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Comment: Revised based on reply from Tracy.

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For more information about the 2.4 updates, refer to the caNanoLab 2.4 Release Note - 2021-06-24.  

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Open Source Technologies

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Downloads for caNanoLab are available at the caNanoLab GitHub Repository:(TBD: Need 2.4 info.)

https://github.com/CBIIT/cananolab/tree/cananolab-2.2-it-11releases

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Download the following file:

(TBD: Need 2.4 info.)

https://github.com/CBIIT/cananolab/archive/cananolab-refs/tags/2.34.10-it-07qa6.zip

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Installation and Deployment

(TBD: Need 2.4 info.)

Step 1.

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To migrate from caNanoLab 2.3

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to caNanoLab 2.

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a   Execute the following script:

https://github.com/CBIIT/cananolab/blob/cananolab-2.3-it-114.0-qa6/software/cananolab-webapp/db-scripts/2.3/caNanoLab224.0/db_update_2.4.0.sql

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Action

1

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

Info
titleWindows 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).

2

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_2.3\software\cananolab-webapp
C:\caNanoLab_2.3\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-1.4769.jar 
target/dist/common/caNanoLab_modules.cli 
target/dist/common/caNanoLab_setup.cli 
target/dist/common/caNanoLab_deploy.cli

target/dist/common/wikihelp.properties

3

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.)

4

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

  • caNanoLab.war
  • bcprov-jdk15on-1.4769.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
5

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, the following output appears in the window.

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

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The migration of access control data has been implemented as a series of REST services. These services must be invoked in the following order for all access data to be migrated from CSM to Spring Security.

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Action

1

Migrates all user accounts and grants them all the default Public role and Curator role to curators in CSM.

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

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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

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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

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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

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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

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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
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c  Restart the application server after the above step to migrate data is completed.

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