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.
Note
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 #
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Environment: |
Demo / Test / Production / Other |
Version of i2b2: |
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|---|---|---|---|
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Domain ID: |
Domain Name: |
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Setup Date: |
Setup By: |
Installation Order and Resources #
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Installation Order |
Checklist Name |
Install Guide Resource |
|---|---|---|
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1. System and Software Requirements |
Requirements Checklist |
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2. Data Installation |
Data Checklist |
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3. Deploying the server-common |
Server-Common Checklist |
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4. PM Cell Installation |
PM Checklist |
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5. i2b2 Admin Installation |
i2b2 Admin Checklist |
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6. i2b2 Web Client Installation |
i2b2 Web Client Checklist |
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7. i2b2 Workbench Installation |
i2b2 Workbench Checklist |
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8. ONT Cell Installation |
ONT Checklist |
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9. CRC Cell Installation |
CRC Checklist |
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10. WORK Cell Installation |
WORK Checklist |
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11. FR Cell Installation |
FR Checklist |
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12. IM Cell Installation |
IM Checklist |
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13. Setting up i2b2 |
Initial i2b2 Setup Checklist |
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.
- 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.
Note
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.
- Update the
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).
Important
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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Database / |
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|---|---|---|---|---|
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Crcdata |
Data Repository (CRC) |
i2b2demodata |
i2b2demodata |
demouser |
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Hivedata |
Project Management (PM) |
i2b2hive |
i2b2hive |
demouser |
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Imdata |
Identity Management (IM) |
i2b2imdata |
i2b2imdata |
demouser |
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Metadata |
Ontology Management (ONT) |
i2b2metadata |
i2b2metadata |
demouser |
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Pmdata |
Project Management (PM) |
i2b2pm |
i2b2pm |
demouser |
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Workdata |
Workplace (WORK) |
i2b2workdata |
i2b2workdata |
demouser |
Tip
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.
- Need to add an additional
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.
Important
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 #
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Step |
File Name or Comment |
Completed |
|---|---|---|
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Database Requirements |
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Installed a Database Management System supported by i2b2
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Oracle / PostgreSQL / SQLServer |
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Browser Requirements |
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Installed a web browser supported by i2b2
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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
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Only required for Linux Machines |
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Installed IIS on your web server
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Only required for Windows Machines |
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Installed Php: Hypertext Preprocessor on your web server
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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
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Optional |
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Data Checklist #
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Step |
File Name or Comment |
Completed |
|---|---|---|
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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
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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
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Type of data loaded: |
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Hivedata |
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Set the database properties
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db.properties |
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Created the Hivedata tables
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Loaded the data into the Hivedata tables
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Type of data loaded: |
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Imdata |
Optional Cell |
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Set the database properties
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db.properties |
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Created the Imdata tables
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Loaded the data into the Imdata tables
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Type of data loaded: |
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Metadata |
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Set the database properties
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db.properties |
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Created the Metadata tables
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Loaded the data into the Metadata tables
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Type of data loaded: |
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Pmdata |
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Set the database properties
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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
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Type of data loaded: |
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Workdata |
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Set the database properties
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db.properties |
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Created the Workdata tables
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Loaded the data into the Workdata tables
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Type of data loaded: |
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Server-Common Checklist #
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Step |
File Name or Comment |
Completed |
|---|---|---|
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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 #
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Step |
File Name or Comment |
Completed |
|---|---|---|
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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
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.
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Step |
File Name or Comment |
Completed |
|---|---|---|
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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
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See note at end of this table |
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Added the domain information for your environment
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i.e. test and production |
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Verified the installation of the i2b2 Admin |
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Note
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.
i2b2 Web Client Checklist #
Warning
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 |
|---|---|---|
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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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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
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Optional |
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Added the i2b2demo domain for your i2b2 demo environment
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Added the domain information for your environment
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i.e. test and production |
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Verified the installation of the i2b2 Web Client |
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Note
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.
i2b2 Workbench Checklist #
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Step |
File Name or Comment |
Completed |
|---|---|---|
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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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Verified the installation of the i2b2 Workbench |
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ONT Checklist #
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Step |
File Name or Comment |
Completed |
|---|---|---|
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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
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Location of the Hivedata tables |
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Set the Project Management Cell Integration Properties
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Settings to locate and communicate with the PM Cell |
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Set the File Management Cell Properties
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Settings to locate and communicate with the FRC Cell |
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Set the CRC Cell Properties
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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
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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 #
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Step |
File Name or Comment |
Completed |
|---|---|---|
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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
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Settings to locate and communicate with the FRC cell |
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Set the Project Management Cell Properties
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Settings to locate and communicate with the PM Cell |
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Configured the datasource lookups for the CRC Loader |
CRCLoaderApplicationContext.xml |
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Configured the following CRC properties |
crc.properties |
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Set the Project Management Cell Properties
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Settings to locate and communicate with the PM Cell |
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Set the CRC Datasource Lookup Properties
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Location of your hivedata tables and the type of database |
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Set the Ontology Cell Properties
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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
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Optional performance property |
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Set the Analysis plug-in: Queue properties
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Optional performance property |
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Set the Setfinder query: Timeout properties
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Optional performance property |
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Set the Setfinder query: Lockout properties
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Optional performance property |
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Set the Setfinder query: Temp table properties
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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 #
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Step |
File Name or Comment |
Completed |
|---|---|---|
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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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Configured the following Workplace properties |
workplace.properties |
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Set the Metadata Schema Name
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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 #
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Step |
File Name or Comment |
Completed |
|---|---|---|
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Configured the File Repository build properties |
build.properties |
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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 |
|---|---|---|
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Configured the IM build properties |
build.properties |
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Configured the IM application directory properties |
im_application_directory.properties |
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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 |
|---|---|---|
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Hive Data Management |
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Updated the Help URL for your environment
|
Optional |
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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
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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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