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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, 7 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 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: $1 -d <db_name> -m <mode>"
7 echo
8 echo "-d <db_name> the graph database name "
9 echo "-m <mode> create/index/unindex/drop tables "
10 echo
11 }
12
13 #
14 #Set default value for variables
15 #
16 graphDb=""
17 mode=""
18 h="white"
19
20 while getopts d:m: opt
21 do
22 case "$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 $graphDb <<ENDSQL
125 SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL";
126 DROP INDEX NODE_GRAPH_IDX ON single_model_node;
127 DROP INDEX EDGE_GRAPH_IDX ON single_model_edge;
128 ENDSQL
129 fi
130
131 if [ "$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

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svn:executable *