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For any general information about the application, application support, or to report a bug, contact Application Support (NCIAppSupport@nih.gov). |
Topics in this document include:
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For more information about the 2.3 updates, refer to the caNanoLab 2.3 Release Notes. (TBD?)
Open Source Technologies
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 the following page:
http://www.mysql.com/downloads/workbench/
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Product | Link | ||||||||
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Java Software Development Kit (JDK) version 8.0 and set JAVA_HOME | http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html
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Wildfly version 8.2.0.Final |
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Jakarta Ant version 1.9.x and set ANT_HOME environment variable | http://archive.apache.org/dist/ant/binaries/
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MySQL version 5.1.x | http://dev.mysql.com/downloads/mysql/5.1.html
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Apache Maven 3.3.x or higher | https://archive.apache.org/dist/maven/maven-3
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Obtaining the caNanoLab Source Code
Downloads for caNanoLab are available at the caNanoLab GitHub Repository:
https://github.com/CBIIT/cananolab/tree/cananolab-2.2-it-11
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The caNanoLab Software License License applies.
Ant Build Properties
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Step 1. Extract caNanoLab
Download the following file:
https://github.com/CBIIT/cananolab/archive/cananolab-2.3.1-it-07.zip
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Extract the above file to Extract the GitHub location to a location on your local system, for example, C:\caNanoLab_2.3. and navigate into the “software” directory to reach the source. (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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Step 1. DB changes to be deployed to migrate to caNanoLab 2.3 from caNanoLab 2.1
a Execute the following
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script:
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Step 2. caNanoLab installation instructions to upgrade to 2.3
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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, the following output appears in the window.
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The migration of access control data has been implemented as a series of ReST 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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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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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
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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
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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
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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
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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 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
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. The Welcome/Login page appears.
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