<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.
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. |
Environment: | Demo / Test / Production / Other | Version of i2b2: |
|
---|---|---|---|
Domain ID: | Domain Name: | ||
Setup Date: | Setup By: |
Installation Order | Checklist Name | Install Guide Resource |
---|---|---|
1. System and Software Requirements | Requirements Checklist | |
2. Data Installation | Data Checklist | |
3. Deploying the server-common | Server-Common Checklist | |
4. PM Cell Installation | PM Checklist | |
5. i2b2 Admin Installation | i2b2 Admin Checklist | |
6. i2b2 Web Client Installation | i2b2 Web Client Checklist | |
7. i2b2 Workbench Installation | i2b2 Workbench Checklist | |
8. ONT Cell Installation | ONT Checklist | |
9. CRC Cell Installation | CRC Checklist | |
10. WORK Cell Installation | WORK Checklist | |
11. FR Cell Installation | FR Checklist | |
12. IM Cell Installation | IM Checklist | |
13. Setting up i2b2 | Initial i2b2 Setup Checklist |
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.
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) |
2. At least two datasources have to be defined in the ds.xml files for the ONT, CRC, WORK, and IM Cells. |
|
3. The PM Cell has only one datasource (PMBootsrapDS) defined and it points to the location of the Pmdata tables. |
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. |
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. |
|
5. The <driver-class> and <driver> for each <datasource> needs to be defined correctly for the type of database you are connecting to. |
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. |
6. The <username> and <password> for each <datasource> needs to match the database users you setup during the data installation. |
The following table shows the usernames and passwords for the i2b2 demo environment. |
|
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. |
7. Multiple projects with different data sources. |
|
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.
Step | File Name or Comment | Completed | ||
---|---|---|---|---|
Database Requirements | ||||
| Oracle / PostgreSQL / SQLServer | |||
Browser Requirements | ||||
| Firefox / Internet Explorer / Safari | |||
i2b2 Server Requirements | ||||
| ||||
| ||||
| ||||
| ||||
| ||||
| ||||
| ||||
| ||||
Web Server Requirements | ||||
| Only required for Linux Machines | |||
| Only required for Windows Machines | |||
| Required for both Linux and Windows Machines | |||
i2b2 Software Requirements | Downloaded zip files from i2b2.org | |||
| ||||
| ||||
| ||||
| ||||
| Optional |
Step | File Name or Comment | Completed | ||
---|---|---|---|---|
Extracted the i2b2 data package to a directory of your choice | YOUR_I2B2_DATA_DIR | |||
Created database user accounts for all the i2b2 schemas | ||||
Crcdata | ||||
| db.properties | |||
| ||||
| ||||
| Type of data loaded: | |||
Hivedata | ||||
| db.properties | |||
| ||||
| Type of data loaded: | |||
Imdata | Optional Cell | |||
| db.properties | |||
| ||||
| Type of data loaded: | |||
Metadata | ||||
| db.properties | |||
| ||||
| Type of data loaded: | |||
Pmdata | ||||
| db.properties | |||
| ||||
| ||||
| Type of data loaded: | |||
Workdata | ||||
| db.properties | |||
| ||||
| Type of data loaded: |
Step | File Name or Comment | Completed | |
---|---|---|---|
Extracted the i2b2 source code to a directory of your choice | YOUR_I2B2_SRC_DIR | ||
Configured the build properties | build.properties | ||
Deployed edu.harvard.i2b2.server-common |
Step | File Name or Comment | Completed | |
---|---|---|---|
Configured the PM build properties | build.properties | ||
Configured the datasources for the PM Cell | pm-ds.xml | ||
Deployed edu.harvard.i2b2.pm | |||
Verified the installation of the PM Cell |
|
Step | File Name or Comment | Completed | ||
---|---|---|---|---|
Copied Admin files to your web server directory | ||||
Configured the Domain information for your Admin Module | See note at end of this table | |||
| See note at end of this table | |||
| i.e. test and production | |||
Verified the installation of the i2b2 Admin |
The i2b2 Admin is pre-configured with the following domain information:
If you comment out or remove this domain then i2b2 will not work in your demo environment. |
|
Step | File Name or Comment | Completed | ||
---|---|---|---|---|
Extracted the i2b2 Web Client code to a directory of your choice | YOUR_I2B2_WC_DIR | |||
Copied Web Client files to your web server directory | ||||
Configured the Proxy information for your environment | ||||
| ||||
| ||||
| ||||
| ||||
| ||||
| ||||
Configured the Domain information for your Web Client | See note at end of this table | |||
| Optional | |||
| ||||
| i.e. test and production | |||
Verified the installation of the i2b2 Web Client |
The i2b2 Web Client is pre-configured with the following domain information:
If you comment out or remove this domain then i2b2 Web Client will not be able to connect to the public i2b2 site. |
Step | File Name or Comment | Completed | |
---|---|---|---|
Extracted the i2b2 Workbench files to a directory of your choice | YOUR_I2B2_WB_DIR | ||
Configured the Workbench properties with the location of your hive | i2b2workbench.properties | ||
Verified the installation of the i2b2 Workbench |
Step | File Name or Comment | Completed | ||
---|---|---|---|---|
Configured the Ontology build properties | build.properties | |||
Configured the Ontology application directory properties | ontology_application_directory.properties | |||
Configured the following Ontology properties | ontology.properties | |||
| Location of the Hivedata tables | |||
| Settings to locate and communicate with the PM Cell | |||
| Settings to locate and communicate with the FRC Cell | |||
| Settings to locate and communicate with the CRC Cell | |||
| ||||
Set the metadata delimiter property | ||||
Configured the data sources for the Ontology Cell | ont-ds.xml | |||
Deployed edu.harvard.i2b2.ontology | ||||
Updated the ONT Cell Data in the i2b Admin Module | ||||
Verified the installation of the Ontology Cell |
Step | File Name or Comment | Completed | ||
---|---|---|---|---|
Configured the CRC build properties | build.properties | |||
Configured the CRC application directory properties | crc_application_directory.properties | |||
Configured the following CRC Loader properties | edu.harvard.i2b2.crc.loader.properties | |||
| Settings to locate and communicate with the FRC cell | |||
| Settings to locate and communicate with the PM Cell | |||
Configured the datasource lookups for the CRC Loader | CRCLoaderApplicationContext.xml | |||
Configured the following CRC properties | crc.properties | |||
| Settings to locate and communicate with the PM Cell | |||
| Location of your hivedata tables and the type of database | |||
| Settings to locate and communicate with the ONT Cell | |||
| ||||
| Optional performance property | |||
| Optional performance property | |||
| Optional performance property | |||
| Optional performance property | |||
| Optional performance property | |||
Configured the data sources for the CRC Cell | crc-ds.xml | |||
Deployed edu.harvard.i2b2.crc | ||||
Updated the CRC Cell Data in the i2b Admin Module | ||||
Updated the metadata key in the CRC Tables | QT_BREAKDOWN_PATH table | |||
Verified the installation of the CRC Cell |
Step | File Name or Comment | Completed | ||
---|---|---|---|---|
Configured the Workplace build properties | build.properties | |||
Configured the Workplace application directory properties | workplace_application_directory.properties | |||
Configured the following Workplace properties | workplace.properties | |||
| Location of the Hivedata tables | |||
| Settings to locate and communicate with the PM Cell | |||
Configured the data sources for the Workplace Cell | work-ds.xml | |||
Deployed edu.harvard.i2b2.workplace | ||||
Updated the WORK Cell Data in the i2b Admin Module | ||||
Verified the installation of the Workplace Cell |
Step | File Name or Comment | Completed | ||
---|---|---|---|---|
Configured the File Repository build properties | build.properties | |||
Configured the File Repository application directory properties | fr_application_directory.properties | |||
Configured the following File Repository properties | edu.harvard.i2b2.fr.properties | |||
| Settings to locate and communicate with the PM Cell | |||
Deployed edu.harvard.i2b2.fr | ||||
Updated the FRC Cell Data in the i2b Admin Module |
Step | File Name or Comment | Completed | ||
---|---|---|---|---|
Configured the IM build properties | build.properties | |||
Configured the IM application directory properties | im_application_directory.properties | |||
Configured the following IM properties | ontology.properties | |||
| Location of the Hivedata tables | |||
| Settings to locate and communicate with the PM Cell | |||
| ||||
| Optional 3rd party EMPI Service | |||
Configured the data sources for the IM Cell | im-ds.xml | |||
Deployed edu.harvard.i2b2.im | ||||
Updated the IM Cell Data in the i2b Admin Module |
Step | File Name or Comment | Completed | ||
---|---|---|---|---|
Hive Data Management | ||||
| Optional | |||
| ||||
| ||||
Cell Data Management | ||||
| ||||
| ||||
User Management | ||||
| ||||
| ||||
Project Management | ||||
| ||||
| i.e. Unit Conversion for Numerical Observations or Enable Process Timing | |||
| ||||
| ||||
Setup i2b2 Authentication Method of Active Directory | Optional | |||
| ||||
| ||||
| ||||
Setup i2b2 Authentication Method of LDAP | Optional | |||
| ||||
| ||||
| ||||
| ||||
| ||||
| ||||
| ||||
| ||||
|