owl/trunk/createGraphDb.sh

#!/bin/sh
function usage {
        echo
        echo "Script to create/link/index a graph database. "
        echo
        echo "Usage: $1 -d <db_name> -m <mode>"
        echo
        echo "-d <db_name>      the graph database name "
        echo "-m <mode>         create/index/unindex tables "
        echo
} 

#
#Set default value for variables
#
graphDb=""
mode=""
h="white"

while getopts d:m: opt
do
  case "$opt" in
        d) graphDb="$OPTARG";;
        m) mode="$OPTARG";;
  esac
done

if [ -z "$graphDb" ] || [ -z "$mode" ]
then
        echo "Missing or more arguments"
        usage $0
        exit 1
fi

arch=`uname -m`
case "$arch" in
    i686)
        mysqldir=/project/tla/dist/mysql-i686
    ;;
    x86_64)
        mysqldir=/project/tla/dist/mysql
    ;;
    *)
        mysqldir=/project/tla/dist/mysql-i686
    ;;
esac

mysqlbin=$mysqldir/bin/mysql
master=white
db=test

if [ "$mode" == "CREATE" ]
then
$mysqlbin -pnieve -h $h -B -N $db <<ENDSQL
        SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
        CREATE DATABASE IF NOT EXISTS ${graphDb}
                DEFAULT CHARACTER SET latin1 DEFAULT COLLATE latin1_general_cs;
ENDSQL
$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL1
        SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
        CREATE TABLE chain_graph LIKE abstract.chain_graph;
        CREATE TABLE single_model_graph LIKE abstract.single_model_graph;
        CREATE TABLE single_model_node LIKE abstract.single_model_node;
        CREATE TABLE single_model_edge LIKE abstract.single_model_edge;
        CREATE TABLE pdb_residue_info LIKE abstract.pdb_residue_info;
        
        ALTER TABLE chain_graph
                MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
                MODIFY pchain_code VARCHAR(2) NOT NULL,
                MODIFY scops INT,
                MODIFY caths INT,
                MODIFY entry_id INT,
                MODIFY assembly_id INT,
                MODIFY chain_id INT,
                MODIFY model_id INT;
        
        ALTER TABLE single_model_graph
                MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT;
        
        ALTER TABLE single_model_node
                MODIFY ssid VARCHAR(5),
                MODIFY sheet_serial CHAR(1);
                
        ALTER TABLE single_model_edge
                MODIFY i_ssid VARCHAR(5),
                MODIFY i_sheet_serial CHAR(1),
                MODIFY j_ssid VARCHAR(5),
                MODIFY j_sheet_serial CHAR(1);          
ENDSQL1
fi

if [ "$mode" == "INDEX" ]
then
$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
        SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";   
        CREATE INDEX NODE_GRAPH_IDX ON single_model_node (graph_id);
        CREATE INDEX EDGE_GRAPH_IDX ON single_model_edge (graph_id);    
        CREATE INDEX CHAIN_IDX ON pdb_residue_info (pdb_code, chain_code, pdb_chain_code);
ENDSQL
fi

if [ "$mode" == "UNINDEX" ]
then
$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
        SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";   
        DROP INDEX NODE_GRAPH_IDX ON single_model_node;
        DROP INDEX EDGE_GRAPH_IDX ON single_model_edge; 
ENDSQL
fi
Revision:	413
Committed:	Wed Nov 21 21:23:19 2007 UTC (16 years, 10 months ago) by filippis
File size:	2653 byte(s)
Log Message:	createGraphDb.sh -pchain_code is now modified to VARCHAR(2) from CHAR(1) due to pdbase_chain_code -index for pdb_residue_info table added
Line	User	Rev	File contents
1	filippis	409	#!/bin/sh
2			function usage {
3			echo
4			echo "Script to create/link/index a graph database. "
5			echo
6			echo "Usage: $1 -d <db_name> -m <mode>"
7			echo
8			echo "-d <db_name> the graph database name "
9			echo "-m <mode> create/index/unindex tables "
10			echo
11			}
12
13			#
14			#Set default value for variables
15			#
16			graphDb=""
17			mode=""
18			h="white"
19
20			while getopts d:m: opt
21			do
22			case "$opt" in
23			d) graphDb="$OPTARG";;
24			m) mode="$OPTARG";;
25			esac
26			done
27
28			if [ -z "$graphDb" ] \|\| [ -z "$mode" ]
29			then
30			echo "Missing or more arguments"
31			usage $0
32			exit 1
33			fi
34
35			arch=`uname -m`
36			case "$arch" in
37			i686)
38			mysqldir=/project/tla/dist/mysql-i686
39			;;
40			x86_64)
41			mysqldir=/project/tla/dist/mysql
42			;;
43			*)
44			mysqldir=/project/tla/dist/mysql-i686
45			;;
46			esac
47
48			mysqlbin=$mysqldir/bin/mysql
49			master=white
50			db=test
51
52			if [ "$mode" == "CREATE" ]
53			then
54			$mysqlbin -pnieve -h $h -B -N $db <<ENDSQL
55			SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
56			CREATE DATABASE IF NOT EXISTS ${graphDb}
57			DEFAULT CHARACTER SET latin1 DEFAULT COLLATE latin1_general_cs;
58			ENDSQL
59			$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL1
60			SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
61			CREATE TABLE chain_graph LIKE abstract.chain_graph;
62			CREATE TABLE single_model_graph LIKE abstract.single_model_graph;
63			CREATE TABLE single_model_node LIKE abstract.single_model_node;
64			CREATE TABLE single_model_edge LIKE abstract.single_model_edge;
65			CREATE TABLE pdb_residue_info LIKE abstract.pdb_residue_info;
66
67			ALTER TABLE chain_graph
68			MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
69	filippis	413	MODIFY pchain_code VARCHAR(2) NOT NULL,
70	filippis	409	MODIFY scops INT,
71			MODIFY caths INT,
72			MODIFY entry_id INT,
73			MODIFY assembly_id INT,
74			MODIFY chain_id INT,
75			MODIFY model_id INT;
76
77			ALTER TABLE single_model_graph
78			MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT;
79
80			ALTER TABLE single_model_node
81			MODIFY ssid VARCHAR(5),
82			MODIFY sheet_serial CHAR(1);
83
84			ALTER TABLE single_model_edge
85			MODIFY i_ssid VARCHAR(5),
86			MODIFY i_sheet_serial CHAR(1),
87			MODIFY j_ssid VARCHAR(5),
88			MODIFY j_sheet_serial CHAR(1);
89			ENDSQL1
90			fi
91
92			if [ "$mode" == "INDEX" ]
93			then
94			$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
95			SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
96			CREATE INDEX NODE_GRAPH_IDX ON single_model_node (graph_id);
97			CREATE INDEX EDGE_GRAPH_IDX ON single_model_edge (graph_id);
98	filippis	413	CREATE INDEX CHAIN_IDX ON pdb_residue_info (pdb_code, chain_code, pdb_chain_code);
99	filippis	409	ENDSQL
100			fi
101
102			if [ "$mode" == "UNINDEX" ]
103			then
104			$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
105			SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
106			DROP INDEX NODE_GRAPH_IDX ON single_model_node;
107			DROP INDEX EDGE_GRAPH_IDX ON single_model_edge;
108			ENDSQL
109			fi