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root/owl/tags/aglappe-jung-0.1.1/createGraphDb.sh
Revision: 419
Committed: Thu Nov 22 14:09:18 2007 UTC (11 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/createGraphDb.sh
File size: 2653 byte(s)
Log Message:
Re-branching for JUNG2 development
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

Properties

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svn:executable *