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title
title

Welcome to the caIntegrator 1.3 Local Installation Guide.

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Section
Info
titleTo Get Support

For any general information about the application, application support, or to report a bug, contact Application Support.

To Print the Guide
You can create a PDF of the guide. For instructions refer to the tip How do I print multiple pages? Exporting Multiple Pages to PDF. If you want to print a single page, refer to How do I print a page? Printing a Page.

Topics in this document include:

Table of Contents
minLevel2

Introduction

This caIntegrator v.1.3 Installation Guide provides you with the instructions to install and configure a fresh caIntegrator v.1.3 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.

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  1. Downloading and installing required software
  2. Setting environment variables
  3. Downloading caIntegrator v.1.3 distribution files
  4. Installing
    1. GUI Installer Method
    2. Command-Line Method
  5. Configuring JBoss servers and MySQLserver to run as a service
  6. Post-Installation Tasks
    1. Using UPT to Add caIntegrator Users

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Required Software Name and Version

Description

Java 2 Platform Standard Edition 6.0 Update 18 (J2SE 6.0). Be sure to download the correct Java SDK for your operating environment. For example, for Linux AMD 64, you would download jdk for Linux, linux-amd64-rpm.bin. For Windows, you might download jdk for Windows,windows-i586-p.exe.

The J2SE Development Kit (JDK) supports creating J2SE applications.

Apache Ant, 1.7.0

Apache Ant is a Java-based build tool.

MySQL, 5.0.45

MySQL is an open-source database software application.

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  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_18
    export ANT_HOME=<some_path>/apache-ant-1.7.0
    export PATH=$JAVA_HOME/bin:$ANT_HOME/bin:$PATH
  2. Log out and log back in so that the system recognizes your changes.

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  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 Ja*va SDK installation, enter java –version from a command prompt. You should see java version "1.6.0_18".
  3. To verify your Ant installation, enter: ant –version from a command prompt. You should see: Apache Ant version 1.7.0 compiled on December 13 2006.
Windows

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

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  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_18".
  3. To verify your Ant installation, enter ant –version

    Info
    titleOther environment variables

    Environment variables for caIntegrator and, optionally, UPT are modified and set in those sections of this document: #Installing a New caIntegrator v.1.3 and #Downloading and Installing UPT (Optional).

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Tip
titleTip

You should consult the following three links to successfully set up secure and well-performing MySQL servers, in preparation for installing caIntegrator:

Tip
titleMore Tips
  • Record the MySQL root username/password chosen during the MySQL installation process, as you will need to use this as your database.system.user/ database.system.password later in the UPT installation process, should you choose to install UPT.
  • Note the MySQL port chosen during the MySQL installation process, as you will need to use this as your database.port later in both the caIntegrator and UPT (if installing UPT) installation processes.

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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.

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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

For instructions on how to install UPT 4.2, refer to the chapter, UPT Installation and Deployment, in the caCORE_CSM_v42_ProgrammersGuide.

Info
titleUPT and CSM

UPT 4.2 is backwards compatible to previous versions of CSM. When you provision the application in UPT 4.2, you will be asked to specify the CSM version caIntegrator is using. You should enter version 4.2 .

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The various installation files for caIntegrator v.1.3 are between 150-250MB in size. All of the files can be downloaded from the caIntegrator distribution folderGForge files archive.

  • For a new command-line installer, download the caIntegrator_install_1_3.zip file (around 175MB).
  • For a command-line upgrade installer, download the caIntegrator_upgrade_1_3.zip file (about 175 MB).
  • For a GUI installer that you can use to do a fresh caIntegrator installation, download the caIntegrator_gui_distribution_1_3.jar file (about 207 MB).

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

Tip
titleServer components in caIntegrator v.1.3

These server components are installed and configured as part of the caIntegrator v.1.3 installation. You do not need to do anything further to download or install these components.

  • JBoss 4.0.5 (hosts the caIntegrator application)

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  1. Open a command prompt in the directory where you downloaded the caIntegrator_gui_distribution_1_3.jar. Enter this command to invoke the GUI installer: java –jar caIntegrator_gui_distribution_1_3.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 do. 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.
    example values, described in textImage Modified
  9. JBoss Installation Options
    example JBoss installation options, described in textImage Modified
  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.
    illustration of process, described in textImage Modified
  11. If your JBoss is externally accessible then fill out the JBoss External Hostname Configuration page. Otherwise, leave it blank and continue.
  12. Specify the authentication type that caIntegrator should use. Database is the most likely choice if you aren't sure what to select here.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. Review the summary of the information you entered.
  18. 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.
  19. When you are informed that the process is finished, click Done in the lower right corner of the wizard to close the installer.
  20. 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.
  21. 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.

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  1. From the directory where you downloaded the caIntegrator_distribution_1_3.zip described in Downloading caIntegrator v.1.3 files, 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 caIntegrator_distribution_1_3.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

      Info
      titleAbout setting property values

      Setting the property values is an important step in the installation process. Before you complete steps 2 & 3, review #Working with Properties Files.

  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.

    Info
    titleOther 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.

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Note
titleBEFORE YOU BEGIN
  • Important: Backup the 1.2 database. You need to create a reliable copy of your entire caIntegrator database.
  • Important: Backup the current installation of caIntegrator and artifacts from the original installation, such as properties files.

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When you installed the previous version of caIntegrator 1.2, you configured the install.properties file. To complete the upgrade to caIntegrator 1.3, you must use some of the values from the original install.properties to configure values in the upgrade installer wizard GUI, or the upgrade.properties file if you are doing a command-line method of upgrade.

See steps 3 & 4 in #Upgrade Using Command Line Installer for more information.

Upgrade Using the GUI Installer

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To perform an upgrade to caIntegrator 1.3 using the GUI Installation Wizard, follow these steps:

  1. Because of the application name change in v.1.3, in the JBOSS home directory, locate the war file containing the previous release of caIntegrator2 and delete it. For example, find this file: JBOSS_HOME/server/default/deploy/caintegrator2.war and delete the file named caintegrator2.war.

    Warning
    titleWatch .war file name

    In this same directory, there may be a different file named caintegrator.war (without the number 2 in the name) which you should not delete.

  2. Open a command prompt in the directory where you downloaded the caIntegrator_gui_distribution_1_3.jar and invoke the GUI installer using this: java –jar caIntegrator_gui_distribution_1_3.jar.
  3. 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.
  4. Review the release notes.
  5. You must accept the license agreement to continue.
  6. Select the Upgrade installation type.
  7. Configure the JBoss Server-related upgrade settings.
    If the path pointing to the caIntegrator installation to be upgraded is incorrect, an error message appears.
  8. 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.
  9. Review the summary of gathered information.
  10. Click Next to proceed through the next two pages. Review the selected upgrade installation type and the upgrade destination.
  11. After you click Next from reviewing the installation destination, the installer runs. The installation wizard displays the installation progress and completion.
  12. When you are informed that the process is finished, click Done in the lower right corner to close the installation wizard.
  13. 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.

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To perform an upgrade to caIntegrator 1.3 using the command-line, follow these steps:

  1. Because of the application name change in v.1.3, in the JBOSS home directory, locate the war file containing the previous release of caIntegrator2 and delete it. For example, find this file: JBOSS_HOME/server/default/deploy/caintegrator2.war and delete the file named caintegrator2.war.

    Warning
    titleWatch .war file name

    In this same directory, there may be a different file named caintegrator.war (without the number 2 in the name) which you should not delete.

  2. From the directory where you downloaded the upgrade zip file, extract 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 caIntegrator_upgrade_1_3.zip . You must have a ZIP tool installed.

      Info
      titleDirectory for unzipped files

      It is recommended that you use a new directory for the unzipped files, rather than the one you used to unzip the installer for the previous version(s) of caIntegrator. This location will be referred to as the <upgrade_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 <upgrade_installer directory> henceforth
      Example: <upgrade_installer directory> = C:\caintegrator2_1_2_upgrade_installer
  3. Edit the default properties in the <upgrade_installer_directory>/upgrade.properties file. Before doing so, review #Working with Properties Files.
    To do so, open both properties files, the one you configured originally when you installed the previous version of caIntegrator. (<install. properties file>)and the <upgrade_installer_directory>/upgrade.properties file.
    For the latest details about configuring the properties for your updated environment, refer to the BDA Properties page.

    Info
    titleNote

    The upgrade.properties file does not have as many attributes, so you will not need to transfer all values you set in the previous installation file.

  4. Record these property values.

    Info
    titleModifying 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.

  5. From the command line, navigate to <upgrade_installer_directory>/ (Example:cd C:\caIntegrator_upgrade_installer), and type ant . This initiates the upgrade process. The anticipated duration is anywhere 1-15 minutes depending on your system's speed, power and memory.
    The installer upgrades your existing caIntegrator database on your MySQL server, and starts your existing JBoss server.
  6. 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.
  7. 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.

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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-4.0.5.GA/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" .

    Info
    titlePhysical 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
    titleWarning

    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 4.0.5 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 for more information.

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Info
titleJBoss & MySQL as services

MySQL and the JBoss server that make up caIntegrator, and the JBoss server optionally installed for UPT, must run continually as services. The instructions in this section cover all of these scenarios. For a caIntegrator deployment, there are at least three servers, and if UPT is installed, four servers:

  • JBoss 4.0.4 for UPT (optional)
  • JBoss 4.0.5 (for caIntegratorapplication)
  • MySQL 5.0.45

Running JBoss as a Service

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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

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Contacting Application Support

NCICB CBIIT Application Support

Application Support http://ncicb.nci.nih.gov/NCICB/support
Telephone: 301 240-451276-4384 5541
Toll free: 888-478-4423

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