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caNanoLab application development is best suited for an experienced Java developer who has some familiarity with the following J2EE and related technologies:.
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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. |
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 http://www.mysql.com/downloads/workbench/
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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,
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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 uid 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, |
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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. |
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mysql> select count(*) from information_schema.tables where table_schema='canano' and table_type='BASE TABLE'; |
Data Migration
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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. |
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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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- Ant is installed, and the Ant build properties are set up.
- The database is installed and verified.
- The Wildfly application server is installed on a system (local or remote) and can be started at a designated port. Wildfly install directory is referred to as
<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
. - The default configuration is used for deploying caNanoLab web archive files.
For example, in wildfly-8.2.0.Final, the default configuration is located at the directory<JBOSS_HOME>/standalone
. The caNanoLab web archive file will be deployed at the directory<JBOSS_HOME>standalone/deployments
. - It is possible to configure Apache server to interface with the Wildfly server and set up a virtual host for the caNanoLab application. If you need assistance, please contact NCI CBIIT Application Support.
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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. | |||||
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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 now 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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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.
Since release 1.5.2, as a part of the database seed data, two There are three default user groups are created: Public and Curator. The group Public
- Group Public is assigned role R (read-only) public protocols, samples and publications.
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- Group Researcher is assigned
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- Role R (read-only) for all protocols, samples, and publications in the system.
- Group Curator is assigned role CURD (create, update, read and delete) to all protocols, samples and publications in the system.
When a user first logs into caNanoLab, the user is automatically added to the Public group and can can see all public data. The user needs to be added to the Researcher or Curator group in the UPT tool in order to have Curator access.
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Since release 1.5.2, a user must be assigned as a caNanoLab administrator to see the ADMINISTRATION 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. |
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UPT Example
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 | Launch the UPT tool at http://<APP_SERVER_URL>/upt52/Home.action and login as the super admin. If you are NOT using LDAP for user authentication, the default user account/password for super admin is superadmin/superadmin. Enter csmupt as the application name when prompted at the UPT log in. If you are using LDAP for user authentication, use the LDAP login name and password of the user assigned as the super admin as specified in the Ant build properties file.
NOTE: The NoteThe user superadmin with initial the password superadmin was created as a part of the database setup. Only a superadmin user can assign users to be caNanoLab administrators. | |||||||
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 it 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:
Repeat the steps to update the database connection information for the caNanoLab application. | |||||||
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 | Select User > Select an Existing User, and click Search. Select admin from the User list. Click ViewDetails, then AssociatedGroups. Select Curator from the pre-defined group list and assign it to the user. Click UpdateAssociations to commit the change. |
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Follow similar steps to create other application user accounts as appropriate.NOTES:
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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. |
Publicly-available data can be browsed through Browse caNanoLab links on the home page without logins.
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