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#!/bin/sh |
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function usage { |
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echo |
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echo "Script to create/link/index a graph database. " |
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echo |
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echo "Usage: $1 -d <db_name> -m <mode>" |
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echo |
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echo "-d <db_name> the graph database name " |
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echo "-m <mode> create/index/unindex tables " |
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echo |
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} |
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|
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# |
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#Set default value for variables |
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# |
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graphDb="" |
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mode="" |
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h="white" |
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|
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while getopts d:m: opt |
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do |
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case "$opt" in |
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d) graphDb="$OPTARG";; |
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m) mode="$OPTARG";; |
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esac |
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done |
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|
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if [ -z "$graphDb" ] || [ -z "$mode" ] |
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then |
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echo "Missing or more arguments" |
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usage $0 |
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exit 1 |
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fi |
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|
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arch=`uname -m` |
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case "$arch" in |
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i686) |
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mysqldir=/project/tla/dist/mysql-i686 |
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;; |
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x86_64) |
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mysqldir=/project/tla/dist/mysql |
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;; |
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*) |
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mysqldir=/project/tla/dist/mysql-i686 |
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;; |
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esac |
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|
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mysqlbin=$mysqldir/bin/mysql |
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master=white |
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db=test |
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|
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if [ "$mode" == "CREATE" ] |
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then |
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$mysqlbin -pnieve -h $h -B -N $db <<ENDSQL |
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SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL"; |
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CREATE DATABASE IF NOT EXISTS ${graphDb} |
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DEFAULT CHARACTER SET latin1 DEFAULT COLLATE latin1_general_cs; |
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ENDSQL |
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$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL1 |
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SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL"; |
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CREATE TABLE chain_graph LIKE abstract.chain_graph; |
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CREATE TABLE single_model_graph LIKE abstract.single_model_graph; |
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CREATE TABLE single_model_node LIKE abstract.single_model_node; |
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CREATE TABLE single_model_edge LIKE abstract.single_model_edge; |
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CREATE TABLE pdb_residue_info LIKE abstract.pdb_residue_info; |
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|
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ALTER TABLE chain_graph |
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MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT, |
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MODIFY pchain_code VARCHAR(2) NOT NULL, |
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MODIFY scops INT, |
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MODIFY caths INT, |
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MODIFY entry_id INT, |
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MODIFY assembly_id INT, |
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MODIFY chain_id INT, |
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MODIFY model_id INT; |
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|
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ALTER TABLE single_model_graph |
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MODIFY graph_id INT UNSIGNED NOT NULL AUTO_INCREMENT; |
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|
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ALTER TABLE single_model_node |
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MODIFY ssid VARCHAR(5), |
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MODIFY sheet_serial CHAR(1); |
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|
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ALTER TABLE single_model_edge |
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MODIFY i_ssid VARCHAR(5), |
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MODIFY i_sheet_serial CHAR(1), |
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MODIFY j_ssid VARCHAR(5), |
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MODIFY j_sheet_serial CHAR(1); |
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ENDSQL1 |
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fi |
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|
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if [ "$mode" == "INDEX" ] |
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then |
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$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL |
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SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL"; |
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CREATE INDEX NODE_GRAPH_IDX ON single_model_node (graph_id); |
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CREATE INDEX EDGE_GRAPH_IDX ON single_model_edge (graph_id); |
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CREATE INDEX CHAIN_IDX ON pdb_residue_info (pdb_code, chain_code, pdb_chain_code); |
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ENDSQL |
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fi |
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|
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if [ "$mode" == "UNINDEX" ] |
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then |
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$mysqlbin -pnieve -h $h -B -N $graphDb <<ENDSQL |
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SET sql_mode = "NO_UNSIGNED_SUBTRACTION,TRADITIONAL"; |
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DROP INDEX NODE_GRAPH_IDX ON single_model_node; |
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DROP INDEX EDGE_GRAPH_IDX ON single_model_edge; |
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ENDSQL |
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fi |
