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As of release 1.1, the caNanoLab domain model has been caGrid enabled. In other words, a caNanoLab grid data service can be deployed and registered with caGrid production index server, allowing sharing of public nanomaterial information across the caGrid. In release 1.5, the caNanoLab grid service has been updated to use caGrid 1.3. For more information, see {+} https://cabig.nci.nih.gov/workspaces/Architecture/caGrid+.

Targeted Developer

The 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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The following open source technologies power a caNanoLab release 1.5.4 web application:

Open Source Technologies

Java Software Development Kit (JDK) version 6.0: http://www.oracle.com/technetwork/java/javase/downloads/jdk6-downloads-1637591.html Image Added
JBoss version 5.1.0: http://sourceforge.net/projects/jboss/files/JBoss/JBoss-5.1.0.GA/ Image Added
Jakarta Ant version 1.7.x: http://archive.apache.org/dist/ant/binaries/ Image Added
MySQL version 5.1.x: http://dev.mysql.com/downloads/mysql/5.1.html Image Added

Info

title	Note

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.

The caNanoLab web application has been tested within NCICBIIT against JBoss servers (version 5.1.0) hosted on Windows XP and RedHat Linux systems, and against MySQL 5.1.x databases hosted on RedHat Linux systems and Windows XP systems. Prior to release 1.2.1, the caNanoLab web application had been tested against Oracle 9i databases hosted on Sun Solaris systems, and Oracle 10g XE database hosted on Windows XP.
Download each of the tools listed in the bulleted list above 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/ Image Added

Grid Service

Setting up a caNanoLab grid service is optional. It is recommended that you install the grid service only after you successfully install the web application and become familiar with submitting and searching data through the web application.

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Follow these steps to set the build and deploy properties required for building and deploying the caNanoLab system.

Step

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Action

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1.

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Extract caNanoLab

Extract the caNanoLab_1.5.4.zip to a location on your local system, for

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example, C:\caNanoLab_1.5.4. This location is referred as

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<CANANOLAB_SOURCE> throughout the document. Verify that the following five

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folders exist in the directory <CANANOLAB_SOURCE>:

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build

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cananolab-db

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cananolab-grid

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cananolab-webapp

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common

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Step 2. Edit Ant Properties

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

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 double back slashes
or a single forward slash / should be used as the file separator if working on Windows platform.
admin.email: the email address that receives requests for new user accounts, for example, NCICBIIT application support email for the NCICBIIT installation
ldap.authentication.enabled: a Boolean flag for whether or not using LDAP for user authentication in caNanoLab, for example, true

Note: Please note that default value is true. If you are not using LDAP for user
authentication, please set this value to false and leave properties 4) through 9) blank.
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 label for LDAP, for example, cn

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Step

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Action

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superadmin.login.name: the LDAP login name for the user account who is the super admin of the UPT tool. See page 14 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, localhost
database.port: the database port number, for example, 3306
database.user: the database user name used in the caNanoLab application, for example, cananolab_app
database.password: the password for the database user specified above,

for example, go!234
database.system.user: the system database user name that has privileges to create a database, create tables, grant user accesses to a database, for example, root
database.system.password: the password for the system database user

specified above, for example, rootpass
jboss.server.dir: the JBoss server directory, for example,

C:/apps/jboss-5.1.0.GA/server/default

Note: The following properties 17) through 34) are only required if you setting up a grid service. These properties contain metadata about the grid service that are required for the grid index server to visually map the location of a grid service in the caGrid portal, and are useful during grid service auto-discovery. If you are not setting up a caNanoLab grid service, you may leave these properties blank.
application.base.path.linux: a directory on the Linux system that stores the downloaded external software, such as the Globus WS Core binary files, for example, ${user.home}/apps

Note: This property is currently optional for building the web application and
the database, and is only required for building the grid service on a Linux system.
application.base.path.windows: a directory on the Windows system that stores the downloaded external software, such as the Globus WS Core binary files, for example, C:/apps
grid.indexserver: the grid index server from which the caNanoLab grid data services can be automatically discovered, for example, http://cagrid- index.nci.nih.gov:8080/wsrf/services/DefaultIndexService, NCICBIIT's production caGrid index server
grid.service.hostname: virtual host name for the JBoss server hosting the grid service, for example, cananolab.nci.gov
grid.service.port: port number configured for the JBoss server hosting the caNanoLab grid service, for example, 80
grid.service.protocol: protocol configured for the JBoss server hosting the caNanoLab grid service, for example, http
application.owner: owner of the caNanoLab grid service, for example,

NCICBIIT
country: the country in which the caNanoLab grid service is running, for

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Step

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Action

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example, US
1. city: the city at which the caNanoLab grid service is running, for example,
  
  Rockville
2. zipcode: the zip code at which the caNanoLab grid service is running, for example, 20852
3. state: the state at which the caNanoLab grid service is running, for
  
  example, MD
4. street1: the first part of the street at which the caNanoLab grid service is running, for example, 2115 East Jefferson Street
5. street2: the second part of the street at which the caNanoLab grid service is running
6. affiliation: the affiliation of the person who is responsible for maintaining the caNanoLab grid service, for example, NCICBIIT.
7. email: the email of the person who is responsible for maintaining the caNanoLab grid service, for example, NCICBIIT@pop.nih.gov
8. phone: the phone number of the person who is responsible for maintaining the caNanoLab grid service
9. first.name: the first name of the person who is responsible for maintaining the caNanoLab grid service
10. last.name: the last name of the person who is responsible for maintaining the caNanoLab grid service.

Database Technology

Assumptions and Requirements

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Step

Action

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_1.5.4\build C:\caNanoLab_1.5.4\build>ant install:new:cananolab-db

Successful execution of the Ant script creates the database schema and seed data required the caNanoLab 1.5.4 release.

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_1.5.4\build C:\caNanoLab_1.5.3\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 has been created, either through 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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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_1.5.4\build C:\caNanoLab_1.5.4\build>ant update:cananolab-db Successful execution of the Ant script updates the database schema and seed data required the caNanoLab 1.5.4 release.	Step	Action
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_1.5.4\build C:\caNanoLab_1.5.4\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.
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 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 replaced by the real LDAP login name that corresponds to the old login name. The token should be replaced by 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 replaced by the real LDAP login name that corresponds to the old login name. The token should be replaced by the old login name. Note: if the created_by field contains the word "COPY" in it, update it with have a prefix ":", where the token should be replaced by the real LDAP login name that corresponds to the old login name who created the data. If you don't 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 has been successful.

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Ant has been installed. Ant build properties have been set up, as described on pages 3 through 5. The database has been installed and verified, as described on pages 6 through 9. The JBoss application server has been installed on a system (local or remote) and can be started at a designated port. JBoss install directory is referred 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 be deployed at the directory <JBOSS_HOME>server/default/deploy.

It is possible to configure Apache server to interface with the JBoss server and set up a virtual host for the caNanoLab application, if you need assistance, please contact NCICBIIT Application Support (info provided at the end).

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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_1.5.4\build C:\caNanoLab_1.5.4\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>:
Step	Action
<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: 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 and the grid service 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: <!-- ================ --> <!-- Limit categories --> <!-- ================ --> <!-- edited for caNanoLab --> <category name="org.hibernate">
Step	Action
<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 have been 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 Welcome/Login page.

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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. Use csmupt* as the application name when prompted at the UPT log in. If you are using LDAP for user authentication, please use the LDAP login name and password of the user who has been assigned as the super admin as specified in the Ant build properties file on page 5. 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, you can skip this step. If you are not using LDAP for authentication, you can follow this step to reset the password for *superadmin: Select User* > Select an Existing User. Click on Search and select *superadmin* and click on View Details. Update the User Password field and Confirm Password field and click on Update to commit the change.
3	Logged in as the super admin, 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 > Select an Existing Application; click Search. Select caNanoLab from the application list. Click View Details, then Associated Admins. Assign this user to be an administrator for the caNanoLab application. Click Update Association to commit the change. Note: if you using LDAP for user authentication, any user login names created in the UPT tool should 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; 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 org.hibernate.dialect.MySQLDialect Application Database Driver com.mysql.jdbc.Driver Note: Please refer to page 5 for appropriate values for these fields. Values for Application Database Dialect and Application Database Driver should 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 View Details, then Associated Groups. Select Curator from the pre-defined group list and assign it to the user. Click Update Associations to commit the change.

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

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Content

Space Tools

Versions Compared

Old Version 8

New Version 9

Key

Targeted Developer

Open Source Technologies

Grid Service

Step

1.

Extract caNanoLab

Step 2. Edit Ant Properties

Database Technology

Assumptions and Requirements

Verification

Verification