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Welcome to the caNanoLab 2.1 Installation Guide.
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Edit the Ant properties file, build.properties
, at <CANANOLAB_SOURCE>/build
by specifying values for the following properties.
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,
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admin.email | The email address that receives requests for new user accounts, for example, the NCICBIIT application support email for the NCICBIIT installation. | |||||
ldap.authentication.enabled | A Boolean flag to indicate whether or not to use LDAP for user authentication in caNanoLab, for example,
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ldap.host.url | The URL of the LDAP server used for user authentication. | |||||
ldap.searchable.base | The location in the directory from which the LDAP search begins. | |||||
ldap.userId.label | The buid label for LDAP, for example, | |||||
superadmin.login.name | The LDAP login name for the user account who is the super admin of the UPT tool. See User Provisioning Tool (UPT) for details on setting up UPT. | |||||
superadmin.first.name | The LDAP first name for the user account who is the super admin of the UPT tool. | |||||
superadmin.last.name | The LDAP last name for the user account who is the super admin of the UPT tool. | |||||
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 user specified above, for example, | |||||
database.system.user | The system database user name with privileges to create a database, create tables, grant user accesses to a database, for example, | |||||
database.system.password | The password for the system database user specified above, for example, | |||||
jboss.server.dir | The Wildfly server directory, for example, |
Database Technology
Assumptions and Requirements
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Follow these steps to initialize your MySQL database system.
Step | Action |
1 | Execute the Ant build script Example: Issue the following commands to execute the Ant script:
Successful execution of the Ant script creates the database schema and seed data required the caNanoLab 2.1 release. |
2 | If you are NOT using LDAP for user authentication, you can skip this step. If you are using LDAP for authentication, execute the Ant build script Example: Issue the following commands to execute the Ant script:
Successful execution of the Ant script updates the default UPT super admin with the user name entered in the build properties file. |
Verification
Once the MySQL database is created, either through a new setup or through data migration (described in the next section), verify that the following numbers of database objects are created:
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Follow these steps to complete the required data migration from release 1.5.3, 1.5.4, or 1.5.5. in MySQL to release 2.1 in MySQL.
Step | Action | |||||
1 | Execute the Ant build script Example: Issue the following commands to execute the Ant script:
Successful execution of the Ant script updates the database schema and seed data required the caNanoLab 2.1 release. | |||||
2 | If you are NOT using LDAP for user authentication, you can skip this step. If you are using LDAP for authentication, execute the Ant build script Example: Issue the following commands to execute the Ant script:
Successful execution of the Ant script updates the default UPT super admin with the user name entered in the build properties file. | |||||
3 | If you are NOT using LDAP for user authentication, you can skip this step. If you are using LDAP for authentication, and you already have user accounts in the system and you have data created by these users whose login names are not their LDAP login IDs, you need to perform the following update:
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After data migration, refer to the Verification section to verify that the migration is successful.
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Follow these steps to install and deploy caNanoLab.
Step | Action | |||||
1 | Set up an environment variable
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2 | Execute the Ant build script build.xml located at 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
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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
This configuration file is read when Wildfly server starts. | |||||
4 |
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5. | Start JBoss application server in Standalone mode. This script assumes the CLI port is running at 19990. If it is different, you need to update port number at the second line in the script.
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Verification
Once the deployment artifacts are deployed and the Wildfly application server is correctly configured, you can start the Wildfly application server, which in turn starts the caNanoLab application.
Open the URL http://<APP_SERVER_URL>/caNanoLab/
, for example, http://localhost:8080/caNanoLab
. The Welcome/Login page displays.
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The following steps illustrate an example use of the UPT tool to create a new user, assign the user to be a caNanoLab administrator, and assign the user to the Curator group.
Step | Action | |||||
1 |
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2 | If you are using LDAP for user authentication, skip this step. If you are not using LDAP for authentication, follow this step to reset the password for superadmin:
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3 | Log in as the super admin, and follow these steps to create a new user and assign the user to be a caNanoLab administrator:
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4 | Before the newly-created user can log into the UPT application, logged in as the super admin, follow these steps to update the required database connection information for the csmupt and caNanoLab applications under the Application tab:
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5 | Log out of the UPT tool and log back in as admin. Use caNanoLab as the application name when prompted at the UPT log in. | |||||
6 |
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Follow similar steps to create other application user accounts as appropriate.
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Send an email to the NCI CBIIT application support group: ncicbiit@mail.nih.gov
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