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Download caNanoLab from the GitHub location to a location on your local system, for example, C C:\caNanoLab_2.1.1. This location is referred to as <CANANOLABas <CANANOLAB_SOURCE> throughout SOURCE> throughout the document. Verify that the following five folders exist in the directory <CANANOLABdirectory <CANANOLAB_SOURCE>\software:

build
cananolab-db
cananolab-grid
cananolab-webapp
common

Step 2. Edit Ant Properties

Edit the Ant properties file, build.properties, at <CANANOLABat <CANANOLAB_SOURCE>/build by build by specifying values for the following properties.

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Execute the following scripts in the order specified below.
1. Create the following table:
  CREATE TABLE favorite_data (
  favorite_data_id bigint(20) DEFAULT NULL,
  data_id bigint(20) DEFAULT NULL,
  data_type varchar(200) DEFAULT NULL,
  data_name varchar(200) DEFAULT NULL,
  login_name varchar(200) DEFAULT NULL,
  protocol_file_id bigint(20) DEFAULT NULL,
  pubmed_id bigint(20) DEFAULT NULL,
  editable tinyint(1) DEFAULT '0',
  description text,
  protocol_file_title varchar(200) DEFAULT NULL
2. https://github.com/CBIIT/common-security-module/blob/master/software/common/resources/db/db-upgrade/mysql/MigrationScript5.0MySQL.sql
3. https://github.com/CBIIT/common-security-module/blob/master/software/common/resources/db/db-upgrade/mysql/MigrationScript5.1MySQL.sql
4. Execute the following script to reset password for all the accounts:
  update csm_user set password = 'zJPWCwDeSgG8j2uyHEABIQ==';
  update csm_user set first_time_login = 1;
Migrate encryption from 4.x CSM database.
CSM 5.0 has introduced using AES encryption to encrypt CSM User information while storing it in CSM_USER table. If you are upgrading CSM from 4.x to 5.x, apart from migrating the database, you will need to run encryption migration. This step expects that the PASSWORD column values in CSM_USER are not altered from the original values created through the CSM API.
1. Download the CSM UPT v5.2 distribution file into a designated folder (for example, c:\csm_52). Note the folder name and location.
2. Extract the contents of the downloaded csm_upgrade5.2.zip into a designated folder, for example, c:\csm_52\csm_upgrade5.2
3. In the designated folder, find and modify the upgrade.properties file. Update the database properties with the upgraded database connection details.
4. Open the cmd window and navigate toc:\csm_52\csm_upgrade5.2 .
5. Runant -Dproperties.file=upgrade.properties migration:run.

`Step 2. Upgrade to caNanoLab 2.1.1`

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Action

Set up an environment variable JBOSSvariable JBOSS_HOME to HOME to point to the Wildfly installation directory.

Info

title	Windows Platform

If working on the Windows platform, use either double back slashes // or a single forward slash / as the file separator, for example:
JBOSS_HOME=C:/wildfly-8.2.0.Final (C:\wildfly-8.2.0.Final would fail)

Execute the Ant build script build.xml located at <CANANOLAB_SOURCE>/build with the target, deploy:cananolab-webpp.

For example, issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.1\build a C:\caNanoLab_2.1\build>ant deploy:cananolab-webapp

Successful execution of the Ant script generates the following artifacts that include two deployable web archive war files, configuration files, and libraries for running the web application in the Wildfly environment. The Ant script also places these artifacts in the appropriate directories under <JBOSS_HOME>. Artifacts generated are also available in the following folder under <CANANOLAB_SOURCE>:

target/dist/cananolab- webapp/caNanoLab.war
target/dist/common/ApplicationSecurityConfig.xml
target/dist/common/csmupt.csm.new.hibernate.cfg.xml
target/dist/common/csmupt423.csm.new.hibernate.cfg.xml
target/dist/common/login-config.xml
target/dist/common/mysql-connector-java-5.1.26.jar
target/dist/common/upt-ds.xml
target/dist/common/properties-service.xml
target/dist/common/upt-ds.xml
target/dist/common/uptEAR.ear
target/dist/common/bcprov-jdk15on-1.47.jar
target/dist/common/caNanoLab_modules.cli
target/dist/common/caNanoLab_setup.cli
target/dist/common/caNanoLab_deploy.cli
target/dist/common/csmapi-5.2.jar

We recommend increasing the JBoss JVM heap size to 2G bytes and permanent generation (permgen) memory space to 256M bytes by updating the file <JBOSS_HOME>/bin/standalone.conf with the following JAVA_OPTS:

JAVA_OPTS="-Xms512m -Xmx2048m -XX:PermSize=128m
-XX:MaxPermSize=256m -Dsun.rmi.dgc.client.gcInterval=3600000
-Dsun.rmi.dgc.server.gcInterval=3600000"

This configuration file is read when the Wildfly server starts.

For a standalone server, pass the JVM settings either as command line arguments when executing the $JBOSS_HOME/bin/standalone.sh script, or by declaring them in $JBOSS_HOME/bin/standalone.conf.
For Windows users, the script to execute is %JBOSS_HOME%/bin/standalone.bat while the JVM settings can be declared
in%JBOSS_HOME%/bin/standalone.conf.bat

Create a new directory structure (C:/local/content/caNanoLab/artifacts) and move the following artifacts:
- csmapi-5.2.jar
- caNanoLab.war
- uptEAR.ear
- bcprov-jdk15on-1.47.jar
- mysql-connector-java-5.1.26.jar
- caNanoLab_modules.cli
- caNanoLab_setup.cli
- caNanoLab_deploy.cli
Create a new directory structure (C:/local/content/caNanoLab/config) and move the following artifacts:
- ApplicationSecurityConfig.xml
- csmupt.csm.new.hibernate.cfg.xml
- wikihelp.properties

Start JBoss application server in Standalone mode. This script assumes the CLI port is running at 19990. If it is different, update the port number in the second line in the script.

Windows environment:

jboss-cli.bat --file=C:/local/content/caNanoLab/artifacts/caNanoLab_modules.cli
Press <ENTER>.

Linux environment:

jboss-cli.sh --file=C:/local/content/caNanoLab/artifacts/caNanoLab_modules.cli
Press <ENTER>.

Run the remaining caNanoLab_setup.cli and caNanoLab_deploy.cli that deploys the caNanoLab and csmUPT. After successful completion, the following output appears in the window.

{"outcome"=> "success"}
{"outcome"=> "success"}
{"outcome"=> "success"}
{"outcome"=> "success"}
{
"outcome"=> "success",
"result"=> undefined
}

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Step 2. Edit Ant Properties

`Step 2. Upgrade to caNanoLab 2.1.1`