Welcome to the caNanoLab 2.1.1 Installation Guide.
To Get Support
For any general information about the application, application support, or to report a bug, contact Application Support.
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Topics in this document include:
Introduction to caNanoLab
For more information about the 2.1.1 updates, see the caNanoLab 2.1.1 Release Note.
Open Source Technologies
Download each of the following tools and follow the installation instructions provided with each respective product for your environment.
MySQL Administrator
Contact a MySQL database administrator for proper configuration the MySQL database. For MySQL database configuration and maintenance, we suggest downloading the MySQL workbench (Suite of GUI tools) .
Product | Link |
---|---|
Java Software Development Kit (JDK) version 7.0 and set JAVA_HOME | http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html |
Wildfly version 8.2.0.Final | |
Jakarta Ant version 1.8.x and set ANT_HOME environment variable | |
MySQL version 5.1.x |
Obtaining the caNanoLab Source Code
Downloads for caNanoLab are available at the caNanoLab GitHub Repository.
The caNanoLab Software License applies.
Ant Build Properties
Setting Properties
Follow these steps to set the build and deploy properties required for building and deploying caNanoLab.
Step 1. Download caNanoLab from GitHub
Download caNanoLab from the GitHub location to a location on your local system, for example, C:\caNanoLab_2.1. This location is referred to as <CANANOLAB_SOURCE> throughout the document. Verify that the following five folders exist in the directory <CANANOLAB_SOURCE>\software:
- 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.
Property | Description |
---|---|
file.repository.dir | A directory on the system that hosts the Wildfly application server for storing uploaded files, for example, C:/apps/caNanoLab. |
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. caNanoLab 2.1 and beyond does not support LDAP authentication. Set this to false. |
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 that the user specified above, for example, go!234. |
database.system.user | The system database user name with privileges to create a database, create tables, and grant user accesses to a database, for example, root. |
database.system.password | The password for the system database that the user specified above, for example, rootpass. |
jboss.server.dir | The Wildfly server directory, for example: |
Installation and Deployment
Deploy database changes for migration to CSM 5.2
- Execute the following scripts in the order specified below.
- Create the following table:
- Execute the following scripts in the order specified below.
CREATE TABLE favorite_data (
favorite_data_id bigint(20) DEFAULT NULL,
data_id bigint(20) DEFAULT NULL,
data_type varchar(200) DEFAULT NULL,
data_name varchar(200) DEFAULT NULL,
login_name varchar(200) DEFAULT NULL,
protocol_file_id bigint(20) DEFAULT NULL,
pubmed_id bigint(20) DEFAULT NULL,
editable tinyint(1) DEFAULT '0',
description text,
protocol_file_title varchar(200) DEFAULT NULL
);
- {+}https://github.com/CBIIT/common-security-module/blob/master/software/common/resources/db/db-upgrade/mysql/MigrationScript5.0MySQL.sql+
- {+}https://github.com/CBIIT/common-security-module/blob/master/software/common/resources/db/db-upgrade/mysql/MigrationScript5.1MySQL.sql+
- Execute the following script to reset password for all the accounts:
update csm_user set password = 'zJPWCwDeSgG8j2uyHEABIQ==';
update csm_user set first_time_login = 1;
- Migrate encryption from 4.x CSM database
CSM 5.0 has introduced using AES encryption to encrypt CSM User information while storing it in CSM_USER table. If you are upgrading CSM from 4.x to 5.x, apart from migrating the database, you will need to run encryption migration. This step expects that the PASSWORD column values in CSM_USER are not altered from the original values created through the CSM API.
- Download the CSM UPT v5.2 distribution file into a designated folder (for example, c:\csm_52). Be sure to note the folder name and location.
- Extract the contents of the downloaded csm_upgrade5.2.zip into a designated folder, for example, c:\csm_52\csm_upgrade5.2
- In the designated folder, find and modify the upgrade.properties file. Update the database properties with the upgraded database connection details.
- Open the cmd window and navigate to:
c:\csm_52\csm_upgrade5.2
- Run:
ant -Dproperties.file=upgrade.properties migration:run.
caNanoLab installation instructions to upgrade to 2.1.1
Follow these steps to install and deploy caNanoLab.
# | Action |
---|---|
1 | Set up an environment variable JBOSS_HOME to point to the Wildfly installation directory. |
2 | Execute the Ant build script build.xml located at <CANANOLAB_SOURCE>/build with the target, deploy:cananolab-webpp. |
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 <JBOSS_HOME>/bin/standalone.conf with the following JAVA_OPTS: |
4 |
|
5 | Start JBoss application server in Standalone mode. This script assumes the CLI port is running at 19990. If it is different, update the port number in the second line in the script.
|
Verification
Once the deployment artifacts are deployed and the Wildfly application server is correctly configured, you can 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.