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Print the Guide If you want to print a single page, refer to Printing a Page. |
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For more information about the 2.2 updates, see refer to the caNanoLab 2.2 Release Notes.
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Download each of the following tools and follow the installation instructions provided with each respective product for your environment. Assistance from a MySQL database administrator is expected to properly configure the MySQL database. For MySQL database configuration and maintenance, it is also helpful to download the MySQL workbench (suite of GUI tools) at at http://www.mysql.com/downloads/workbench/
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Follow these steps to set the build and deploy properties required for building and deploying caNanoLab.
Step 1. Extract caNanoLab
Extract the GitHub location to a location on your local system, for example, C:\caNanoLab_2.2
(This location is referred as <CANANOLAB_SOURCE> throughout the document). Verify that the following five folders exist in the directory <CANANOLAB_SOURCE>:
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file.repository.dir | A directory on the system that hosts the Wildfly application server for storing uploaded files, for example,
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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, for example, | |||||
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 | |||||
database.server | The name of the server hosting the database, for example, | |||||
database.port | The database port number, for example, | |||||
database.user | The database user name used in the caNanoLab application, for example, | |||||
database.password | The password for the database that the user specified above, for example, | |||||
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, | |||||
database.system.password | The password for the system database that the user specified above, for example, | |||||
jboss.server.dir | The Wildfly server directory, for example:
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Installation and Deployment
Step 1. DB changes to be deployed to migrate to caNanoLab 2.2 from caNanoLab 2.1
a a Execute the following scripts in the order specified below:
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Step 2. caNanoLab installation instructions to upgrade to 2.2
a Follow Follow these steps to deploy the caNanoLab application.
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1 | Set up an environment variable JBOSS_HOME to point to the Wildfly installation directory.
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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:
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>:
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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:
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 | |||||
4 | Create a new directory structure
Create a new directory structure
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5 | Start JBoss application server in Standalone mode. From
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:
For Linux environment:
Run the remaining After successful completion, | you should see the following output appears in the window.
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b Migrate Migrate access control data from CSM 5.2 to Spring Security.
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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 |
2 | 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 |
3 | 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 |
4 | 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 |
5 | 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 |
6 | 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 Restart the application server after the above step to migrate data is completed.
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Open the URL, http://<APP_SERVER_URL>/caNanoLab/
, for example, http://localhost:8080/caNanoLab . The Welcome/Login page displays.
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