Download 3.1.2 DB Properties

GTC Technical Instructions
Version 1.0
GTC Technical Instructions
Table of Contents
1 Scope ....................................................................................................................................... 3
2 Database Setup ........................................................................................................................ 3
3 GTC Web Application ............................................................................................................... 3
3.1
Managing property files ....................................................................................................... 3
3.1.1
ANT build properties ........................................................................................................ 3
3.1.2
DB Properties .................................................................................................................. 3
3.1.3
Junit Properties ................................................................................................................ 3
3.2
Integration, Assembly and Deployment ............................................................................... 4
3.3
Elaboration of shell script execution .................................................................................... 4
4 Data Sync Utilities .................................................................................................................... 5
4.1
Managing Property files ....................................................................................................... 5
4.1.1
DB Properties .................................................................................................................. 5
4.2
SVN Folder Structure – Data Sync Utilities ......................................................................... 5
4.3
Integration, Assembly and Deployment ............................................................................... 6
4.4
Elaboration of shell script execution .................................................................................... 6
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1 Scope
Scope of this document is limited to technical instructions on integration, assembly and
deployment of GTC web application (Beta) and data sync utilities.
2 Database Setup
Please download all SQL script for database setup from following URL.
http://gaggle.systemsbiology.net/svn/gaggle/GTC/trunk/SQL
Please execute following downloaded SQL script on MySQL server if required databases are not
exits.
1)
2)
3)
4)
gtcmain.sql
kegggenomicdatabaseDDL.sql
ncbigenomicdatabaseDDL.sql
stringdatabaseDDL.sql
*STRING: Please load flat file using following command
LOAD DATA INFILE '<your_system_path>\protein.links.detailed.v8.0.txt' INTO TABLE proteinlinkdata FIELDS
TERMINATED BY '\t' LINES TERMINATED BY '\n' IGNORE 1 LINES;
*Please note: “stringdatabaseDDL.sql” file will create database and tables as per application
requirements. Above mentioned load command will load flat file into database. Utilities will run on
flat file database and populate gtc string database.
*BioNET: Reload data dump.
3 GTC Web Application
3.1 Managing property files
3.1.1
ANT build properties
Please specify tomcat home directory path, do not include “webapps” folder.
3.1.2
DB Properties
Location of file: <your system path>\BetaGTCWebApp\ JavaSource\ org\
systemsbiology\ gtc\ properties\db.properties.
Please specify MySQL server name, port number, user id, password, master
database name.
*Do not to change master database name ‘gtcmain’.
3.1.3
Junit Properties
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Location of file: <your system path>\BetaGTCWebApp\ JUnitTest\ org\
systemsbiology\ gtc\ jUnitProperties

AnnotationBO.properties
Please specify absolute location of “anno.jnlp” file on your system.

CytoscapeBO.properties
Please specify absolute location of “cy2.6.1.jnlp” file on your system.

GenomeBrowserBO.properties
Please specify absolute location of “genomebrowser.jnlp” file on your system.

OrthologyTranslatorBO.properties
Please specify absolute location of “OrthologyTranslator.jnlp” file on your
system.

OrganismDataDAO.properties
Please specify organism id as per organism table of gtcmain database for
'sourceSpeciesName' and 'targetSpeciesName' specified in
OrthologyTranslatorBO.properties

TranslatorBO.properties
Please specify absolute location of “translator.jnlp” file on your system.
3.2 Integration, Assembly and Deployment
1) Synchronize latest code from gaggle svn repository i.e.
“http://gaggle.systemsbiology.net/svn/gaggle/GTC/trunk/BetaGTCWebApp/” with
local mapped svn folder.
2) Implement change requests or enhancements in required files.
3) Check-in all modified files to svn repository.
4) To deploy latest changes login to gtc.systemsbiology.net using putty.
5) Get into /usr/src/gtc/ directory.
6) Execute “GTCWebAppDeploymentScript.sh” to deploy latest code to
http://gtc.systemsbiology.net/ under “/gtc” context.
3.3 Elaboration of shell script execution
Following is brief elaboration “GTCWebAppDeploymentScript.sh” execution.
1) Archiving current deployed application under “/usr/src/gtc/Archives/” folder with
BetaGaggleTool<yymmdd> name.
2) Delete current deployed version of GTC web app.
3) Download latest code from gaggle svn repository using “svn checkout” command.
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4) After successful download, call ant script for code compile, junit test run, WAR
generation and deploying new version of gtc web app into tomcat.
5) After successful execution of ant script restart tomcat.
6) Please use http://gtc.systemsbiology.net/gtc/ URL for review.
4 Data Sync Utilities
4.1 Managing Property files
4.1.1
DB Properties
Please specify MySQL server name/IP, port number, user id and password.
*Please do not change DBName property.
Following is list of properties files for each data sync utility






\ DataUtils\BioNET\Bionet.properties.
\DataUtils\DataCount\DataCount.properties
\DataUtils\GenomeMap\GenomeMap.properties
\DataUtils\KEGG\kegggenomicdatabase.properties
\DataUtils\NCBI\ncbigenomicdatabase.properties
\DataUtils\STRING\STRINGV1.2.properties
*Please note: No need of building JAR for any utility using ANT script after changing
db properties as mentioned above.
4.2 SVN Folder Structure – Data Sync Utilities
Following is svn repo path for all data sync utilities.
http://gaggle.systemsbiology.net/svn/gaggle/GTC/trunk/DataUtils/
# BioNET/
# DataCount/
# GenomeMap/
# KEGG/
# NCBI/
# STRING/
Each data sync utility svn folder is consisting of following items.
1)
2)
3)
4)
Document explaining how to run utility.
SVN folder for latest code for e.g. BioNetUtility/ inside BioNET/
Properties file for database credentials.
Shell script to execute utility in background except for “DataCount”
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5) Log file for progress tracking.
4.3 Integration, Assembly and Deployment
“Bio Net Utility” is used as an example for explaining utility integration and deployment
process. Following steps will remain same for all utilities.
1) Synchronize latest code from gaggle svn repository i.e.
“http://gaggle.systemsbiology.net/svn/gaggle/GTC/trunk/DataUtils/BioNET/BioNetUtilit
y/” with local mapped svn folder.
2) Implement change requests or enhancements in required files.
3) Check-in all modified files to svn repository.
4) To deploy latest changes login to gtc.systemsbiology.net using putty.
5) Get into “/usr/src/gtc/DataSyncUtilities/” directory.
6) Execute “BioNET.sh” to deploy latest code.
4.4 Elaboration of shell script execution
“Bio Net Utility” is used as an example. Following steps will remain same for all utilities.
1) Archiving current deployed utility version under /usr /src /gtc
/DataSyncUtilities/Archives/BioNET” folder with BioNETDataSyncUtility<yymmdd>
name.
2) Deleting current version of utility.
3) Download latest code from gaggle svn repository using “svn checkout” command.
4) After successful download, calling ant script for compiling and jar generation. Copy new
version of jar under “dist/” folder of “/usr /src /gtc /DataSyncUtilities
/BioNET/BioNetUtility/”.
5) To run utility in background, please execute shell script as explained into “BioNET
Extractor Utility.doc”
6) In this it will be “/usr/src/gtc/DataSyncUtilities/BioNET/bionet.sh”.
*Please note: For Integration and deployment to need to use “/usr /src /gtc
/DataSyncUtilities/BioNET.sh” and for running utility in background you need to use “/usr /src
/gtc/DataSyncUtilities/BioNET/bionet.sh”
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