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/drop 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 scop_graph LIKE abstract.scop_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 scop_graph
                MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
                MODIFY pchain_code VARCHAR(2) NOT NULL,
                MODIFY sunid INT UNSIGNED,
                MODIFY sccs VARCHAR(10),
                MODIFY domain_type ENUM('UNKNOWN', 'WHOLECHAIN', 'SINGLEFRAGMENT', 'MULTIFRAGMENT', 'MULTICHAIN'),
                MODIFY num_chain INT,
                MODIFY num_fragment INT,
                MODIFY caths INT,
                MODIFY num_chain_res INT,
                MODIFY chain_scops INT,
                MODIFY entry_id INT,
                MODIFY assembly_id INT,
                MODIFY chain_id VARCHAR(35),
                MODIFY model_id INT;
        
        ALTER TABLE single_model_graph
                MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT;
        
        ALTER TABLE single_model_node
                MODIFY node_id INT AUTO_INCREMENT NOT NULL PRIMARY KEY,
                MODIFY num INT NOT NULL,
                MODIFY ssid VARCHAR(5),
                MODIFY sheet_serial CHAR(1);
                
        ALTER TABLE single_model_edge
                MODIFY i_num INT NOT NULL,
                MODIFY i_ssid VARCHAR(5),
                MODIFY i_sheet_serial CHAR(1),
                MODIFY j_num INT NOT NULL,
                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

if [ "$mode" == "DROP" ]
then
$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
        SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
        DROP TABLE chain_graph; 
        DROP TABLE scop_graph;  
        DROP TABLE single_model_graph;  
        DROP TABLE single_model_node;
        DROP TABLE single_model_edge;
        DROP TABLE pdb_residue_info;    
ENDSQL
fi
Revision:	580
Committed:	Tue Apr 8 10:01:57 2008 UTC (14 years, 4 months ago) by filippis
File size:	3694 byte(s)
Log Message:	createGraphDb: -the node_id in the single_model_node table changed to AUTO_INCREMENT doClassifySingleModels: -the interSS for CR added RIGraph: -write_graph_to_db methods treat the node_id field in the single_model_node table as AUTO_INCREMENT -write_graph_to_motiffile method 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: $1 -d <db_name> -m <mode>"
7			echo
8			echo "-d <db_name> the graph database name "
9	filippis	576	echo "-m <mode> create/index/unindex/drop tables "
10	filippis	409	echo
11			}
12
13			#
14			#Set default value for variables
15			#
16			graphDb=""
17			mode=""
18			h="white"
19
20			while getopts d:m: opt
21			do
22			case "$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	filippis	503	CREATE TABLE scop_graph LIKE abstract.scop_graph;
63	filippis	409	CREATE TABLE single_model_graph LIKE abstract.single_model_graph;
64			CREATE TABLE single_model_node LIKE abstract.single_model_node;
65			CREATE TABLE single_model_edge LIKE abstract.single_model_edge;
66			CREATE TABLE pdb_residue_info LIKE abstract.pdb_residue_info;
67
68			ALTER TABLE chain_graph
69			MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
70	filippis	413	MODIFY pchain_code VARCHAR(2) NOT NULL,
71	filippis	409	MODIFY scops INT,
72			MODIFY caths INT,
73			MODIFY entry_id INT,
74			MODIFY assembly_id INT,
75			MODIFY chain_id INT,
76			MODIFY model_id INT;
77
78	filippis	503	ALTER TABLE scop_graph
79			MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
80			MODIFY pchain_code VARCHAR(2) NOT NULL,
81			MODIFY sunid INT UNSIGNED,
82			MODIFY sccs VARCHAR(10),
83			MODIFY domain_type ENUM('UNKNOWN', 'WHOLECHAIN', 'SINGLEFRAGMENT', 'MULTIFRAGMENT', 'MULTICHAIN'),
84			MODIFY num_chain INT,
85			MODIFY num_fragment INT,
86			MODIFY caths INT,
87			MODIFY num_chain_res INT,
88			MODIFY chain_scops INT,
89			MODIFY entry_id INT,
90			MODIFY assembly_id INT,
91			MODIFY chain_id VARCHAR(35),
92			MODIFY model_id INT;
93
94	filippis	409	ALTER TABLE single_model_graph
95			MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT;
96
97			ALTER TABLE single_model_node
98	filippis	580	MODIFY node_id INT AUTO_INCREMENT NOT NULL PRIMARY KEY,
99	filippis	503	MODIFY num INT NOT NULL,
100	filippis	409	MODIFY ssid VARCHAR(5),
101			MODIFY sheet_serial CHAR(1);
102
103			ALTER TABLE single_model_edge
104	filippis	503	MODIFY i_num INT NOT NULL,
105	filippis	409	MODIFY i_ssid VARCHAR(5),
106			MODIFY i_sheet_serial CHAR(1),
107	filippis	503	MODIFY j_num INT NOT NULL,
108	filippis	409	MODIFY j_ssid VARCHAR(5),
109			MODIFY j_sheet_serial CHAR(1);
110			ENDSQL1
111			fi
112
113			if [ "$mode" == "INDEX" ]
114			then
115			$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
116			SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
117			CREATE INDEX NODE_GRAPH_IDX ON single_model_node (graph_id);
118			CREATE INDEX EDGE_GRAPH_IDX ON single_model_edge (graph_id);
119	filippis	413	CREATE INDEX CHAIN_IDX ON pdb_residue_info (pdb_code, chain_code, pdb_chain_code);
120	filippis	409	ENDSQL
121			fi
122
123			if [ "$mode" == "UNINDEX" ]
124			then
125			$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
126			SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
127			DROP INDEX NODE_GRAPH_IDX ON single_model_node;
128			DROP INDEX EDGE_GRAPH_IDX ON single_model_edge;
129			ENDSQL
130			fi
131	filippis	576
132			if [ "$mode" == "DROP" ]
133			then
134			$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
135			SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
136			DROP TABLE chain_graph;
137			DROP TABLE scop_graph;
138			DROP TABLE single_model_graph;
139			DROP TABLE single_model_node;
140			DROP TABLE single_model_edge;
141			DROP TABLE pdb_residue_info;
142			ENDSQL
143			fi