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Welcome to the caNanoLab 2.0 Installation Guide.

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Follow these steps to initialize your MySQL database system:

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.

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 2.0 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 need to perform the following 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 is replaced by the real LDAP login name that corresponds to the old login name. 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 is replaced by the real LDAP login name that corresponds to the old login name. 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 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.

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 JBOSS_HOME to point to the JBoss installation directory.

Note: Use either double back slashes // or a single forward slash / 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 -->

Verification

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). 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

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.
  • Click on Update to commit the change.

3

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 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.

 

Follow similar steps to create other application user accounts as appropriate.

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NCICBIIT Application Support

ncicbiit@mail.nih.gov

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