Developers Getting Started With i2b2
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<a href="https://community.i2b2.org/wiki/download/attachments/7405617/Appendix%20B%20-%20Install%20Checklist.pdf "><img src="https://community.i2b2.org/wiki/download/attachments/851970/printer.png" alt="Printable version of this worksheet" title="Printable version of this worksheet" align=right></a>



This checklist is designed to assist you in the installation of the i2b2 Server and Clients. It is organized to coincide with the installation chapters. The items appear in the checklist in the order in which they need to occur during the installation.


Info
titleNote

This checklist is not a replacement for the i2b2 Installation Guide. The guide itself contains detailed information, important notes and warnings as well as helpful tips.


Installation Overview


Environment:

Demo / Test / Production / Other   

Version of i2b2:

                                

Domain ID:


Domain Name:


Setup Date:


Setup By:




Installation Order and Resources


Installation Order

Checklist Name

Install Guide Resource

1. System and Software Requirements   

Requirements Checklist

Chapter 2. Requirements

2. Data Installation

Data Checklist

Chapter 3. Data Installation

3. Deploying the server-common

Server-Common Checklist   

Chapter 4. i2b2 Server-Common Install

4. PM Cell Installation

PM Checklist

Chapter 5. Project Management (PM) Cell Install

5. i2b2 Admin Installation

i2b2 Admin Checklist

Chapter 6. i2b2 Administration Module Install

6. i2b2 Web Client Installation

i2b2 Web Client Checklist

Chapter 7. i2b2 Web Client Install

7. i2b2 Workbench Installation

i2b2 Workbench Checklist

Chapter 8. i2b2 Workbench Install

8. ONT Cell Installation

ONT Checklist

Chapter 9. Ontology Management (ONT) Cell Install   

9. CRC Cell Installation

CRC Checklist

Chapter 10. Data Repository (CRC) Cell Install

10. WORK Cell Installation

WORK Checklist

Chapter 11. Workplace (WORK) Cell Install

11. FR Cell Installation

FR Checklist

Chapter 12. File Repository (FR) Cell Install

12. IM Cell Installation

IM Checklist

Chapter 13. Identity Management (IM) Cell Install

13. Setting up i2b2

Initial i2b2 Setup Checklist

Chapter 14. Initial Setup of i2b2 in Admin



Things To Keep In Mind


For the most part the installation of the different i2b2 Core Cells involves steps that are very similar. For instance, they all have a build.properties file where you will need to set the jboss.home and axis2.war.name properties for the cell you will be deploying.


Based on feedback provided by our users, a common area for confusion and errors seems to be around the configuration of the data sources for each cell. Here are some things to keep in mind that will hopefully eliminate or at least minimize any confusion around defining your datasources.

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1. The PM, ONT, CRC, WORK, and IM cells each have a ds.xml file that needs to be updated before deploying the cell. (pm-ds.xml, ont-ds.xml, crc-ds.xml, work-ds.xml, and im-ds.xml)


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2. At least two datasources have to be defined in the ds.xml files for the ONT, CRC, WORK, and IM Cells.


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  • The BootstrapDS datasource points to the DB_LOOKUP tables that are part of the Hivedata tables.
  • The DemoDS datasource points to the tables for the cell you are configuring.


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3. The PM Cell has only one datasource (PMBootsrapDS) defined and it points to the location of the Pmdata tables.


Info
titleNote

Depending on how you have setup your database environment the Pmdata tables may or may not be in the same location as your Hivedata tables.



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4. The <connection-url> for every <datasource> defined in each ds.xml file needs to be updated with information that is specific to your environment.


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  • Update the <connection-url> with the correct JDBC information for your type of database.
  • The address in the URL needs to point to either the location of your hivedata tables (BootstratpDS) or the tables for your cell (DemoDS).


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5. The <driver-class> and <driver> for each <datasource> needs to be defined correctly for the type of database you are connecting to.


Note
titleImportant

Depending on your environment, the default of localhost may not be appropriate for you. Some systems require the I.P. address instead of the alias name.



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6. The <username> and <password> for each <datasource> needs to match the database users you setup during the data installation.


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The following table shows the usernames and passwords for the i2b2 demo environment.


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Data Package   


Cell Owner

Database /
Schema Name   


User Name


Password   

Crcdata

Data Repository (CRC)

i2b2demodata

i2b2demodata   

demouser

Hivedata

Project Management (PM)

i2b2hive

i2b2hive

demouser

Imdata

Identity Management (IM)

i2b2imdata

i2b2imdata

demouser

Metadata

Ontology Management (ONT)   

i2b2metadata

i2b2metadata

demouser

Pmdata

Project Management (PM)

i2b2pm

i2b2pm

demouser

Workdata

Workplace (WORK)

i2b2workdata

i2b2workdata

demouser




Tip
titleTip

Obviously the passwords and possible the usernames will be different for those databases that contain your real patient data. The Install Worksheet (Appendix A) can be used to document and organize the settings for your environment. The worksheet is particularly useful if you are setting up multiple environments and need to keep track of the settings for each environment.



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7. Multiple projects with different data sources.


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  • Need to add an additional <datasource> section for each project data source.
  • In addition to updating the connection-url, drivers and database user information you also need to update both the jndi-name and pool-name to reflect the name of the other projects.


Note
titleImportant

Any changes made to a cell's ds.xml file after it has been deployed will require you to re-deploy the cell in order for the changes to take effect.



In addition to the ds.xml files, several cells have additional "data configurations" defined in their property files. These additional data configurations are typically defining the schema / database name and location of your Hivedata tables so the cells can lookup relevant information.


Installation Checklists

Requirements Checklist


Step

File Name or Comment

Completed

Database Requirements




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Installed a Database Management System supported by i2b2


Oracle / PostgreSQL / SQLServer


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Browser Requirements




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Installed a web browser supported by i2b2


Firefox / Internet Explorer / Safari


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i2b2 Server Requirements




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Installed Java JDK 8.0 on your i2b2 Server




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Installed WildFly 17.0.0 Application Server on your i2b2 Server




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Set WildFly logging level to INFO




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Documented WildFly port; if other than 9090 then install scripts have to be updated




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Setup WildFly to run as either a Linux or Windows service




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Installed Apache Ant 1.9.6 on your i2b2 Server




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Installed Apache Axis2 1.6.2 on your i2b2 Server




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Set your system environment variables on your i2b2 Server




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Web Server Requirements




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Installed/Configured cURL on your web server


Only required for Linux Machines


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Installed IIS on your web server


Only required for Windows Machines


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Installed Php: Hypertext Preprocessor on your web server


Required for both Linux and Windows Machines


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i2b2 Software Requirements

Downloaded zip files from i2b2.org



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i2b2 data installation scripts




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i2b2 core source code




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i2b2 Web Client code




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i2b2 Workbench application for Macintosh or Windows




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i2b2 VMWare image of the i2b2 Core Server


Optional


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Data Checklist


Step

File Name or Comment

Completed

Extracted the i2b2 data package to a directory of your choice

YOUR_I2B2_DATA_DIR


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Created database user accounts for all the i2b2 schemas



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Crcdata




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Set the database properties


db.properties


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Created the Crcdata tables




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Created the stored procedures




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Loaded the data into the Crcdata tables


Type of data loaded:
    i2b2 demo data or your local data


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Hivedata




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Set the database properties


db.properties


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Created the Hivedata tables




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Loaded the data into the Hivedata tables


Type of data loaded:
    i2b2 demo data or your local data


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Imdata

Optional Cell



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Set the database properties


db.properties


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Created the Imdata tables




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Loaded the data into the Imdata tables


Type of data loaded:
    i2b2 demo data or your local data


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Metadata




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Set the database properties


db.properties


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Created the Metadata tables




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Loaded the data into the Metadata tables


Type of data loaded:
    i2b2 demo data or your local data


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Pmdata




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Set the database properties


db.properties


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Created the Pmdata tables




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Created the PM triggers




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Loaded the data into the Pmdata tables


Type of data loaded:
    i2b2 demo data or your local data


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Workdata




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Set the database properties


db.properties


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Created the Workdata tables




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Loaded the data into the Workdata tables


Type of data loaded:
    i2b2 demo data or your local data


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Server-Common Checklist


Step

File Name or Comment

Completed

Extracted the i2b2 source code to a directory of your choice

YOUR_I2B2_SRC_DIR


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Configured the build properties

build.properties


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Deployed edu.harvard.i2b2.server-common



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PM Checklist


Step

File Name or Comment

Completed

Configured the PM build properties

build.properties


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Configured the datasources for the PM Cell

pm-ds.xml


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Deployed edu.harvard.i2b2.pm



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Verified the installation of the PM Cell



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i2b2 Admin Checklist


Warning
titleWarning


The Admin Module and the Web Client each have their own folder that contains the necessary files to run the respective application. Both the admin and webclient folders contain files with similar names which can be a source of confusion. Therefore it is important to make sure you are editing the files in the admin folder and not the ones that reside in the webclient folder.


In addition to the above, you also want to make sure you are editing the admin files in your webserver directory and not the ones that reside in YOUR_I2B2_SRC_DIR.


Step

File Name or Comment

Completed

Copied Admin files to your web server directory



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Configured the Domain information for your Admin Module

See note at end of this table



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Commented out or removed the pre-configured domain of i2b2demo


See note at end of this table


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Added the domain information for your environment


i.e. test and production


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Verified the installation of the i2b2 Admin



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Info
titleNote

The i2b2 Admin is pre-configured with the following domain information:


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The domain is i2b2demo


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The URL points to the local PM in your i2b2 demo environment


If you comment out or remove this domain then i2b2 will not work in your demo environment.


i2b2 Web Client Checklist


Warning
titleWarning


The Admin Module and the Web Client each have their own folder that contains the necessary files to run the respective application. Both the admin and webclient folders contain files with similar names which can be a source of confusion. Therefore it is important to make sure you are editing the files in the webclient folder and not the ones that reside in the admin folder.


In addition to the above, you also want to make sure you are editing the web client files in your webserver directory and not the ones that reside in YOUR_I2B2_WC_DIR.


Step

File Name or Comment

Completed

Extracted the i2b2 Web Client code to a directory of your choice

YOUR_I2B2_WC_DIR


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Copied Web Client files to your web server directory



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Configured the Proxy information for your environment




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Using the default PHP proxy file that is included with the i2b2 Software




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Update security configurations in the PHP proxy




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Level2

Verified the correct proxy is defined in the Web Client's config file (i2b2_config_data.js)




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Not using the default PHP proxy file that is included with the i2b2 Software




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Write your own proxy file




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Update the urlProxy in the Web Client's config file to reflect the correct proxy (i2b2_config_data.js)




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Configured the Domain information for your Web Client

See note at end of this table



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Commented out, or removed the default domain of HarvardDemo


Optional


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Added the i2b2demo domain for your i2b2 demo environment




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Level1

Added the domain information for your environment


i.e. test and production


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Verified the installation of the i2b2 Web Client



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Info
titleNote

The i2b2 Web Client is pre-configured with the following domain information:


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The domain is HarvardDemo


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The URL points to the public i2b2 in your i2b2.org site


If you comment out or remove this domain then i2b2 Web Client will not be able to connect to the public i2b2 site.


i2b2 Workbench Checklist


Step

File Name or Comment

Completed

Extracted the i2b2 Workbench files to a directory of your choice

YOUR_I2B2_WB_DIR


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Configured the Workbench properties with the location of your hive

i2b2workbench.properties


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Level1


Verified the installation of the i2b2 Workbench



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ONT Checklist


Step

File Name or Comment

Completed

Configured the Ontology build properties

build.properties


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Configured the Ontology application directory properties

ontology_application_directory.properties


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Configured the following Ontology properties

ontology.properties


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Set the Metadata Schema Name


Location of the Hivedata tables


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Set the Project Management Cell Integration Properties


Settings to locate and communicate with the PM Cell


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Set the File Management Cell Properties


Settings to locate and communicate with the FRC Cell


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Set the CRC Cell Properties


Settings to locate and communicate with the CRC Cell


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Set the Ontology Service Account Properties




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Set the metadata delimiter property

indent




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Configured the data sources for the Ontology Cell

ont-ds.xml


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Deployed edu.harvard.i2b2.ontology



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Updated the ONT Cell Data in the i2b Admin Module



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Verified the installation of the Ontology Cell



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CRC Checklist


Step

File Name or Comment

Completed

Configured the CRC build properties

build.properties


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Configured the CRC application directory properties

crc_application_directory.properties


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Configured the following CRC Loader properties

edu.harvard.i2b2.crc.loader.properties



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Set the File Management Cell Properties


Settings to locate and communicate with the FRC cell


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Set the Project Management Cell Properties


Settings to locate and communicate with the PM Cell


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Configured the datasource lookups for the CRC Loader

CRCLoaderApplicationContext.xml
edu.harvard.i2b2.crc.loader.properties


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Configured the following CRC properties

crc.properties



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Set the Project Management Cell Properties


Settings to locate and communicate with the PM Cell


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Set the CRC Datasource Lookup Properties


Location of your hivedata tables and the type of database


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Set the Ontology Cell Properties


Settings to locate and communicate with the ONT Cell


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Set the CRC Service Account Properties




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Set the PDO paging properties


Optional performance property


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Set the Analysis plug-in: Queue properties


Optional performance property


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Set the Setfinder query: Timeout properties


Optional performance property


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Set the Setfinder query: Lockout properties


Optional performance property


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Set the Setfinder query: Temp table properties


Optional performance property


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Configured the data sources for the CRC Cell

crc-ds.xml


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Deployed edu.harvard.i2b2.crc



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Updated the CRC Cell Data in the i2b Admin Module



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Updated the metadata key in the CRC Tables

QT_BREAKDOWN_PATH table


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Verified the installation of the CRC Cell



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WORK Checklist


Step

File Name or Comment

Completed

Configured the Workplace build properties

build.properties


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Configured the Workplace application directory properties

workplace_application_directory.properties


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Level1


Configured the following Workplace properties

workplace.properties



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Set the Metadata Schema Name


Location of the Hivedata tables


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Set the Project Management Cell Integration Properties


Settings to locate and communicate with the PM Cell


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Configured the data sources for the Workplace Cell

work-ds.xml


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Deployed edu.harvard.i2b2.workplace



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Updated the WORK Cell Data in the i2b Admin Module



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Verified the installation of the Workplace Cell



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FR Checklist


Step

File Name or Comment

Completed

Configured the File Repository build properties

build.properties


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Level1


Configured the File Repository application directory properties

fr_application_directory.properties


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Configured the following File Repository properties

edu.harvard.i2b2.fr.properties



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Set the Project Management Cell Integration Properties


Settings to locate and communicate with the PM Cell


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Deployed edu.harvard.i2b2.fr



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Updated the FRC Cell Data in the i2b Admin Module



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IM Checklist


Step

File Name or Comment

Completed

Configured the IM build properties

build.properties


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Level1


Configured the IM application directory properties

im_application_directory.properties


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Level1


Configured the following IM properties

ontology.properties



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Set the Metadata Schema Name


Location of the Hivedata tables


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Set the Project Management Cell Properties


Settings to locate and communicate with the PM Cell


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Set the Patient in Project Property




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Set the EMPI Service Properties


Optional 3rd party EMPI Service


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Configured the data sources for the IM Cell

im-ds.xml


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Deployed edu.harvard.i2b2.im



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Updated the IM Cell Data in the i2b Admin Module



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Initial i2b2 Setup Checklist


Step

File Name or Comment

Completed

Hive Data Management




indent
Level1

Updated the Help URL for your environment


Optional


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Level1



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Verified Domain Name is entered correctly in i2b2 Admin




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Defined the type of environment




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Cell Data Management




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Verified the information for each of your cells is entered correctly; particularly the cell id and cell url




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Defined any cell specific parameters




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User Management




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Entered at least one i2b2 user in i2b2 Admin




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Defined any user specific parameters




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Project Management




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Entered at least one project in i2b2 Admin




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Defined any project specific parameters


i.e. Unit Conversion for Numerical Observations or Enable Process Timing


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At least one user given access to the project and defined their level of access




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Defined any project-user parameters




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Setup i2b2 Authentication Method of Active Directory

Optional


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Added parameter for authentication method




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Added parameter for PDC Domain of your NT domain




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Added parameter for the connection URL of your NT domain




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Setup i2b2 Authentication Method of LDAP

Optional


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Added parameter for authentication method




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Added parameter for the connection URL of your LDAP server




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Added parameter for search base




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Added parameter for distinguished name




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Added parameter for security authentication




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Added parameter for ssl




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Added parameter for security layer




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Added parameter for privacy strength




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Added parameter for max buffer




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