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Welcome to the caNanoLab 2.1.1 Installation Guide.

Info

title	To Get Support

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	support - include
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For any general information about the application, application support, or to report a bug, contact Application Support.
To Print the Guide
If you want to print a single page, refer to Printing a pagePage.

Topics in this document include:

...

For more information about the 2.1.1 updates, see refer to the caNanoLab 2.1.1 Release Note.

...

Download each of the following tools and follow the installation instructions provided with each respective product for your environment.

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title	MySQL Administrator

...

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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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

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Wildfly version 8.2.0.Final

http://wildfly.org/downloads/

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Jakarta Ant version 1.8.x and set ANT_HOME environment variable

http://archive.apache.org/dist/ant/binaries/

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MySQL version 5.1.x

http://dev.mysql.com/downloads/mysql/5.1.html

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Obtaining the caNanoLab Source Code

Downloads for caNanoLab are available at the caNanoLab GitHub Repository.

The caNanoLab Software License 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.

...

Extract caNanoLab

...

...
Extract the GitHub location to a location on your local system, for example,
...
C:\caNanoLab_2.1.1 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 `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 .

Note

Info

title	Writable Directory

This directory should be writable by the user that starts the Wildfly server, and this directory should be created prior to starting the application.

If working on Windows platform, use

Use either double-back slashes or a single forward slash / as the file separator if working on Windows platform.

admin.email

The email address that receives requests for new user accounts, for example, the

NCICBIIT

NCI CBIIT application support email for the

NCICBIIT

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

`localhost`.
database.port	The database port number, for example,

3306

`3306`.
database.user	The database user name used in the caNanoLab application, for example,

cananolab

`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

`root`.
database.system.password	The password for the system database that the user specified above, for example,

rootpass

rootpass.

jboss.server.dir

The Wildfly server directory, for example:

C:/apps/wildfly-8.2.0.Final/standalone

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Installation and Deployment

...

Step 1. DB changes to be deployed to migrate to CSM 5.2

a Execute the following scripts in the order specified below.

{+}

1. 1. 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

...

1. 1. 1. https://github.com/CBIIT/common-security-module/blob/master/software/common/resources/db/db-upgrade/mysql/MigrationScript5.0MySQL.sql

{+}

1. 1. 1. https://github.com/CBIIT/common-security-module/blob/master/software/common/resources/db/db-upgrade/mysql/MigrationScript5.1MySQL.sql

1. 1. 2. Execute the following script to reset

password

1. 1. 1. passwords for all of the accounts: update csm_user set password = 'zJPWCwDeSgG8j2uyHEABIQ=='; update csm_user set first_time_login = 1;

b Migrate encryption from 4.x CSM database.

CSM 5.0 has introduced using AES encryption to

...

encrpt 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

...

would need to run encryption migration. This step expects

...

PASSWORD column values in CSM_USER are not altered from the their original values created through

...

CSM API.

1. 1. 1. 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.
    2. Extract the contents

of the downloaded csm

1. 1. 1. of the downloaded csm_upgrade5.2.

zip into

1. 1. 1. zip into a designated folder

1. 1. 1. (for example, c:\csm_52\csm_upgrade5.2).
    2. In the designated folder, find and modify

the upgrade

1. 1. 1. the upgrade.

properties file. Update the database properties

1. 1. 1. properties file. Database properties must be updated with the upgraded database connection details.
    2. Open the cmd window and navigate to

1. 1. 1. c:\csm_52\csm_upgrade5.2
    2. Run

1. 1. 1. "ant -Dproperties.file=upgrade.properties migration:run".

Step 2. 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

variable JBOSS_

HOME to

HOME to point to the Wildfly installation directory.

Info

Note

title

If working on the Windows platform, use

Windows Platform

Use either double back slashes // or a single forward slash / as the file separator if working on Windows platform, for example

, JBOSS_HOME=C:/wildfly-8.2.0.Final (C:\wildfly-8.2.0.Final would fail).

Execute the Ant build script build.xml located

at <CANANOLAB

at <CANANOLAB_SOURCE>/

build with

build with the target

deploy:cananolab-webpp .

For example, issue

Example : Issue the following commands to execute the Ant script:

C:\>cd C:\caNanoLab_2.1\build

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

, and also places these artifacts in the appropriate directories

under <JBOSS

under <JBOSS_

HOME>

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

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

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

sever

server, pass in the JVM settings either as command line arguments when executing

the $JBOSS

the $JBOSS_HOME/bin/standalone.

sh script

sh script, or by declaring them

in $JBOSS

in $JBOSS_HOME/bin/standalone.conf.
(For Windows users, the script to execute

is %JBOSS_HOME%/bin/standalone.

bat
…while

bat while the JVM settings can be declared

in%JBOSS

in `%JBOSS_HOME%/bin/standalone.conf.bat`.)
4	1. Create a new directory

structure (

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

Start JBoss application server in Standalone mode.

This script

From <install-dir>/bin:

./standalone.sh --server-config=standalone-full.xml

The cli scripts assumes the CLI port is running at 19990. If it is different, update the port number

at the second line in the script.

For Windows environment:

jboss-cli.bat --file=C:/local/content/caNanoLab/artifacts/caNanoLab_modules.

cli Press

cli and press <ENTER>.

For Linux environment:

jboss-cli.sh --file=

/local/content/caNanoLab/artifacts/caNanoLab_modules.cli

Press

and press <ENTER>.

Run the

remaining caNanoLab

remaining caNanoLab_setup.

cli and caNanoLab

cli and caNanoLab_deploy.

cli that

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 correctly configured,

...

shutdown and restart 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

...

appears.

...

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Key

Obtaining the caNanoLab Source Code

Ant Build Properties

Setting Properties

Step 1.

Extract caNanoLab

Step 2. Edit Ant Properties

Installation and Deployment

Step 1. DB changes to be deployed to migrate to CSM 5.2

a Execute the following scripts in the order specified below.

b Migrate encryption from 4.x CSM database.

Step 2. caNanoLab installation instructions to upgrade to 2.1.1

Verification