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 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 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
Revision:	503
Committed:	Tue Jan 8 19:51:39 2008 UTC (14 years, 7 months ago) by filippis
File size:	3310 byte(s)
Log Message:	createGraphDb: -scop_graph table added -!!!!residue serial fields (num, i_num, j_num) are changed to unsigned !!!!ProtStructGraph: -interSSE variable added -getResidueSerial abstract method added -restrictContactsBetweenSs method added !!!!AIGraph: -getResidueSerial method added RIGraph: -!!!!getResidueSerial method added -scop graphs are written to db correctly -interSSE variable taken into account for CR db field DbRIgraph: -changes made so to be able to read from db using a scop id -interSSE and minSeqSep are set now in get_db_graph_info() -!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs. testDbRIGraph added: It reads one graph from a source db based either -on pdbcode, chaincode and graph properties or -on scop id and graph properties or -on a graph id and it writes the graph to a destination db. Pdb: -unused scop regions are now removed in restrictToScopDomain -unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet -!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence CatalSiteSet: - removeCatalSiteRes(int resser) method added CatalyticSite: -remRes(int resser) method added Scop: -remove(ScopRegion e) method added genDbGraph:Comments only added to demonstrate new functionality. -comment added to show how to use restrictContactsBetweenSs -comment added to show how to use restrictToScopDomain -runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results -runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
Line	File contents
1	#!/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 $graphDb <<ENDSQL1
60	SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
61	CREATE TABLE chain_graph LIKE abstract.chain_graph;
62	CREATE TABLE scop_graph LIKE abstract.scop_graph;
63	CREATE TABLE single_model_graph LIKE abstract.single_model_graph;
64	CREATE TABLE single_model_node LIKE abstract.single_model_node;
65	CREATE TABLE single_model_edge LIKE abstract.single_model_edge;
66	CREATE TABLE pdb_residue_info LIKE abstract.pdb_residue_info;
67
68	ALTER TABLE chain_graph
69	MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
70	MODIFY pchain_code VARCHAR(2) NOT NULL,
71	MODIFY scops INT,
72	MODIFY caths INT,
73	MODIFY entry_id INT,
74	MODIFY assembly_id INT,
75	MODIFY chain_id INT,
76	MODIFY model_id INT;
77
78	ALTER TABLE scop_graph
79	MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT,
80	MODIFY pchain_code VARCHAR(2) NOT NULL,
81	MODIFY sunid INT UNSIGNED,
82	MODIFY sccs VARCHAR(10),
83	MODIFY domain_type ENUM('UNKNOWN', 'WHOLECHAIN', 'SINGLEFRAGMENT', 'MULTIFRAGMENT', 'MULTICHAIN'),
84	MODIFY num_chain INT,
85	MODIFY num_fragment INT,
86	MODIFY caths INT,
87	MODIFY num_chain_res INT,
88	MODIFY chain_scops INT,
89	MODIFY entry_id INT,
90	MODIFY assembly_id INT,
91	MODIFY chain_id VARCHAR(35),
92	MODIFY model_id INT;
93
94	ALTER TABLE single_model_graph
95	MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT;
96
97	ALTER TABLE single_model_node
98	MODIFY num INT NOT NULL,
99	MODIFY ssid VARCHAR(5),
100	MODIFY sheet_serial CHAR(1);
101
102	ALTER TABLE single_model_edge
103	MODIFY i_num INT NOT NULL,
104	MODIFY i_ssid VARCHAR(5),
105	MODIFY i_sheet_serial CHAR(1),
106	MODIFY j_num INT NOT NULL,
107	MODIFY j_ssid VARCHAR(5),
108	MODIFY j_sheet_serial CHAR(1);
109	ENDSQL1
110	fi
111
112	if [ "$mode" == "INDEX" ]
113	then
114	$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
115	SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
116	CREATE INDEX NODE_GRAPH_IDX ON single_model_node (graph_id);
117	CREATE INDEX EDGE_GRAPH_IDX ON single_model_edge (graph_id);
118	CREATE INDEX CHAIN_IDX ON pdb_residue_info (pdb_code, chain_code, pdb_chain_code);
119	ENDSQL
120	fi
121
122	if [ "$mode" == "UNINDEX" ]
123	then
124	$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
125	SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
126	DROP INDEX NODE_GRAPH_IDX ON single_model_node;
127	DROP INDEX EDGE_GRAPH_IDX ON single_model_edge;
128	ENDSQL
129	fi