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Welcome to the caNanoLab 2.1 Installation Guide.
For any general information about the application, application support, or to report a bug, contact Application Support. |
Topics in this document include:
For more information about the 2.1 updates, see the caNanoLab 2.1 Release Note.
caNanoLab application development is best suited for an experienced Java developer who has some familiarity with the following J2EE and related technologies.
Unix/Linux environment, Windows XP environment or Mac OS environment (Configuring environment variables; Installing Ant, JDK, Apache Tomcat and JBoss servers)
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The caNanoLab web application has been tested within NCI CBIIT against Wildfly servers (version 8.2.0) hosted on Windows XP and RedHat Linux systems, and against MySQL 5.1.x databases hosted on RedHat Linux systems and Windows XP systems.
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 http://www.mysql.com/downloads/workbench/
Downloads for caNanoLab are available at caNanoLab GitHub Repository . The caNanoLab Software License applies.
The caNanoLab source distribution caNanoLab_2.1.zip is downloaded, and Ant is installed.
In caNanoLab release 2.1, the Ant build script automatically installs the web application. |
Follow these steps to set the build and deploy properties required for building and deploying caNanoLab.
Extract the caNanoLab_2.1.zip to a location on your local system, for example, C:\caNanoLab_2.1
. This location is referred as <CANANOLAB_SOURCE>
throughout the document. Verify that the following five folders exist in the directory <CANANOLAB_SOURCE>
:
build
cananolab-db
cananolab-grid
cananolab-webapp
common
Edit the Ant properties file, build.properties
, at <CANANOLAB_SOURCE>/build
by specifying values for the following properties.
Property | Description | |
---|---|---|
file.repository.dir | A directory on the system that hosts the Wildfly application server for storing uploaded files, for example,
| |
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,
| |
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, |
superadmin.last.name
and database.server
in Step 2. Edit Ant Properties.If you:
If you have a previously installed caNanoLab running on a Wildfly server, stop the server before running the database scripts. |
If you are installing the caNanoLab application for the first time or want to install a new schema for release 2.1, follow the steps below to set up the required MySQL schema objects and the seed data for release 2.1.
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. |
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:
Tables 72
Example: Issue the following query at the MySQL prompt, logging in as root
:
mysql> select count(*) from information_schema.tables where table_schema='canano' and table_type='BASE TABLE'; |
If you are installing caNanoLab 2.1 for the first time or installing a new caNanoLab release 2.1 schema, you can skip this section. |
This installation guide only discusses the steps for migrating from release 1.5.3, 1.5.4, or 1.5.5. in MySQL to release 2.1 in MySQL. If you have previously installed caNanoLab in MySQL prior to release 1.5.1, you need to migrate to release 1.5.1 first, one release at a time. The 1.5.5 installation guide is available at caNano Lab Release Notes, but previous installation guides are available at the caNanoLab Archive page.
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.
<JBOSS_HOME>
in the document. The Wildfly application server host URL is referred as <APP_SERVER_URL>
, for example, cananolab-dev.nci.nih.gov:19080
.<JBOSS_HOME>/standalone
. The caNanoLab web archive file will be deployed at the directory <JBOSS_HOME>standalone/deployments
.Follow these steps to install and deploy caNanoLab.
Step | Action | |
1 | Set up an environment variable
| |
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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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.
Before a user can log in to the caNanoLab application to submit and search data, you must first create a user account through the UPT web interface. The caNanoLab application makes use of the NCI CBIIT's User Provisioning Tool (UPT), a separate web application, for user account management. The concepts of users, groups, roles, protection groups are defined according the CSM/UPT principles. See the CSM documentation for details on these concepts and the use of the UPT tool.
There are three default user groups:
When a user first logs into caNanoLab, the user is automatically added to the Public group and can see all public data. The user needs to be added to the Researcher or Curator group in order to have access.
Since release 1.5.2, a user must be assigned as a caNanoLab administrator to see the Administration menu in the application to log into the UPT tool or update site preferences, such as the site logo. A user must be assigned as a caNanoLab administrator AND assigned to the Curator group to be able to execute the transfer ownership function. |
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.
Since release 1.5.2, if you are not using LDAP for user authentication, superadmin or caNanoLab administrators maintain the passwords for user accounts. The UPT tool does not allow users to manage their own passwords. |
Send an email to the NCI CBIIT application support group: ncicbiit@mail.nih.gov
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