caNanoLab 2.1.1 Installation Guide

Welcome to the caNanoLab 2.1.1 Installation Guide.

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Topics in this document include:

Introduction to caNanoLab

Welcome to the cancer Nanotechnology Laboratory (https://cananolab.cancer.gov). caNanoLab is a data sharing portal that supports the international biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. caNanoLab provides support to annotate nanomaterials with characterizations resulting from physico-chemical, in vitro, and in vivo assays and share characterizations and associated nanotechnology protocols in a secure environment.

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 of 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	http://wildfly.org/downloads/
Jakarta Ant version 1.8.x and set ANT_HOME environment variable	http://archive.apache.org/dist/ant/binaries/
MySQL version 5.1.x	http://dev.mysql.com/downloads/mysql/5.1.html

Obtaining the caNanoLab Source Code

Downloads for caNanoLab are available at the caNanoLab GitHub Repository.

The caNanoLab Software License applies.

Setting the Ant Build Properties

Follow these steps to set the build and deploy properties required for building and deploying caNanoLab 2.1.1.

Step 1. Download caNanoLab from GitHub

Download caNanoLab from the GitHub location to a location on your local system, for example, C:\caNanoLab_2.1.1. 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`. Writable Directory This directory should be writable by the user that starts the Wildfly server and created prior to starting the application. If working on Windows platform, use either double-back slashes or a single forward slash `/` as the file separator.
admin.email	The email address that receives requests for new user accounts, for example, the NCI CBIIT application support email for the NCI CBIIT installation.
ldap.authentication.enabled	A Boolean flag to indicate whether or not to use LDAP for user authentication. caNanoLab 2.1.1 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: `C:/apps/wildfly-8.2.0.Final/standalone`

Installing and Deploying caNanoLab 2.1.1

Follow these steps to build and deploy caNanoLab 2.1.1.

Step 1. Deploy Database Changes for Migrating to CSM 5.2

Execute the following scripts in the order specified below.
1. Create the following table:
  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
2. https://github.com/CBIIT/common-security-module/blob/master/software/common/resources/db/db-upgrade/mysql/MigrationScript5.0MySQL.sql
3. https://github.com/CBIIT/common-security-module/blob/master/software/common/resources/db/db-upgrade/mysql/MigrationScript5.1MySQL.sql
4. 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.
1. Download the CSM UPT v5.2 distribution file into a designated folder (for example, c:\csm_52). Note the folder name and location.
2. Extract the contents of the downloaded csm_upgrade5.2.zip into a designated folder, for example, c:\csm_52\csm_upgrade5.2
3. In the designated folder, find and modify the upgrade.properties file. Update the database properties with the upgraded database connection details.
4. Open the cmd window and navigate to c:\csm_52\csm_upgrade5.2.
5. Run ant -Dproperties.file=upgrade.properties migration:run.

Step 2. Upgrade to caNanoLab 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. Windows Platform If working on the Windows platform, use either double back slashes `//` or a single forward slash / as the file separator, for example: `JBOSS_HOME=C:/wildfly-8.2.0.Final (C:\wildfly-8.2.0.Final would fail)`
2	Execute the Ant build script build.xml located at `<CANANOLAB_SOURCE>/build` with the target, `deploy:cananolab-webpp`. For example, issue the following commands to execute the Ant script: `C:\>cd C:\caNanoLab_2.1\build a C:\caNanoLab_2.1\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 Wildfly environment. The Ant script also places these artifacts in the appropriate directories under `<JBOSS_HOME>`. Artifacts generated are also available in the following folder under `<CANANOLAB_SOURCE>`: `target/dist/cananolab- webapp/caNanoLab.war` `target/dist/common/ApplicationSecurityConfig.xml` `target/dist/common/csmupt.csm.new.hibernate.cfg.xml` `target/dist/common/csmupt423.csm.new.hibernate.cfg.xml` `target/dist/common/login-config.xml` `target/dist/common/mysql-connector-java-5.1.26.jar` `target/dist/common/upt-ds.xml` `target/dist/common/properties-service.xml` `target/dist/common/upt-ds.xml` `target/dist/common/uptEAR.ear` `target/dist/common/bcprov-jdk15on-1.47.jar` `target/dist/common/caNanoLab_modules.cli` `target/dist/common/caNanoLab_setup.cli` `target/dist/common/caNanoLab_deploy.cli` `target/dist/common/csmapi-5.2.jar`
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`: `JAVA_OPTS="-Xms512m -Xmx2048m -XX:PermSize=128m` `-XX:MaxPermSize=256m -Dsun.rmi.dgc.client.gcInterval=3600000` `-Dsun.rmi.dgc.server.gcInterval=3600000"` This configuration file is read when the Wildfly server starts. For a standalone server, pass the JVM settings either as command line arguments when executing the `$JBOSS_HOME/bin/standalone.sh` script, or by declaring them in `$JBOSS_HOME/bin/standalone.conf`. For Windows users, the script to execute is `%JBOSS_HOME%/bin/standalone.bat` while the JVM settings can be declared `in%JBOSS_HOME%/bin/standalone.conf.bat`
4	Create a new directory structure (`C:/local/content/caNanoLab/artifacts`) and move the following artifacts: `csmapi-5.2.jar` `caNanoLab.war` `uptEAR.ear` `bcprov-jdk15on-1.47.jar` `mysql-connector-java-5.1.26.jar` `caNanoLab_modules.cli` `caNanoLab_setup.cli` `caNanoLab_deploy.cli` Create a new directory structure (`C:/local/content/caNanoLab/config`) and move the following artifacts: `ApplicationSecurityConfig.xml` `csmupt.csm.new.hibernate.cfg.xml` `wikihelp.properties`
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. Windows environment: `jboss-cli.bat --file=C:/local/content/caNanoLab/artifacts/caNanoLab_modules.cli` Press <ENTER>. Linux environment: `jboss-cli.sh --file=C:/local/content/caNanoLab/artifacts/caNanoLab_modules.cli` Press <ENTER>. Run the remaining `caNanoLab_setup.cli` and `caNanoLab_deploy.cli` that deploys the caNanoLab and csmUPT. After successful completion, the following output appears in the window. `{"outcome"=> "success"}` `{"outcome"=> "success"}` `{"outcome"=> "success"}` `{"outcome"=> "success"}` `{` `"outcome"=> "success",` `"result"=> undefined` `}`

Verification

Once the deployment artifacts are deployed and the Wildfly application server is configured correctly, 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.

Content

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