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Property

Description

file.repository.dir

A directory on the system that hosts the Wildfly application server for storing uploaded files, for example, C:/apps/caNanoLab. Note

Info

title	Writable Directory

This directory should be writable by the user that starts the Wildfly server and created prior to starting the application. If working on Windows platform, use either double-back slashes or a single forward slash / as the file separator.

admin.email

The email address that receives requests for new user accounts, for example, the NCI CBIIT application support email for the NCI CBIIT installation.

ldap.authentication.enabled

A Boolean flag to indicate whether or not to use LDAP for user authentication. caNanoLab 2.1.1 and beyond does not support LDAP authentication. Set this to false.

database.server

The name of the server hosting the database, for example, localhost.

database.port

The database port number, for example, 3306.

database.user

The database user name used in the caNanoLab application, for example, cananolab_app.

database.password

The password for the database that the user specified above, for example, go!234.

database.system.user

The system database user name with privileges to create a database, create tables, and grant user accesses to a database, for example, root.

database.system.password

The password for the system database that the user specified above, for example, rootpass.

jboss.server.dir

The Wildfly server directory, for example:

C:/apps/wildfly-8.2.0.Final/standalone

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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). Be sure to note 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.

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Action

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

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 <CANANOLABat <CANANOLAB_SOURCE>/build with build with the target, deploy 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 <JBOSSunder <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 <JBOSSfile <JBOSS_HOME>/bin/standalone.conf with conf with the following JAVAfollowing 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 $JBOSSthe $JBOSS_HOME/bin/standalone.sh scriptsh script, or by declaring them in $JBOSSin $JBOSS_HOME/bin/standalone.conf.
For Windows users, the script to execute is %JBOSS_HOME%/bin/standalone.bat
…while 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.

For Windows environment:

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

For Linux environment:

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

Run the remaining caNanoLabremaining caNanoLab_setup.cli and caNanoLabcli and caNanoLab_deploy.cli that 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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Once the deployment artifacts are deployed and the Wildfly application server is configured correctly configured, you can start the Wildfly application server, which in turn starts the caNanoLab application.

Open the URL, http://<APP_SERVER_URL>/caNanoLab/, for example:

http://localhost:8080/caNanoLab

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