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Welcome to the caNanoLab 2.1 Installation Guide.
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To Print the Guide You can create a PDF of the guide. For instructions refer to the tip Printing multiple pages. If you want to print a single page, refer to Printing a pagePage. |
Topics in this document include:
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Include Page | Updates 2.0 | Updates 2.0
For more information about the 2.1 updates, refer to the caNanoLab 2.1 Release Note.
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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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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General System Requirements
What is caNanoLab Tested Against?
The following open source technologies power a caNanoLab release 2.0 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
- JBoss version 5.1.0: http://sourceforge.net/projects/jboss/files/JBoss/JBoss-5.1.0.GA/
- Jakarta Ant version 1.7.x: http://archive.apache.org/dist/ant/binaries/
- MySQL version 5.1.x: http://dev.mysql.com/downloads/mysql/5.1.html
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.
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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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- Java Software Development Kit (JDK) version 7.0: http://www.oracle.com/technetwork/java/javase/downloads/jdk6-downloads-1637591.html
Multiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include - Wildfly version 8.2.0: http://sourceforge.net/projects/jboss/files/JBoss/JBoss-5.1.0.GA/
Multiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include - Jakarta Ant version 1.8.x: http://archive.apache.org/dist/ant/binaries/
Multiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include - MySQL version 5.1.x: http://dev
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- mysql/5.1.html
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Obtaining the caNanoLab Source
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Code
Downloads for caNanoLab are available at caNanoLab GitHub Repository . The caNanoLab Software License applies.
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Ant Build Ant Build Properties
Assumptions and Requirements
The caNanoLab source distribution caNanoLab_2.01.zip is downloaded. , and Ant is installed.NOTE:
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In caNanoLab release 2. |
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1, the Ant build script automatically installs the web application. |
Setting Properties
Follow these steps to set the build and deploy properties required for building and deploying the caNanoLab system.
Step 1. Extract caNanoLab
Extract the caNanoLab_2.01.zip to a location on your local system, for example, C:\caNanoLab_2.
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. 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
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Edit the Ant properties file, build.properties
, at <CANANOLAB_SOURCE>/build
by specifying values for the following properties:.
Property | Description |
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file.repository.dir |
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A directory on the system that hosts the |
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Wildfly application server for storing uploaded files, for example, |
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admin.email |
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The email address that receives requests for new user accounts, for example, the NCICBIIT application support email for the NCICBIIT installation. | |
ldap.authentication.enabled |
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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 |
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The URL of the LDAP server used for user authentication. | |
ldap.searchable.base |
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The location in the directory from which the LDAP search begins. | |
ldap.userId.label |
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The |
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buid label for LDAP, for example, |
superadmin.login.name |
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The LDAP login name for the user account who is the super admin of the UPT tool. |
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Refer to User Provisioning Tool (UPT) for details on setting up UPT. |
superadmin.first.name |
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The LDAP first name for the user account who is the super admin of the UPT tool. | |
superadmin.last.name |
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The LDAP last name for the user account who is the super admin of the UPT tool. | |
database.server |
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The name of the server hosting the database, for example, | |
database.port |
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The database port number, for example, | |
database.user |
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The database user name used in the caNanoLab application, for example, | |
database.password |
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The password for the database user specified above, for example, | |
database.system.user |
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The system database user name with privileges to create a database, create tables, grant user accesses to a database, for example, | |
database.system.password |
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The password for the system database user specified above, for example, | |
jboss.server.dir |
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The |
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Wildfly server directory, for example, |
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Database Technology
Assumptions and Requirements
- The Ant build properties are set as described in 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)
superadmin.last.name
anddatabase.server
in Step 2. Edit Ant Properties.
For a Previous Installation
If you installed :
- Installed caNanoLab prior to release 2.
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- 1 against an MySQL database
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OR
Installed release 1.2, release 1.1.1, or release 1.1 against an Oracle database,
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- AND have associated production data in these schemas
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AND would like to continue to use the same data for caNanoLab release 2.
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- 1 in MySQL,
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- Review the following database initialization steps, and then go directly to section, Data Migration.
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If you have a previously installed caNanoLab |
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running on a |
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Wildfly server, stop the server before running the database scripts. |
For a New Installation
If you are installing the caNanoLab application for the first time or want to install a new schema for release 2.01, follow the steps below to set up the required MySQL schema objects and the seed data for release 2.01.
Initializing the MySQL Database
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:
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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:
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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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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. |
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1 for the first time or installing a new caNanoLab release 2. |
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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 MySQL to release 2.0 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 the main caNanoLab wiki page 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 2.0 1 in MySQL:.
Step | Action |
1 | Execute the Ant build script Example: Issue the following commands to execute the Ant script:
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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:
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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.
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Assumptions and Requirements
- Ant is installed, and the Ant build properties are set up.
- The database is installed and verified.
- The
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- Wildfly application server is installed on a system (local or remote) and can be started at a designated port.
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- Wildfly install directory is referred to as
<JBOSS_HOME>
in the document. The
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- Wildfly application server host URL is referred as
<APP_SERVER_URL>
, for example,cananolab-dev.nci.nih.gov:19080
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- The default configuration is used for deploying caNanoLab web archive files.
For example, in
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- wildfly-8.2.0.Final, the default configuration is located at the directory
<JBOSS_HOME>/
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standalone
. The caNanoLab web archive file will be deployed at the directory<JBOSS_
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HOME>standalone/
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deployments
.- It is possible to configure Apache server to interface with the
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- Wildfly server and set up a virtual host for the caNanoLab application. If you need assistance,
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- contact caNanoLab-Support@ISB-CGC.org.
Installation and Deployment
Follow these steps to install and deploy caNanoLab:.
Step | Action |
1 | Set up an environment variable |
Wildfly installation directory.
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2 | Execute the Ant build script build.xml located at Example: Issue the following commands to execute the Ant script:
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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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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:
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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.
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Please locate the file <JBOSS_HOME>/server/default/conf/log4j.xml and add to the beginning of the section Limit categories the following text:
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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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Verification
Once the deployment artifacts are deployed and the JBoss Wildfly application server is correctly configured, you can now start the JBoss 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 displaysappears.
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 NCICBIITNCI 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 Refer to 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:
- Group Public
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- is assigned role R (read-only) public protocols, samples and publications.
- Group Researcher is assigned Role R (read-only)
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- for all protocols, samples, and publications
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- 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 see can view 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.NOTE:
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Since release 1.5.2, a user must be assigned as a caNanoLab administrator to see the |
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Administration menu |
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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. |
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 |
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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. | |||
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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.
- 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
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- caNanoLab-Support@ISB-CGC.org and request that the caNanoLab technical team give you a demonstration of the UPT tool in the context of the caNanoLab application.
Contacting Application Support
NCICBIIT Application Support
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