix);
+
+
 /**
  * @brief Recovers an obiblob from an OBIDMS column containing indices referring to obiblobs,
  *        using the index of the element in the line, and the column pointer, in the context of a view.

src/utils.c

@@ -18,6 +18,7 @@
 #include <dirent.h>
 #include <unistd.h>
 #include <time.h>
+#include <math.h>
 
 #include "utils.h"
 #include "obidebug.h"
@@ -35,6 +36,43 @@
  **********************************************************************/
 
 
+int digit_count(index_t i)
+{
+	int n_digits;
+
+	if (i == 0)
+		n_digits = 1;
+	else
+		n_digits = floor(log10(llabs(i))) + 1;
+
+	return n_digits;
+}
+
+
+char* build_word_with_idx(const char* prefix, index_t idx)
+{
+	char* word;
+	int   n_digits;
+
+	n_digits = digit_count(idx);
+	word = (char*) malloc((strlen(prefix) + 1+ n_digits + 1)*sizeof(char));
+	if (word == NULL)
+	{
+		obi_set_errno(OBI_MALLOC_ERROR);
+		obidebug(1, "\nError allocating memory for a character string");
+		return NULL;
+	}
+	if (sprintf(word, "%s_%lld", prefix, idx) < 0)
+	{
+		obi_set_errno(OBI_UTILS_ERROR);
+		obidebug(1, "\nProblem building a word from a prefix and an index");
+		return NULL;
+	}
+
+	return word;
+}
+
+
 int count_dir(char* dir_path)
 {
 	struct dirent* dp;

src/utils.h

@@ -17,6 +17,7 @@
 #include <sys/stat.h>
 
 #include "obidms.h"
+#include "obitypes.h"
 
 
 #define FORMATTED_TIME_LENGTH (1024)    /**< The length allocated for the character string containing a formatted date.
@@ -25,6 +26,35 @@
                                 	   	 */
 
 
+/**
+ * @brief Counts the number of digits of a number.
+ *
+ * @param i The number.
+ *
+ * @returns The number of digits of the number.
+ *
+ * @since July 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int digit_count(index_t i);
+
+
+/**
+ * @brief Builds a word from a prefix and an index, with the form prefix_index.
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param prefix The prefix for the word.
+ * @param idx The index to use as suffix.
+ *
+ * @returns The built word.
+ *
+ * @since July 2017
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+char* build_word_with_idx(const char* prefix, index_t idx);
+
+
 /**
  * @brief Counts the number of files and directories in a directory.
  *