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root/owl/tags/aglappe-1.1.2/createGraphDb.sh
Revision: 576
Committed: Tue Apr 1 15:56:06 2008 UTC (11 years, 5 months ago) by filippis
Original Path: trunk/createGraphDb.sh
File size: 3636 byte(s)
Log Message:
RIGraph:Now you can store unweighted graphs in db and also select the db that contains the ids for the single models.
-paramater weighted added to write_graph_to_db and write_graph_to_db_fast methods. If true, it works as before (atomWeight is written to db field weight) else the db field weight gets always value 1. Methods without this parameter still exist and work as before.
-protected field singleModelsDb and corresponding methods getSingleModelsDb and setSingleModelsDb have been added. All constructors set the singleModelsDb field to DEFAULT_SINGLEMODELS_DB which equals to "ioannis". Changes have been also made to write_graph_to_db and write_graph_to_db_fast methods to deal with the singleModelsDb field.

DbRIGraph, testDbRIGraph:Changes have been also made to address the reading of (un)weighted graphs from db.

doClassifySingleModels.sh has been added. You can create your own table with ids for the single models wherever you want.

createGraphDs.sh: mode to drop tables has been 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 503 MODIFY num INT NOT NULL,
99 filippis 409 MODIFY ssid VARCHAR(5),
100     MODIFY sheet_serial CHAR(1);
101    
102     ALTER TABLE single_model_edge
103 filippis 503 MODIFY i_num INT NOT NULL,
104 filippis 409 MODIFY i_ssid VARCHAR(5),
105     MODIFY i_sheet_serial CHAR(1),
106 filippis 503 MODIFY j_num INT NOT NULL,
107 filippis 409 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 $graphDb <<ENDSQL
115     SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
116     CREATE INDEX NODE_GRAPH_IDX ON single_model_node (graph_id);
117     CREATE INDEX EDGE_GRAPH_IDX ON single_model_edge (graph_id);
118 filippis 413 CREATE INDEX CHAIN_IDX ON pdb_residue_info (pdb_code, chain_code, pdb_chain_code);
119 filippis 409 ENDSQL
120     fi
121    
122     if [ "$mode" == "UNINDEX" ]
123     then
124     $mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
125     SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
126     DROP INDEX NODE_GRAPH_IDX ON single_model_node;
127     DROP INDEX EDGE_GRAPH_IDX ON single_model_edge;
128     ENDSQL
129     fi
130 filippis 576
131     if [ "$mode" == "DROP" ]
132     then
133     $mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL
134     SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
135     DROP TABLE chain_graph;
136     DROP TABLE scop_graph;
137     DROP TABLE single_model_graph;
138     DROP TABLE single_model_node;
139     DROP TABLE single_model_edge;
140     DROP TABLE pdb_residue_info;
141     ENDSQL
142     fi

Properties

Name Value
svn:executable *