SR26

README

@@ -4,14 +4,14 @@ information produced by the USDA.
 You must first create a new user and database, make sure that these are
 referred to in createdb.sh.
 
-Then make sure you have a recent copy of mdb-tools.  These tools are used to
+Then make sure you have a recent copy of mdbtools.  These tools are used to
 convert the sr22 data from access format into SQL.
 
-Edit create_db.sh to reflect your local MySQL installation, user, password, and
-database.
+Edit createdb.sh to reflect your local MySQL installation: user, password, and
+database.  Also set the version number of the SR database you wish to use.
 
 Then:
 
-    make sr22
+    ./createdb.sh
 
-This should insert all the data into your mysql database!
+This should download and insert all the data into your mysql database!

createdb.sh

@@ -4,35 +4,52 @@
 #  (http://www.ars.usda.gov/Services/docs.htm?docid=18879)
 # draws heavily on http://blog.moybella.net/2007/03/10/converting-microsoft-access-mdb-into-csv-or-mysql-in-linux/
 
-SR22=data/sr22.mdb # data from the USDA in m$ access format
+VER=26
 MYSQLUSER=youruser
 MYSQLPASS=yourpass
 MYSQLDB=ndb
 MYSQLCONN="mysql -u $MYSQLUSER --password=$MYSQLPASS $MYSQLDB"
-TABLES=`mdb-tables $SR22` # a list of tables in our input
-
-# create the database if it doesn't exist
-
-echo creating database $MYSQLDB
-echo "CREATE DATABASE IF NOT EXISTS $MYSQLDB;" | $MYSQLCONN || exit 1
+MDB=data/sr${VER}.mdb # data from the USDA in m$ access format
+
+# If we already ahve MDB file, do nothing.
+if [[ -f data/sr${VER}.mdb ]]
+then
+	# do nothing
+	true
+
+# If we have the ZIP file, extract MDB.
+elif [[ -f data/sr${VER}db.zip ]]
+then
+	unzip data/sr${VER}db.zip sr${VER}.mdb
+	mv sr${VER}.mdb data/
+
+# Otherwise, download ZIP and extract MDB.
+else
+	wget http://www.ars.usda.gov/SP2UserFiles/Place/12354500/Data/SR${VER}/dnload/sr${VER}db.zip || exit 1
+	mv sr${VER}db.zip data/
+	unzip data/sr${VER}db.zip sr${VER}.mdb
+	mv sr${VER}.mdb data/
+fi
 
 # put the schema into the database
-
 echo creating schema in $MYSQLDB
-#mdb-schema $SR22 | $MYSQLCONN
-# The above should work, but the schema requires manual tweaking.
-# The schema that mdb-schema produces from the sr22 access database does not
-# match mysql's spec.
-# Instead we use this hand-edited schema:
-$MYSQLCONN <sr22.sql
 
+# If custom schema is available, use it. If not, use what is available.
+if [[ -f sr${VER}.sql ]]
+then
+	$MYSQLCONN <sr${VER}.sql
+else	
+	mdb-schema --drop-table $MDB mysql | $MYSQLCONN
+fi
+
+TABLES=`mdb-tables $MDB` # a list of tables in our input
 echo adding tables to $MYSQLDB
+
 for table in $TABLES
 do
-    echo adding $table
-    mdb-export -H $SR22 $table > $table.sql
-        mysqlimport -L -u $MYSQLUSER --password=$MYSQLPASS --fields-terminated-by="," --fields-enclosed-by="\"" $MYSQLDB $table.sql
-        rm $table.sql
+	echo adding $table
+	mdb-export -I mysql $MDB $table | sed '1i BEGIN;' | sed '$ a COMMIT;' | $MYSQLCONN
 done
 
 echo done
+

sr22.sql

@@ -141,7 +141,7 @@ CREATE TABLE ABBREV
 	Beta_Carot			DOUBLE, 
 	Beta_Crypt			DOUBLE, 
 	Lycopene			DOUBLE, 
-	Lut_Zea			DOUBLE,  -- this was Lut+Zea
+	`Lut+Zea`		DOUBLE,  -- this was Lut+Zea
 	Vit_E			DOUBLE, 
 	Vit_D_mcg			DOUBLE, 
 	ViVit_D_IU			DOUBLE,