caIntegrator 1.4 Local Installation Guide

Welcome to the caIntegrator 1.4 Local Installation Guide. Topics in this document include:

Introduction

This caIntegrator v.1.4 Installation Guide provides you with the instructions to install and configure a fresh caIntegrator v.1.4 application. The caIntegrator installation installs and configures a JBoss application server and creates a caIntegrator-specific schema within a pre-existing database on a preinstalled MySQL server.

Directions are given in this document for both Linux and Windows operating systems.

Overview of caIntegrator Installation

The process for installing caIntegrator v.1.4 includes the following tasks described in this document:

1. Downloading and installing required software
2. Setting environment variables
3. Downloading caIntegrator v.1.4 distribution files
4. Installing
   
   1. GUI Installer Method
   2. Command-Line Method
5. Configuring JBoss servers and MySQL server to run as a service
6. Post-Installation Tasks
   
   1. Using UPT to Add caIntegrator Users

caIntegrator v.1.4 Software and Technology Requirements

Operating System

The caIntegrator v.1.4 installation has been tested on Linux Red Hat Enterprise Linux AS 4 64/32-bit (for AMD chipset) and the Windows XP/2003 environments. While the installation may work in other Linux and Windows environments, it has only been tested in these environments.

Required Software---Not Included in caIntegrator

Many of the servers and services that make up caIntegrator are automatically installed as part of this caIntegrator v.1.4 installation. However, prior to the installation, you must download and install the following required tools and recommended versions in the order they are listed in the table. The software name, version, description, and URL hyperlinks (for download) are indicated in the table. Complete the directions for installing each, as directed on the corresponding website.

Java SDK Installation

When you install the Java SDK, you will be prompted to select the installation directory. Record the path, as this directory will be used when you set the environment variables.

Apache Ant Installation

• Unzip the Apache Ant distribution files using a command line unzip tool or a zip utility, such as WinZip.

• After extracting the zip, you must set the environment variables, described in the following section, so that Ant is available in the system PATH.

Apache Ant Environment Variables

Linux

To set the environmental variables in Linux, follow these steps:

1. As the root user, enter the following in the /etc/profile file. A PATH variable should already be created in this file, so be sure to define the JAVA_HOME and ANT_HOME export before the PATH export. Replace <some_path> with the correct path fragment for Java and Ant installations.
   export JAVA_HOME=<some_path>/jdk1.6.0_31
export ANT_HOME=<some_path>/apache-ant-1.8.2 ;
   export PATH=$JAVA_HOME/bin:$ANT_HOME/bin:$PATH
2. Log out and log back in so that the system recognizes your changes.

Verifying the Environment Variables in Linux

To verify that environment variables have been set correctly, follow these steps:

1. From the command line, enter:
   echo $JAVA_HOME
echo $ANT_HOME
   Both of these commands should return the location where you installed these tools.
2. To verify your Java SDK installation, enter java --version from a command prompt. You should see java version "1.6.0_31".
3. To verify your Ant installation, enter: ant --version from a command prompt. You should see: Apache Ant version 1.8.2

Windows

To set the environmental variables in Windows, follow these steps:

1. In Windows, select Control Panel, then select the System application. In the System Properties window, select the Advanced tab.
2. On the Advanced tab, click the Environment Variables button. To add a new system variable, select the New button.
   
   1. In the Variable n ame text box, enter JAVA_HOME .
   2. In the Variable v alue text box, enter the location of your Java installation.
3. Click the New button again.
   
   1. In the Variable name text box, enter ANT_HOME .
   2. In the Variable value text box, enter the location of your Ant installation.
4. Select the PATH system environment variable, and select the Edit button. This opens the Edit System Variable dialog box.
5. In the Variable value text box, prepend the following text in front of the text that already exists in the Variable Value field.
   %JAVA_HOME%\bin;%ANT_HOME%\bin;
6. Click OK.

Verifying the Environment Variables in Windows

To verify the environment variables have been set correctly, follow these steps:

1. From the command line, enter:
   echo %JAVA_HOME% *
   echo %ANT_HOME% *
   Both of these commands should return the location where you installed these tools.
2. To verify your Java SDK installation, enter java --version from a command prompt. You should see java version "1.6.0_31".

3. To verify your Ant installation, enter ant --version

   Other environment variables

   Environment variables for caIntegrator and, optionally, UPT are modified and set in those sections of this document: caIntegrator 1.4 Local Installation Guide and caIntegrator 1.4 Local Installation Guide.

MySQL Installation and Configuration

A MySQL 5.1 server must be downloaded, installed and running in order for the caIntegrator installation to work successfully.

To download and install MySQL, follow the steps outlined on the MySQL website

Working with Properties Files

An important component of command-line installation of either caIntegrator or UPT is configuring properties files. Prior to initiating a command-line installation, property variables must be modified. Note the following points about changing or entering variables.

Paths in Properties Files

The paths in the *.properties files should use forward slashes. For example, you would use application.base.path=C:/apps/caIntegrator-app, not application.base.path=C:\apps\caIntegrator-app. If you use backslashes, you will experience undesirable results.

Spaces in Path Property Values

You should not specify paths with spaces included as property values. In Windows, note that the C:\Documents and Settings{ }<username> path contains spaces and should not be used, or anything similar. If you are using Windows, use a path such as C:/apps/caIntegrator. Spaces are fine for property values which do not represent a path.

More About Property Values

In each *.properties file, any property value marked with uppercase REPLACE_* must be manually updated with the appropriate value.

• In each *.properties file, any property value marked with lowercase replace_* may be optionally updated with the appropriate value.
• If there is reference to a database.system.user for your MySQL server, you can determine which users have full privileges to create and manage other databases, by executing show grants from a MySQL prompt to determine the correct level of privileges.

Downloading and Installing UPT (Optional)

If you wish to manage user accounts for your caIntegrator application, you must install UPT.

Overview of UPT

UPT is used to provision users in the caIntegrator application. Each CBIIT application installs with its own Common Security Module (CSM) schema that has sample/default users and a role/permissions structure. To add additional users you must provision the caIntegrator application in the UPT. Then you can assign users to caIntegrator.

You can download UPT 4.2.3 and installation instructions.

Installing caIntegrator v.1.4 Application and Services

To newly install the caIntegrator v.1.4 application and services, follow the steps in these sections:

• caIntegrator 1.4 Local Installation Guide
• caIntegrator 1.4 Local Installation Guide
  • caIntegrator 1.4 Local Installation Guide
  • caIntegrator 1.4 Local Installation Guide
• caIntegrator 1.4 Local Installation Guide
  • caIntegrator 1.4 Local Installation Guide
• caIntegrator 1.4 Local Installation Guide
  • caIntegrator 1.4 Local Installation Guide

Downloading caIntegrator v.1.4 Files

To download the caIntegrator v.1.4 files, follow this step:

The various installation files for caIntegrator v.1.4 are between 150-200MB in size. All of the files can be downloaded from the caIntegrator distribution folder.

• For a new command-line installer or command-line upgrade installer, download the caintegrator2-install-1.4.zip file (around 165MB).
• For a GUI installer that you can use to do a fresh caIntegrator installation, download the caintegrator2_gui_distribution_1.4.jar-201207171753.jar file (about 190 MB).

Remember the download location, as you will be using this file to run the installation in the steps that follow.

Installing a New caIntegrator v.1.4

You can perform a new installation of caIntegrator v.1.4 using either of these two methods:

• A GUI Installation wizard. Instructions for this method start in the following section.
• A command-line installation. For instructions, see caIntegrator 1.4 Local Installation Guide.

GUI Installer Method of Installation

For detailed information on all of the GUI installer fields, refer to the BDA Properties page.

For performing an installation using the GUI Installer, follow these steps:

1. Open a command prompt in the directory where you downloaded the caintegrator2_gui_distribution_1.4.jar-201207171753.jar. Enter this command to invoke the GUI installer: java --jar caintegrator2_gui_distribution_1.4.jar-201207171753.jar .
2. The Installation Wizard opens to facilitate the installation process. Click Next to proceed through the pages of the wizard, beginning with progressing past the Welcome page.
3. Review the release notes.
4. You must accept the license agreement.
5. Select the Install installation type. For a new installation, select Install.
6. Select Browse to navigate to the directory where you would like to install caIntegrator. The directory then displays in the text box. If the folder does not yet exist, click OK in the dialog box to indicate that you want the folder to be created.
7. Select the type of installation you would like to perform. You can install everything, or just specific components (JBoss or Database only). The remaining sections in this guide assumes you chose to install everything.
8. Continue walking through the pages of the installer. Configure the caIntegrator JBoss server on the next two pages of the installation wizard. The screen shots show example values. The port values which are specified are the defaults and can be used unless you want to reconfigure the values because of values already in use.
   
9. JBoss Installation Options
   
10. JBoss SSL requires that you have requested and retrieved certificates already. If this does not apply to your installation, leave the values as false and continue.
    
11. If your JBoss is externally accessible then fill out the JBoss External Hostname Configuration page. Otherwise, leave it blank and continue.
12. For a standard installation of caIntegrator, do not use SSO.
13. Specify the authentication type that caIntegrator should use. Database is the most likely choice if you aren't sure what to select here.
14. If you selected LDAP in the previous step (authentication type), enter the appropriate configuration information for LDAP: the LDAP URL and the LDAP Search Back DN.
15. If the authentication type is database, specify the following data base configuration information:
    
    • The Database Host Name
    • The Database Port Example: 3306
    • Database name of the pre-existing database where the caIntegrator schema will be installed
    • The pre-existing Database Application User to be used by caIntegrator to connect to its database.
      Error messages inform you if the following occurs:
      • If the specified database host cannot be reached, or the field is blank.
      • If the specified database does not already exist, or the caIntegrator DB user's credentials are wrong.
16. Specify SMTP mail server connection information so that caIntegrator can send emails from users with new account requests. You must provide the following
    • Mail Server Host Example: localhost
    • Mail Server Port Number Example: 25
    • Mail Server Authentication: default is false.
    • Mail Server starttls: default is false.
17. If jar signing is necessary for the installation, then enable it on the Jar Signing Configuration page. This step is optional and can be skipped.
18. Review the summary of the information you entered.
19. Review the selected installation type and the installation destination.
    After you click Next from reviewing the installation destination, the installer runs. The installation wizard displays the installation progress and completion.
20. When you are informed that the process is finished, click Done in the lower right corner of the wizard to close the installer.
21. To verify caIntegrator installation:
    
    1. Open your web browser to installed instance. The URL follows this format: http://<jboss.server.hostname>:<jboss.server.port>/caintegrator/workspace.action.
    2. Enter ncimanager as the user and changeme as the password. Refer to the <user home>/.installer-caintegrator/caintegrator_installer/install.properties file for the correct values.
22. After successfully installing caIntegrator, make a backup of the <user home>/.installer-caintegrator/caintegrator_installer/install.properties file in a different directory for future reference.

Command-Line Method of Installation

About Properties

An important component of command-line installation is configuring properties.

See also caIntegrator 1.4 Local Installation Guide.

Command-line Installation Steps

To install a new instance of caIntegrator using the command-line, follow these steps:

1. From the directory where you downloaded the caintegrator2-install-1.4.zip described in [caIntegrator 1.4 Local Installation Guide, unzip the Files, using one of these two methods:
   
   1. Open a command prompt and use it to extract this file to a temporary location. For example, you may enter a command such as unzip -q caintegrator2-install-1.4.zip . You must have a ZIP tool installed. This location will be referred to as the <installer_directory> henceforth.

   2. Use WinZip or a similar utility to unzip the files to a temporary location. This location will be referred to as the <installer_directory> henceforth.
      Example: <installer directory> = C:\caIntegrator_installer

      About setting property values

      Setting the property values is an important step in the installation process. Before you complete steps 2 & 3, review caIntegrator 1.4 Local Installation Guide.

2. Open the <installer_directory> / install.properties file, modify the values for your environment and save the file. For the latest details about configuring the properties for your environment, refer to the BDA Properties wiki page.

3. Record the property values you have set.

   Other default values

   You should not need to modify the other default values as we have chosen unique ports to reduce the risk of other applications using the same values. However, be sure to verify that the ports in this file are not being used by other applications.

4. From the command line, navigate to <installer_directory>/(Example:cd C:\caIntegrator_2_0_installer), and type ant . This initiates the installation process. The anticipated duration is anywhere from 1-15 minutes, depending on your system's speed, power and memory.
   The installer installs the caIntegrator schema in the specified pre-existing database on your MySQL server, and installs, configures, and starts the JBoss server for the caIntegrator application.
5. To verify caIntegrator installation, open your web browser to the installed instance. The URL follows this format: http://<jboss.server.hostname>:<jboss.server.port>/caintegrator/workspace.action.
   Refer to the <installer_directory>/install.properties file for the correct values. Enter manager as the user and manager as the password.
6. After successfully installing caIntegrator, make a backup of the <installer_directory>/install.properties file in a different directory for future reference.

Upgrading caIntegrator 1.3 to 1.4

This section describes how to upgrade your product from caIntegrator 1.3 to caIntegrator 1.4. The instructions in this section apply only if you have already installed a caIntegrator version 1.3.

You can perform an upgrade installation of caIntegrator v.1.3 using either of these two methods:

• A GUI Installation wizard. Instructions for this method are found in caIntegrator 1.4 Local Installation Guide.
• A command-line installation. Instructions for this method are found in caIntegrator 1.4 Local Installation Guide.

If you are performing a new installation, go directly to caIntegrator 1.4 Local Installation Guide.

caIntegrator 1.3 Users Upgrading to caIntegrator 1.4

The directions in this section presume that you have a valid and functioning caIntegrator 1.3. It also assumes that Java SDK, Apache Ant and MySQL have all been successfully uploaded and installed, as described on pages caIntegrator 1.4 Local Installation Guide.

Overview of Properties Files

When you installed the previous version of caIntegrator 1.3, you configured the install.properties file. To complete the upgrade to caIntegrator 1.4, you must use some of the values from the original install.properties to configure values in the installer wizard GUI.

See steps 3 & 4 in caIntegrator 1.4 Local Installation Guide for more information.

Upgrading caIntegrator Using the GUI Installer

For detailed information on all of the GUI installer fields, refer to the BDA Properties page.

To perform an upgrade to caIntegrator 1.4 using the GUI Installation Wizard, follow these steps:

1. Because of the upgrade from JBOSS4 to JBOSS5 in the caIntegrator 1.4 release, two GUI installer invocations are required. The first will install the new JBOSS5 in the same directory as the existing JBOSS4 and the second will update the database.
2. Open the install.properties file for the existing 1.3 installation located at <user home>/.installer-caintegrator/caintegrator_installer/install.properties and save it as install.properties_v1.3 to your desktop for reference during the upgrade.
3. Open a command prompt in the directory where you downloaded the caintegrator2_gui_distribution_1.4.jar-201207171753.jar and invoke the GUI installer using this: java --jar caintegrator2_gui_distribution_1.4.jar-201207171753.jar.
4. The Installation Wizard opens to facilitate the installation process. Click Next to proceed through the pages of the wizard, beginning with progressing past the Welcome page.
5. Review the release notes.
6. You must accept the license agreement to continue.
7. Select the Install installation type in step #4.
8. Select JBoss in step #6.
9. Configure the JBoss Server-related settings.
10. Specify the authentication type that caIntegrator is using. If you choose LDAP, configure the LDAP information: the LDAP Host Name, the LDAP Search Base, and the LDAP Search Prefix. An example of the Host Name is ldaps://myldaphost.mydomain.com:636.
11. Review the summary of gathered information.
12. Click Next to proceed through the next two pages.
13. After you click Next from reviewing the installation destination, the installer runs. The installation wizard displays the installation progress and completion.
14. When you are informed that the process is finished, click Done in the lower right corner to close the installation wizard.
15. At this point if you open your web browser to the installed instance you will see a MYSQLGrammerException error displayed.
16. Before invoking the GUI installer again, stop the server.
17. Open a command prompt in the directory where you downloaded the caintegrator2_gui_distribution_1.4.jar-201207171753.jar and invoke the GUI installer using this: java --jar caintegrator2_gui_distribution_1.4.jar-201207171753.jar.
18. The Installation Wizard opens to facilitate the installation process. Click Next to proceed through the pages of the wizard, beginning with progressing past the Welcome page.
19. You must accept the license agreement to continue.
20. Select the Upgrade installation type in step #4.
21. Select Everything in step #6.
22. Configure the JBoss Server-related settings.
23. Specify the authentication type that caIntegrator is using. If you choose LDAP, configure the LDAP information: the LDAP Host Name, the LDAP Search Base, and the LDAP Search Prefix. An example of the Host Name is ldaps://myldaphost.mydomain.com:636.
24. Review the summary of gathered information.Review the selected upgrade installation type and the upgrade destination.
25. Click Next to proceed through the next two pages.
26. After you click Next from reviewing the installation destination, the installer runs. The installation wizard displays the installation progress and completion.
27. To verify the caIntegrator installation, open your web browser to the installed instance. The URL follows this format: http://<jboss.server.hostname>:<jboss.server.port>/caintegrator. Example: http://hostname:47210/caintegrator and enter ncimanager as the user and changeme as the password. Refer to the original install.properties for the correct jboss.server.hostname and jboss.server.port values.
28. Once the update is verified you can delete the JBOSS4 directory.

Upgrading caIntegrator Using the Command-Line Installer

To perform an upgrade to caIntegrator 1.4 using the command-line, follow these steps:

1. Because of the upgrade from JBOSS4 to JBOSS5 in the caIntegrator 1.4 release, two ant commands are required. The first will install the new JBOSS5 in the same directory as the existing JBOSS4 and the second will update the database.
2. Open the install.properties file found in the application.base.path directory and save it to your desktop as install.properties.v1.3.1 for reference during the upgrade.
3. Delete the caintegrator2-install-1.3.1.zip file from its directory such as the application.base.path directory.
4. Download caintegrator2-install-1.4.zip to the directory where the previous install zip file was such as the application.base.path directory. From the directory where you downloaded the install zip file, extract the files, using one of these two methods:
   
   1. Open a command prompt and use it to extract this file. For example, you may enter a command such as unzip -q caintegrator2-install-1.4.zip . You must have a ZIP tool installed.
   2. Use WinZip or a similar utility to unzip the files.
5. When asked if you would like to replace the existing files, respond All.
6. Open the install.properties file and replace all REPLACE_VALUE properties with the values in the install.properties.v1.3.1 file. Before doing so, review caIntegrator 1.4 Local Installation Guide.
   For the latest details about configuring the properties for your updated environment, refer to the BDA Properties page.
7. In the DATABASE SETTINGS section of the install.properties file replace database.re-create=true with database.re-create=false. In the DATABASE SETTINGS section of the install.properties file add the property and value exclude.database=true.

8. Save this file to your desktop as install.properties.v1.4step1. Save this file to your desktop a second time, this time as install.properties. Upload the install.properties file to the application.base.path directory.

   Modifying property values

   You shouldn't need to modify the other default values as we have chosen unique ports to reduce the risk of other applications using the same values. However, be sure to check the *.properties file to verify that the ports in this file are not being used by other applications.

9. From the command line, navigate to the directory where you unzipped the installer file and type ant . This is the first of two ant commands. The anticipated duration is anywhere 1-15 minutes depending on your system's speed, power and memory.
10. When the installer detects that a database exists, it warns you to back it up, which you were instructed to do earlier in this process. Press Y to proceed.
11. If you open the application now in a browser window you will see a MYSQLGrammerException error.
12. Stop the server.
13. Open the install.properties file and revert database.re-create=false back to database.re-create=true. Delete the property and value exclude.database=true.
14. Save this file to your desktop as install.properties.v1.4step2. Save this file to your desktop a second time, this time as install.properties. Upload the install.properties file to the application.base.path directory.
15. From the command line, navigate to the directory where you unzipped the installer file and type ant upgrade:database .
16. Restart the server.
17. To verify caIntegrator installation, open your web browser to the installed instance. The URL follows this format: http://<jboss.server.hostname>:<jboss.server.port>/caintegrator /workspace.action. Example: http://hostname:47210/caintegrator/workspace.action and enter ncimanager as the user and changeme as the password. Refer to the original install.properties for the correct jboss.server.hostname and jboss.server.port values.
18. Once the update is verified you can delete the JBOSS4 directory.

Configuring JBoss

To configure JBoss in Windows, follow these steps.

1. Modify the following entry to the JBoss run.bat file which is located at <application_root_directory>/jboss-5.1.0.GA-nci/bin/run.bat. Find the line that begins with set JAVA_OPTS= -Dbda=bda -Dprogram.name=%PROGNAME% -server and modify the "-Xms256m -Xmx512m" to read "-Xms4096m -Xmx4096m" .

   Physical memory

   If 4096m is higher than the physical memory on the machine, then performance could be severely impacted with performance degradation and errors. 4096m of physical memory is recommended.

   Warning

   Be careful when copying and pasting from this installation guide. No spaces must come before and after the columns. A safe way to ensure that the text has no unwanted space and unwanted characters is to copy the text into a blank text editor such as NotePad first. Then you can correct the spacing and copy-paste back into the run.bat file.

2. Restart your JBoss 5.1.0 server for the changes to take effect. The method of doing this may depend on the start/stop/restart scripts you created after the installation. Most commonly, you can execute shutdown.bat and then run.bat under $JBOSS_HOME/bin. Refer to the publicly available JBoss user's guide

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   for more information.

Configuring JBoss Servers and MySQL Server to Run as Services

Running JBoss as a Service

Before starting the caIntegrator JBOSS server, change the default location for user data. User data consists of various files that are saved by caIntegrator during the deployment and querying of studies. The default location for user data should be changed via the Djava.io.tmpdir jvm parameter in the Jboss run.conf file.

Example jvm parameter: -Djava.io.tmpdir=/local/content/caintegrator/jvmtmp

To run JBoss as a service, follow these steps:

Linux

See http://wiki.jboss.org/wiki/Wiki.jsp?page=StartJBossOnBootWithLinux .

Windows

To run an existing JBoss command line installation as a service, follow the directions for creating a user-defined service at http://support.microsoft.com/kb/137890/EN-US/ . You need to have access to the Windows Resource Kit.

Running MySQL as a Service

To run MySQL as a service, follow these steps:

Linux

See http://www.redhat.com/docs/manuals/enterprise/RHEL-AS-2.1-Manual/cluster-manager/s1-service-mysql.html

.

Windows

When installing MySQL server on Windows, choose the option to run MySQL as a Windows service.

Post-Installation Tasks

Using UPT to Administer caIntegrator Users

To add and administer caIntegrator users in the UPT, refer to the caIntegrator User's Guide

Default Users

The following users are provided by default by the caIntegrator installer.

• ncimanager / changeme
• nciinvestigator / changeme
• cai2admin / changeme - This is the UPT user who will have access to provision caIntegrator users.

Contacting Application Support