Index: /trunk/Mars/hawc/processing/DiskToDB/run-scripts.sh
===================================================================
--- /trunk/Mars/hawc/processing/DiskToDB/run-scripts.sh	(revision 20105)
+++ /trunk/Mars/hawc/processing/DiskToDB/run-scripts.sh	(revision 20106)
@@ -229,4 +229,5 @@
 mkdir -p ./queries
 readonly ONDISK="./queries/insert-OnDisk-${TEL}.sql"
+readonly AUXDISK="./queries/insert-AuxOnDisk-${TEL}.sql"
 readonly RAW="./queries/insert-raw-${TEL}.sql"
 readonly CALIB="./queries/find-calibration2-${TEL}.sql"
@@ -239,6 +240,4 @@
 
 # Create Database of existing files
-# Create SQL query with:
-# (Telescope, Night, RUNID, ISDRSFILE).
 echo "Updating file table"
 bash ./update-file-table2.sh -i -o "${ONDISK}" "${TEL}" "${DIR}/raw"
@@ -246,4 +245,10 @@
 echo "Uploading updated table"
 mysql --defaults-file="${CRED}" < "${ONDISK}"
+
+# Create Database of existing auxiliary files
+bash ./update-aux-table.sh -r -o "${AUXDISK}" "${TEL}" "${DIR}/auxil"
+# Update DataOnDisk tabel in database
+echo "Uploading updated table"
+mysql --defaults-file="${CRED}" < "${AUXDISK}"
 
 # get list of NIGHTS with unprocessed files
Index: /trunk/Mars/hawc/processing/DiskToDB/update-aux-table.sh
===================================================================
--- /trunk/Mars/hawc/processing/DiskToDB/update-aux-table.sh	(revision 20105)
+++ /trunk/Mars/hawc/processing/DiskToDB/update-aux-table.sh	(revision 20106)
@@ -121,6 +121,15 @@
 
 
-echo \
-"\
+	EXT=0
+	NIGHT=`find "${DIR}"/[0-9][0-9][0-9][0-9]/ -type f \
+		| grep -o "/[0-9]\{8\}.${AUX}.fits" \
+		| cut -f2 -d "/" \
+		| cut -f1 -d "."`|| EXT=1
+
+	if [ ${EXT} = "0" ]
+	then
+
+		echo \
+		"\
 INSERT INTO AuxOnDisk_tmp (Telescope, NIGHT, ${AUX})
 VALUES
@@ -128,57 +137,96 @@
 
 
-NIGHT=`find "${DIR}"/[0-9][0-9][0-9][0-9]/ -type f \
-	| grep -o "/[0-9]\{8\}.${AUX}.fits" \
-	| cut -f2 -d "/" \
-	| cut -f1 -d "."`
-
-# Format to (Telescope, NIGHT, FAD_CONTROL_TEMPERATURE),
-QUERY=`paste <(for i in ${NIGHT}; do echo ${TEL}; done) \
-	<(echo "${NIGHT}") \
-	<(for i in ${NIGHT}; do echo "0"; done) \
-	--delimiters "," \
-	| sed 's/^/(/' \
-	| sed 's/$/),/'`
-
-# Write query to OUTPUT file
-echo "${QUERY}" >> ${OUTPUT}
-# Change last comma to semicolon
-sed -i '$s/,$//' "${OUTPUT}"
-
-echo "ON DUPLICATE KEY UPDATE ${AUX} = 0;" >> ${OUTPUT}
-
-# 1) If there is data in the database that is not on disk then set 
-#	${AUX} = NULL for that night
-# 2) Delete all entries from the database that are not on disk
-# 3) ${INSERT} all entries into the database that are on disk
-echo \
-"\
-CREATE TEMPORARY TABLE TableNotDisk_${AUX}
-(
-	Telescope tinyint UNSIGNED NOT NULL,
-	NIGHT int UNSIGNED NOT NULL,
-	FAD_CONTROL_TEMPERATURE tinyint UNSIGNED,
-	BIAS_CONTROL_DYNAMIC_DATA tinyint UNSIGNED,
-	FTM_CONTROL_DATA tinyint UNSIGNED,
-	FTU_CONTROL_DATA tinyint UNSIGNED,
-	Updated_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP 
-		ON UPDATE CURRENT_TIMESTAMP,
-	PRIMARY KEY (Telescope, NIGHT)
-) SELECT * FROM AuxOnDisk
-	WHERE (Telescope, NIGHT) NOT IN 
-	(SELECT Telescope, NIGHT FROM AuxOnDisk_tmp)
-	AND Telescope=${TEL};
-
-UPDATE AuxOnDisk SET ${AUX} = NULL WHERE NIGHT IN 
-	(SELECT NIGHT FROM TableNotDisk_${AUX})
-	AND Telescope=${TEL};
-
-DELETE FROM AuxOnDisk 
-	WHERE (Telescope, NIGHT) NOT IN 
-	(SELECT Telescope, NIGHT FROM AuxOnDisk_tmp)
-	AND Telescope=${TEL};
-
-${INSERT} AuxOnDisk (SELECT * FROM AuxOnDisk_tmp);
-"\ >> ${OUTPUT}
+		# Format to (Telescope, NIGHT, FAD_CONTROL_TEMPERATURE),
+		QUERY=`paste <(for i in ${NIGHT}; do echo ${TEL}; done) \
+			<(echo "${NIGHT}") \
+			<(for i in ${NIGHT}; do echo "0"; done) \
+			--delimiters "," \
+			| sed 's/^/(/' \
+			| sed 's/$/),/'`
+
+		# Write query to OUTPUT file
+		echo "${QUERY}" >> ${OUTPUT}
+		# Change last comma to semicolon
+		sed -i '$s/,$//' "${OUTPUT}"
+
+		echo "ON DUPLICATE KEY UPDATE ${AUX} = 0;" >> ${OUTPUT}
+
+		# 1) If there is data in the database that is not on disk then set 
+		#	${AUX} = NULL for that night
+		# 2) Delete all entries from the database that are not on disk
+		# 3) ${INSERT} all entries into the database that are on disk
+		echo \
+		"\
+		CREATE TEMPORARY TABLE TableNotDisk_${AUX}
+		(
+			Telescope tinyint UNSIGNED NOT NULL,
+			NIGHT int UNSIGNED NOT NULL,
+			FAD_CONTROL_TEMPERATURE tinyint UNSIGNED,
+			BIAS_CONTROL_DYNAMIC_DATA tinyint UNSIGNED,
+			FTM_CONTROL_DATA tinyint UNSIGNED,
+			FTU_CONTROL_DATA tinyint UNSIGNED,
+			Updated_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP 
+				ON UPDATE CURRENT_TIMESTAMP,
+			PRIMARY KEY (Telescope, NIGHT)
+		) SELECT * FROM AuxOnDisk
+			WHERE (Telescope, NIGHT) NOT IN 
+			(SELECT Telescope, NIGHT FROM AuxOnDisk_tmp)
+			AND Telescope=${TEL};
+
+		UPDATE DataOnDisk SET auxiliary = NULL
+			WHERE DataOnDisk.NIGHT IN 
+			(SELECT NIGHT FROM AuxOnDisk_tmp)
+			AND Telescope=${TEL};
+
+		DELETE FROM AuxOnDisk 
+			WHERE (Telescope, NIGHT) NOT IN 
+			(SELECT Telescope, NIGHT FROM AuxOnDisk_tmp)
+			AND Telescope=${TEL};
+
+		${INSERT} AuxOnDisk (SELECT * FROM AuxOnDisk_tmp);
+		"\ >> ${OUTPUT}
+
+	else
+		# 1) If there is data in the database that is not on disk then set 
+		#	${AUX} = NULL for that night
+		# 2) Delete all entries from the database that are not on disk
+		# 3) ${INSERT} all entries into the database that are on disk
+		echo \
+		"\
+		CREATE TEMPORARY TABLE TableNotDisk_${AUX}
+		(
+			Telescope tinyint UNSIGNED NOT NULL,
+			NIGHT int UNSIGNED NOT NULL,
+			FAD_CONTROL_TEMPERATURE tinyint UNSIGNED,
+			BIAS_CONTROL_DYNAMIC_DATA tinyint UNSIGNED,
+			FTM_CONTROL_DATA tinyint UNSIGNED,
+			FTU_CONTROL_DATA tinyint UNSIGNED,
+			Updated_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP 
+				ON UPDATE CURRENT_TIMESTAMP,
+			PRIMARY KEY (Telescope, NIGHT)
+		) SELECT * FROM AuxOnDisk
+			WHERE (Telescope, NIGHT) NOT IN 
+			(SELECT Telescope, NIGHT FROM AuxOnDisk_tmp)
+			AND Telescope=${TEL};
+
+		UPDATE DataOnDisk SET auxiliary = NULL
+			WHERE DataOnDisk.NIGHT IN 
+			(SELECT NIGHT FROM AuxOnDisk_tmp)
+			AND Telescope=${TEL};
+
+		DELETE FROM AuxOnDisk 
+			WHERE (Telescope, NIGHT) NOT IN 
+			(SELECT Telescope, NIGHT FROM AuxOnDisk_tmp)
+			AND Telescope=${TEL};
+
+		${INSERT} AuxOnDisk (SELECT * FROM AuxOnDisk_tmp);
+		"\ >> ${OUTPUT}
+
+
+		echo "No Auxiliary files."
+		continue;
+	fi
+
+
 
 done
Index: /trunk/Mars/hawc/processing/DiskToDB/update-file-table2.sh
===================================================================
--- /trunk/Mars/hawc/processing/DiskToDB/update-file-table2.sh	(revision 20105)
+++ /trunk/Mars/hawc/processing/DiskToDB/update-file-table2.sh	(revision 20106)
@@ -147,6 +147,6 @@
 sed -i '$s/,$/;/' "${OUTPUT}"
 
-# 1) If there is data in the database that is not on disk then set star = 0
-#    for that night
+# 1) If there is data in the database that is not on disk then set 
+#	header = NULL for that night
 # 2) Delete all entries from the database that are not on disk
 # 3) ${INSERT} all entries into the database that are on disk
Index: /trunk/Mars/hawc/processing/DiskToDB/write-calibration-query.sh
===================================================================
--- /trunk/Mars/hawc/processing/DiskToDB/write-calibration-query.sh	(revision 20105)
+++ /trunk/Mars/hawc/processing/DiskToDB/write-calibration-query.sh	(revision 20106)
@@ -218,4 +218,6 @@
 	WHERE NIGHT=${NIGHT}
 	AND Telescope=${TEL}
-	) = 0;
+	) = 0
+	AND NIGHT=${NIGHT}
+	AND Telescope=${TEL};
 "\ >> ${OUTPUT}