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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 | |||||||||
Jakarta Ant version 1.8.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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Extract the GitHub location to a location on your local system, for example, C 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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Property | Description | |||||
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file.repository.dir | A directory on the system that hosts the Wildfly application server for storing uploaded files, for example, C
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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. | |||||
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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a Execute the following scripts in the order specified below:
b Migrate access control data from CSM 5.2 to Spring Security.
The migration of access control data has been implemented as a series of ReST services. These services have to must be invoked in the followed following order for all access data to be migrated from CSM to Spring Security.1.
- Migrates all user accounts and grants them all the default Public role and Curator role to curators in CSM.
https://cananolab.nci.nih.gov/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.
https://cananolab.nci.nih.gov/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.
https://cananolab.nci.nih.gov/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.
https://cananolab.nci.nih.gov/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.
https://cananolab.nci.nih.gov/caNanoLab/rest/datamigration/migratecharaccess
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- Migrates all organizations to ACL tables and grant public access. Also,
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- sets up inheritance of access for POCs of organizations.
https://cananolab.nci.nih.gov/caNanoLab/rest/datamigration/migratesamplesourceaccess
Step 2. caNanoLab installation instructions to upgrade to 2.2
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# | Action | |||||
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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>/build with the target deploy:cananolab-webpp. 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 Cstructure
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 following output in the window.
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Open the URL, http://<APP_SERVER_URL>/caNanoLab/
, for example, http://localhost:8080/caNanoLab . The Welcome/Login page displays.