From 0ee728c4d09afe4177436268569e5cf2aa0355f4 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Sat, 31 Aug 2019 18:29:40 +0200
Subject: [PATCH] C: build_ref_db: now adds a comment with the threshold used
 to build the DB

---
 src/build_reference_db.c | 23 ++++++++++++++++++++++-
 src/build_reference_db.h |  4 ++++
 2 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/src/build_reference_db.c b/src/build_reference_db.c
index 260474c..1948270 100755
--- a/src/build_reference_db.c
+++ b/src/build_reference_db.c
@@ -29,6 +29,7 @@
 #include "obi_lcs.h"
 #include "obidms_taxonomy.h"
 #include "obidmscolumn_array.h"
+#include "libjson/json_utils.h"
 
 
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
@@ -167,6 +168,8 @@ int build_reference_db(const char* dms_name,
 	obifloat_t score_array_writable[1000];
 	bool modified;
 	bool merged;
+	char threshold_str[5];
+	char* new_comments;
 
 	// Discuss keeping the matrix view or not
 	matrix_view_name = calloc((strlen(o_view_name)+strlen("_matrix")+1), sizeof(char));
@@ -185,7 +188,7 @@ int build_reference_db(const char* dms_name,
 								 "",
 								 "",
 								 matrix_view_name,
-								 "{}",  // TODO proper comments?
+								 "{}",
 								 false, false,
 							     threshold, true, 0, true,
 								 1) < 0)
@@ -788,6 +791,24 @@ int build_reference_db(const char* dms_name,
 		}
 	}
 
+	// Add information about the threshold used to build the DB
+	snprintf(threshold_str, 5, "%f", threshold);
+
+	new_comments = obi_add_comment((o_view->infos)->comments, DB_THRESHOLD_KEY_IN_COMMENTS, threshold_str);
+	if (new_comments == NULL)
+	{
+		obidebug(1, "\nError adding a comment (db threshold) to a view, key: %s, value: %s", DB_THRESHOLD_KEY_IN_COMMENTS, threshold_str);
+		return -1;
+	}
+
+	if (obi_view_write_comments(o_view, new_comments) < 0)
+	{
+		obidebug(1, "\nError adding a comment (db threshold) to a view, key: %s, value: %s", DB_THRESHOLD_KEY_IN_COMMENTS, threshold_str);
+		return -1;
+	}
+
+	free(new_comments);
+
 	// Close views and DMS
 	if (obi_save_and_close_view(refs_view) < 0)
 	{
diff --git a/src/build_reference_db.h b/src/build_reference_db.h
index 3f3bc33..5365f68 100755
--- a/src/build_reference_db.h
+++ b/src/build_reference_db.h
@@ -21,6 +21,7 @@
 #define LCA_TAXID_COLUMN_NAME "LCA_TAXID"
 #define LCA_TAXID_ARRAY_COLUMN_NAME "LCA_TAXID"
 #define LCA_SCORE_ARRAY_COLUMN_NAME "LCA_SCORE"
+#define DB_THRESHOLD_KEY_IN_COMMENTS "ref_db_threshold"
 
 
 /**
@@ -28,6 +29,9 @@
  *
  * Note: The columns where the results are written are automatically named and created.
  *
+ * Note: The threshold used to build the db is saved in the view's comments with the key
+ *       defined by the DB_THRESHOLD_KEY_IN_COMMENTS macro.
+ *
  * @param dms_name The name of the DMS.
  * @param refs_view_name The name of the view containing the reference sequences annotated with their taxids.
  * @param taxonomy_name The name of the taxonomy stored in the DMS.