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Info
titleNote

REMOVE? grid reference:    In release 1.5.4, we have upgraded the technology stack for the web application, but the technology stack for the caNanoLab grid service has not been upgraded due to the requirements of caGrid 1.3. If you'd like to install caNanoLab grid service, please refer to the caNanoLab Release 1.5.3 Installation Guide for the required technology stack for installing the caNanoLab grid service.

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The caNanoLab source distribution caNanoLab_2.0.zip has been (NEED TO ADD LINK) is downloaded. Ant has been is installed.

NOTE:  In caNanoLab release 2.0, the Ant build script automatically installs the web application.

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Step 1.  Extract caNanoLab

Extract the caNanoLab_2.0.zip ADD LINK to a location on your local system, for example, C:\caNanoLab_2.0. 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

Step 2. Edit Ant Properties

Edit the Ant properties file, build.properties, at <CANANOLAB_SOURCE>/build by specifying values for the following properties:

  1. file.repository.dir:  A directory on the system that hosts the JBoss application server for storing uploaded files, for example, C:/apps/caNanoLab.
    NOTE: This directory should be writable by the user that starts the JBoss server, and this directory should be created prior to starting the application. Either Use either double-back slashes or a single forward slash / should be used as the file separator if working on Windows platform.
  2. admin.email   The email address that receives requests for new user accounts, for example, the NCICBIIT application support email for the NCICBIIT installation.
  3. ldap.authentication.enabled:   A Boolean flag to indicate whether or not to use LDAP for user authentication in caNanoLab, for example, true.
    NOTE: Please note that the default value is true. If you are not using LDAP for user authentication, set this value to false and leave properties 4) through 9) blank.
  4. ldap.host.url:   The URL of the LDAP server used for user authentication.
  5. ldap.searchable.base:   The location in the directory from which the LDAP search begins.
  6. ldap.userId.label:  The uid label for LDAP, for example, cn.
  7. superadmin.login.name:  The LDAP login name for the user account who is the super admin of the UPT tool. See page 14 User Provisioning Tool (UPT) for details on setting up UPT.
  8. superadmin.first.name:  The LDAP first name for the user account who is the super admin of the UPT tool.
  9. superadmin.last.name : The LDAP last name for the user account who is the super admin of the UPT tool.
  10. database.server:  The name of the server hosting the database, for example, localhost.
  11. database.port:  The database port number, for example, 3306.
  12. database.user: The database user name used in the caNanoLab application, for example, cananolab_app.
  13. database.password: The password for the database user specified above, for example, go!234.
  14. database.system.user:  The system database user name that has with privileges to create a database, create tables, grant user accesses to a database, for example, root.
  15. database.system.password:  The password for the system database user specified above, for example, rootpass.
  16. jboss.server.dir:  The JBoss server directory, for example, C:/apps/jboss-5.1.0.GA/server/default.

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  • The Ant build properties are set as described in section, Step 2. Edit Ant Properties.
  • A MySQL database is set up on a system (local or remote) with a system (or root) account.
  • The system account matches properties 9) and properties 10) in procedure 2 of  Step 2. Edit Ant Properties.

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Step

Action

1

Execute the Ant build script build.xml located at <CANANOLAB_SOURCE>/build with the target install:new:cananolab-db.

Example: Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.0\build C:\caNanoLab_2.0\build>ant install:new:cananolab-db

Successful execution of the Ant script creates the database schema and seed data required the caNanoLab 2.0 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 build.xml located at <CANANOLAB_SOURCE>/build with the target update:cananolab-db:ldap:upt:superadmin

Example: Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.0\build C:\caNanoLab_2.0\build>ant update:cananolab-db:ldap:upt:superadmin

Successful execution of the Ant script updates the default UPT super admin with the user name entered in the build properties file on page 4.

 

Verification

Once the MySQL database icreatesdis 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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Example: Issue the following query at the MySQL prompt, logging in as root:

Code Block
mysql> select count(*) from information_schema.tables where table_schema='canano' and table_type='BASE TABLE';

Data Migration

NOTE:
  If you are installing caNanoLab 2.0 for the first time or installing a new caNanoLab release 2.0 schema, you can skip this section.

This installation guide only discusses the steps for migrating from release 1.5.3 or 1.5.4 or 1.5.5.?? in MySQL to release 2.0 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. Please see the install instructions for each release at  http://gforge.nci.nih.gov/frs/?group_id=69+ for details.The 1.5.5 installation is available at the main caNanoLab wiki page, 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 2.0 in MySQL:

Step

Action

1

Execute the Ant build script build.xml located at <CANANOLAB_SOURCE>/build with the target update:cananolab-db.

Example: Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.0\build C:\caNanoLab_2.0\build>ant update:cananolab-db

Successful execution of the Ant script updates the database schema and seed data required the caNanoLab 2.0 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 build.xml located at <CANANOLAB_SOURCE>/build with the target update:cananolab-db:ldap:upt:superadmin

Example: Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.0\build C:\caNanoLab_2.0\build>ant update:cananolab- db:ldap:upt:superadmin

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 'd need to do perform the following data update:

  • Update the login_name column of the csm_user table with the LDAP login name for each user in the table: 
    Example:     Issue the following query at the MySQL prompt for each user, logging in as root:
    mysql> update csm_user set login_name='' where login_name='';
    ...Where the token should be is replaced by the real LDAP login name that corresponds to the old login name. The token should be replaced by Replace the token with the old login name.

  • Update the created_by column of tables containing the column with the LDAP login name:
    Example:     Issue the following query at the MySQL prompt for each table containing the created_by column, logging in as root:
    mysql> update sample set created_by='' where created_by ='';
    ...Where the token should be is replaced by the real LDAP login name that corresponds to the old login name. The token should be replaced by the Replace the token with old login name.


Note: if the created_by field contains the word "COPY" in it, update it with a prefix : (colon), where the token isreplaced is replaced by the real LDAP login name that corresponds to the old login name who created the data. If you do not know the original login who created the data, use the LDAP login of a curator. If you need assistance on completing the data updates for this step, please contact the caNanoLab technical team.

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Ant is installed, and the Ant build properties areset are set up. The database is installed and verified. The JBoss application server is installed on a system (local or remote) and can be started at a designated port. JBoss install directory is referred to as <JBOSS_HOME> in the document. The JBoss application server host URL is referred as <APP_SERVER_URL>, for example, cananolab-dev.nci.nih.gov:19080.

It is assumed that the default configuration is used for deploying caNanoLab web archive files. For example, in JBoss 5.1.0, the default configuration is located at the directory <JBOSS_HOME>/server/default. The caNanoLab web archive file shall will be deployed at the directory <JBOSS_HOME>server/default/deploy.

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Step

Action

1

Set up an environment variable JBOSS_HOME to point to the JBoss installation directory.

Note: Either double back slashes
or a single forward slash / should be used as the file separator if working on Windows platform, for example, JBOSS_HOME=C:/jboss-5.1.0.GA (C:\jboss-5.1.0.GA would fail).

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:

C:\>cd C:\caNanoLab_2.0\build C:\caNanoLab_2.0\build>ant deploy:cananolab-webapp

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 JBoss environment, and also places these artifacts in the appropriate directories under <JBOSS_HOME>:

Code Block
<CANANOLAB_SOURCE>/target/dist/exploded/cananolab- webapp/caNanoLab.war 
 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/Applica tionSecurityConfig.xml 
 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/csmupt. csm.new.hibernate.cfg.xml 
 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/csmupt4 23.csm.new.hibernate.cfg.xml 
 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/login- config.xml 
 
 <CANANOLAB_SOURCE>/target/dist/exploaded/common/mysql- connector-java-5.0.7.jar 
 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/upt- ds.xml 
 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/propert ies-service.xml 
 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/upt- ds.xml 
 
 <CANANOLAB_SOURCE>/target/dist/exploded/common/uptEAR. ear

3

We recommend increasing the JBoss JVM heap size to 1G bytes and permanent generation (permgen) memory space to 256M bytes by updating the file
<JBOSS_HOME>/bin/run.conf with the following JAVA_OPTS:

Code Block
JAVA_OPTS="-Xms512m -Xmx1024m -XX:PermSize=128m - XX:MaxPermSize=256m -Dsun.rmi.dgc.client.gcInterval=3600000 - Dsun.rmi.dgc.server.gcInterval=3600000"

This configuration file is read when JBoss server starts.

4

When deploying the caNanolab application in a production environment, we also recommend updating the default logging behavior of the JBoss server by turning off the unnecessary loggings thus reducing file system requirements for server log files.

Please locate the file <JBOSS_HOME>/server/default/conf/log4j.xml
and add to the beginning of the section Limit categories the following text:

Code Block
<!-- ================ --> 
 <!-- Limit categories --> 
 <!-- ================ --> 
 
 <!-- edited for caNanoLab --> 
 <category name="org.hibernate">
<priority value="WARN"/> 
 </category> 
 <category name="org.springframework"> 
 <priority value="WARN"/> 
 </category> 
 <category name="org.globus"> 
 <priority value="WARN"/> 
 </category> 
 <category name="gov.nih.nci"> 
 <priority value="ERROR"/> 
 </category> 
 <category name="org.displaytag"> 
 <priority value="ERROR"/> 
 </category> 
 <category name="org.directwebremoting"> 
 <priority value="ERROR"/> 
 </category> 
 <category name="net.sf.ehcache"> 
 <priority value="INFO"/> 
 </category> 
 <category name="com.mchange.v2"> 
 <priority value="INFO"/> 
 </category> 
 <category name="org.jboss"> 
 <priority value="INFO"/> 
 </category> 
 <category name="CSM"> 
 <priority value="ERROR"/> 
 </category> 
 <category name="Authorization"> 
 <priority value="ERROR"/> 
 </category> 
 <!—end of edit for caNanoLab -->

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Once the deployment artifacts are deployed and the JBoss application server is correctly configured, you can now start the JBoss application server, which in turn starts the caNanoLab application.
Open the URL http://<APP_SERVER_URL>/caNanoLab/ ( , for example, http://localhost:8080/caNanoLab). You should see a The Welcome/Login page displays.

User Provisioning Tool (UPT)

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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 NCICBIIT'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 at  http://gforge.nci.nih.gov/frs/?group_id=12+ for details on these concepts and the use of the UPT tool.

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NOTE: Since release 1.5.2, a user must be assigned as a caNanoLab administrator to see the ADMINISTRATION menu item 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 AND assigned to the Curator group to be able to execute the transfer ownership function.

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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 to assign the user to the Curator group.

Step

Action

1

Launch the UPT tool at http://<APP_SERVER_URL>/uptlogin 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 user superadmin with initial password superadmin was created as a part of the database setup. Only superadmin 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:

  • Select User > Select an Existing User.
  • Click on Search and select superadmin, and click on ViewDetails.
  • Update the UserPassword field and ConfirmPassword field, and click .
  • Click on Update to commit the change.

3

Logged Log in as the super admin, and follow these steps to create a new user and assign it to be a caNanoLab administrator:

  • Select User > Create a New User.
  • Create a new user account named admin with an initial password.
  • Select Application>SelectanExistingApplication; , and click Search. Select caNanoLab from the application list.
  • Click ViewDetails, then AssociatedAdmins.
  • Assign this user to be an administrator for the caNanoLab application.
  • Click UpdateAssociation to commit the change.
    Note    : If you are using LDAP for user authentication, any user login names created in the UPT tool must be a valid LDAP log in name.

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:

Select Application > Select an Existing Application, and click Search. Select csmupt from the application list.

Click View Details, then update the following fields:

  • Application Database URL, for example, jdbc://mysql://localhost:3306/canano
  • Application Database User Name, for example, cananolab_app
  • Application Database Password, for example, go!234
  • Application Database Confirm Password, for example, go!234
  • Application Database Dialect, for example, org.hibernate.dialect.MySQLDialect
  • Application Database Driver, for example, com.mysql.jdbc.Driver

Note: Please refer to page 5 Edit Ant Properties for the appropriate values for these fields. Values for Application Database Dialect and Application Database Driver must be exactly entered as shown above.

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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NOTES:  Since release 1.5.2, if you are not using LDAP for user authentication, superadmin or caNanoLab administrators maintains maintain the passwords for user accounts. The UPT tool doesn't 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.

At each new data submission, the user who creates the data and the Curator group are automatically assigned role CURD to the newly-created data.

For more information about how to use the UPT tool for managing user accounts, contact NCICBIIT Application Support at NCICBIIT@pop.nci.at  ncicbiit@mail.nih.gov and request that the caNanoLab technical team give you a demonstration of the UPT tool in the context of the caNanoLab application.

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NCICBIIT Application Support

 http://NCICBIIT.nci.nih.gov/NCICBIIT/support

NCICBIIT@pop.ncincicbiit@mail.nih.govTelephone: 301-451-4384
Toll free: 888-478-4423