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Execute the Ant build script build.xml located at <CANANOLAB_SOURCE>/software/cananolab-webapp/build.xml with the target dist.

Example: Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.2\software\cananolab-webapp
C:\caNanoLab_2.2\software\cananolab-webapp>ant dist 

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, and 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/mysql-connector-java-5.1.26.jar 
target/dist/common/properties-service.xml
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/wikihelp.properties

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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 Wildfly server starts.

For a standalone server, pass in 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.)

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Create a new directory structure C:/local/content/caNanoLab/artifacts and move the following artifacts.

• caNanoLab.war
• 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
• wikihelp.properties

Start JBoss application server in Standalone mode.

From <install-dir>/bin:

./standalone.sh --server-config=standalone-full.xml

The cli scripts assumes the CLI port is running at 19990. If it is different, update the port number at the second line in the script. 

For Windows environment:

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

For Linux environment:

jboss-cli.sh --file= /local/content/caNanoLab/artifacts/caNanoLab_modules.cli and press <ENTER>.

Run the remaining caNanoLab_setup.cli and caNanoLab_deploy.cli that deploys the caNanoLab.

After successful completion, you should see following output in the window.

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

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Migrates all access for samples - RWD access for owner and curator, R access for researcher, RWD and R access for specific users.

http://localhost:8080/caNanoLab/rest/datamigration/migratesampleaccess

Migrates all access for protocols - RWD access for owner and curator, R access for researcher, RWD and R access for specific users.

http://localhost:8080/caNanoLab/rest/datamigration/migrateprotocolaccess

Migrates all access for publications - RWD access for owner and curator, R access for researcher, RWD and R access for specific users.

http://localhost:8080/caNanoLab/rest/datamigration/migratepublicationaccess

Adds all charaterizations to the ACL tables and sets them up with the corresponding sample as parent objects. This sets up the characterizations to inherit the access of their sample.

http://localhost:8080/caNanoLab/rest/datamigration/migratecharaccess

Migrates all organizations to ACL tables and grant public access. Also, sets up inheritance of access for POCs of organizations.

http://localhost:8080/caNanoLab/rest/datamigration/migratesamplesourceaccess