Installation Guide

~ Methods of debugging ~
i2b2-on-OMOP With ENACT-OMOP Ontology v4.1
i2b2 Sponsored Projects
i2b2 Related Projects
i2b2 Installation Guide
i2b2 Cell Messaging
i2b2 Administrator Module
Workplace Cell is Unavailable
Web Client is Not Running
WORK Data Source Configuration
The RPDO2 stored procedure
Target Location and Application Name Do Not Match
Target Location Missing or Not Specified Correctly
Remote Server is Unavailable
Quick Upgrade Guide for i2b2 Web Client 1.8.x
Patient Data Object
PM Service is Not Responding
PM Data Source Configuration
PM Cell is Unavailable
Overview
Ontology Cell is Unavailable
Obtaining i2b2 Software
ONT Data Source Configuration
Message Version is Missing
Licenses
Install Guide for i2b2 Web Client v1.8 on Apache
Informational Diagrams for SAML Setup
Foundations of i2b2 Software
Database Error
Contributing code to i2b2
Chapter 9. i2b2 Virtual Machine for Demonstrations
Chapter 7. Troubleshooting Installation Errors
Chapter 6. Initial Setup of i2b2 in Admin
Chapter 5. Client Installation
Chapter 4. i2b2 Server-Common Install
Chapter 4. Server Install Guide
Chapter 3. Data Installation
Chapter 2. Requirements
Chapter 10. Advanced Data Export Features
Chapter 1. Introduction
CRC Data Source Configuration
CRC Cell is Unavailable
B. Legacy Approach – Build Each Cell from Source
Applying Branding Styles to the i2b2 Web Client v1.8
Application Name is Missing
Appendix B – i2b2 Installation Checklist
Appendix A – Install Worksheet
Appendices
A. Server Install on 1.7.12 and higher
Creating a Custom Data Type / Value Picker (v1.8.1+)
Activity & Usage Monitoring
9.9 Next Steps
9.8 Verify Ontology Installation
9.7 Update ONT Cell Data in i2b2 Standalone Admin
9.6 Start Services
9.5 Deployment
9.4.4 Data Source Configuration
9.4.3.6 Metadata Delimiter Property
9.4.3.5 Ontology Service Account Properties
9.4.3.4 Data Repository Cell Properties
9.4.3.3 File Repository Cell Properties
9.4.3.2 Project Management Cell Properties
9.4.3.1 Set Metadata Schema Name
9.4.3 Configure the Ontology Properties
9.4.2 Configure Ontology Application Directory Properties
9.4.1 Configure Ontology Build Properties
9.4 Configuration
9.3 Stop Services
9.2.1 Source Code and Directory Structure
9.2 Ontology Installation Overview
9.1 Prerequisites
Data Exporter (v 1.8.1)
4. i2b2 Classic Web Client Install (optional)
Patient Counting Scripts (“totalnum”)
8.3.1.2 Access Properties file on Windows
8.3.1.1 Access Properties file on a Macintosh
6.9 Next Steps
6.8.2 Enable Process Timing
6.8.1 Unit Conversion for Numerical Observations
6.7.2 LDAP Authentication
6.7.1 Active Directory Authentication in the Classic Webclient
6.6.5.3 Delete Project User Parameters
6.6.5.2 Edit Project User Parameters
6.6.5.1 Add Project User Parameters
6.6.5 Project User Parameters
6.6.4.2 Edit User Roles for a Project
6.6.4.1 Add User Roles for a Project
6.6.4 Project User Roles
6.6.3.2 Remove a User from a Project
6.6.3.1 Add User to a Project
6.6.3 Project Users
6.6.2.3 Delete Project Parameters
6.6.2.2 Edit Project Parameters
6.6.2.1 Add Project Parameters
6.6.2 Project Parameters
6.6.1.3 Delete a Project
6.6.1.2 Edit Project Data
6.6.1.1 Add a New Project
6.6.1 Project Data
6.6.0. Guide to creating a new project with the admin tool
6.6 Managing i2b2 Projects
6.6 Classic Webclient Admin Tool
6.5.2.3 Delete User Parameters
6.5.2.2 Edit User Parameters
6.5.2.1 Add User Parameters
6.5.2 User Parameters
6.5.1.3 Delete an i2b2 User
6.5.1.2 Edit Existing User
6.5.1.1 Add a New User
6.5.1 User Data
6.5 Optional Parameters
6.5 Managing i2b2 Users
6.4.3 Cell DB-Lookup
6.4.2.3 Delete Cell Parameters
6.4.2.2 Edit Cell Parameters
6.4.2.1 Add Cell Parameters
6.4.2 Cell Parameters
6.4.1.3 Delete a Cell
6.4.1.2 Edit Cell Data
6.4.1.1 Add a New Cell
6.4.1 Cell Data
6.4 Managing i2b2 Cells
6.4 Authentication in i2b2
6.3.4.1 Delete Hive Parameters
6.3.3.2 Edit Hive Parameters
6.3.2.1 Add Hive Parameters
6.3.2 Hive Parameters
6.3.1.1 Edit Hive Data
6.3.1 Hive Data
6.3 i2B2 NEW Admin Help Documentation May 2024
6.3 Managing i2b2 Hive Data
6.2 Chapter Overview
6.1 Prerequisites
6. Update Cell Data in i2b2 Admin
i2b2 SAML: Customize Identity Provider (IdP) Login Button
6.7.3. SAML Authentication (v1.7.13+)
6.5a i2b2 Webclient User Registration (new in 1.7.13)
Chapter 8. SAML Setup for i2b2 (v1.7.13 release)
5.8 Next Steps
5.7 Verify PM Installation
5.5 Deployment
5.4.2 Data Source Configuration
5.4.1 Configure the PM Build Properties
5.4 Configuration
5.3 Stop Services
5.2.1 Source Code and Directory Structure
5.2 PM Installation Overview
5.1 Prerequisites
5. Additional Optional Configuration
The PM Cell is down or the address in the properties file is incorrect (related to SELinux)
4.6 Next Steps
4.5 Deployment
4.4.1 Configure the Server-common Build Properties
4.4 Configuration
4.3 Stop Services
4.2.2 Directory Structure and Working Directory
4.2.1 Extract Source Code
4.2 Server-common Installation Overview
4.1 Prerequisites
4. Verify Installation
3.9.4 Load Workdata Tables
3.9.3 Create Workdata Tables
3.9.2 Set Database Properties
3.9.1 Working Directory
3.9 Workdata Tables
3.8.4 Create PM Triggers
3.8.3 Create PM Tables
3.8.2 Set Database Properties
3.8.1 Working Directory
3.8 PM Tables
3.7.4 Load Metadata Tables
3.7.3 Create Metadata Tables
3.7.2 Set Database Properties
3.7.1 Working Directory
3.7 Metadata Tables
3.6.4 Load IM Tables
3.6.3 Create IM Tables
3.6.2 Set Database Properties
3.6.1 Working Directory
3.6 IM Tables
3.5.4 Load Hive Data
3.5.3 Create Hive Tables
3.5.2 Set Database Properties
3.5.1 Working Directory
3.5 Next Steps
3.5 Hivedata Tables
3.4.5 Load Crcdata Tables
3.4.4 Create Crcdata Stored Procedures
3.4.3 Create Crcdata Tables
3.4.2 Set Database Properties
3.4.1 Working Directory
3.4 Verify Workbench Installation
3.4 Crcdata Tables
3.3.3 Create User Accounts in SQL Server
3.3.2 Define Physical Memory
3.3.2 Create User Accounts in PostgreSQL
3.3.1 Define Hive Location
3.3.1 Create User Accounts in Oracle
3.3 Create Database User Accounts
3.3 Configuration
3.2.2 Directory Structure and Schema Mapping
3.2.1 Extract the i2b2 Data Package
3.2.1 Extract Workbench Executables
3.2 Workbench Installation Overview
3.2 Data Installation Overview
3.11 Multiple Fact Tables
3.10.5 Load PM Tables
3.10 Next Steps
3.1 Workbench Prerequisites
3.0 Prerequisites
3. Start Services
3. Setup SFTP in FR
PM Cell’s getVersion Operation is Not Responding
Password Doesn’t Match or Username Doesn’t Exist
6.7.1 Active Directory Authentication (updated for the 1.8.x webclient)
3. i2b2 Workbench Install (optional)
Chapter 9. Ontology Management (ONT) Cell Install
Chapter 5. Project Management (PM) Cell Install
Chapter 13. Identity Management (IM) Cell Install
12.9 SFTP Setup * Optional *
Chapter 12. File Repository (FR) Cell Install
Chapter 11. Workplace (WORK) Cell Install
Chapter 10. Data Repository (CRC) Cell Install
2.5.2 Internet Information Services (IIS)
2.5.1 Client URL Request Library (cURL)
2.7 Next Steps
2.6.2 Download i2b2 Software
2.6 i2b2 Requirements
2.5.3.2 PHP for Windows
2.5.3.1 PHP for Linux
2.5.3 PHP
2.5.2.1 Verify IIS 7.0 Installation
2.5 Web Server Requirements
2.5 Next Steps
2.4.5.2 Set Variables on Windows Machine
2.4.5.1 Set Variables on Linux Machine
2.4.5 System Environment Variables
2.4.4 Apache Axis2
2.4.3 Apache Ant
2.4.2.4 Run Wildfly as a Windows Service
2.4.2.3 Run Wildfly as a Linux Service
2.4.2.2 Wildfly Logging Configuration
2.4.2.1 Recommended Ports
2.4.2 WildFly Application Server
2.4.1 Java JDK
2.4 i2b2 Server Requirements
2.4 Verify Admin Installation
2.3.1 Operating System Requirements
2.3 Browser Requirements
2.3 Admin Module Install Integrated into Webclient
2.2.3 Configuration
2.2.2 Install Standalone Admin on Web Server
2.2.1 Source Code and Working Directories
2.2 Standalone Admin Module Installation
2.2 Database Requirements
2.1 Prerequisites
2. i2b2 Administration Module Install
2. Update QT_BREAKDOWN_PATH
2. Data Source Configuration
13.9 Next Steps
13.8 Verify IM Installation
13.7 Update IM Cell Data in i2b2 Standalone Admin
13.6 Start Services
13.5 Deployment
13.4.4 Data Source Configuration
13.4.3.4 Other EMPI Service Properties
13.4.3.3 Patient in Project Property
13.4.3.2 Project Management Cell Properties
13.4.3.1 Set Schema Name
13.4.3 Configure the IM Properties
13.4.2 Configure the IM Application Directory Properties
13.4.1 Configure the IM Build Properties
13.4 Configuration
13.3 Stop Services
13.2.1 Source Code and Directory Structure
13.2 Identity Management Installation Overview
13.1 Prerequisites
12.8 Verify FR Installation
12.7 Update FR Cell Data in i2b2 Standalone Admin
12.6 Start Services
12.5 Deployment
12.4.3 Configure the FR Properties
12.4.2 Configure the FR Application Directory Properties
12.4.1 Configure the FR Build Properties
12.4 Configuration
12.3 Stop Services
12.2.1 Source Code and Directory Structure
12.2 File Repository Installation Overview
12.10 Next Steps
12.1 Prerequisites
11.9 Next Steps
11.8 Verify Workplace Installation
11.7 Update WORK Cell Data in i2b2 Standalone Admin
11.6 Start Services
11.5 Deployment
11.4.4 Data Source Configuration
11.4.3.2 Project Management Cell Properties
11.4.3.1 Set Metadata Schema Name
11.4.3 Configure the Workplace Properties
11.4.2 Configure the Workplace Application Directory Properties
11.4.1 Configure the Workplace Build Properties
11.4 Configuration
11.3 Stop Services
11.2.1 Source Code and Directory Structure
11.2 Workplace Installation Overview
11.1 Prerequisites
Data Exporter (v 1.8.2)
10.9 Verify CRC Installation
10.8 Update Path in CRC Tables
10.7 Update CRC Cell Data in i2b2 Standalone Admin
10.6 Start Services
10.5 Deployment
10.4.5 Data Source Configuration
10.4.4.2.5 Setfinder Query – Temp Table Properties
10.4.4.2.4 Setfinder Query – Lockout Properties
10.4.4.2.3 Setfinder Query – Timeout Properties
10.4.4.2.2 Analysis Plug-in – Queue Properties
10.4.4.2.1 PDO Paging Properties
10.4.4.2 Optional Performance Properties
10.4.4.1.4 CRC Service Account Properties
10.4.4.1.3 Ontology Cell Properties
10.4.4.1.2 Data Source Lookup Properties
10.4.4.1.1 Project Management Cell Properties
10.4.4.1 Required Environment Properties
10.4.4 Configure the CRC Properties
10.4.3.3 Data Source Properties for the CRC Loader
10.4.3.2 Project Management Cell Properties for CRC Loader
10.4.3.1 File Repository Cell Properties for CRC Loader
10.4.3 Configure CRC Loader Properties
10.4.2 Configure CRC Application Directory Properties
10.4.1 Configure CRC Build Properties
10.4 Configuration
10.3 Stop Services
10.2.1 Source Code and Directory Structure
10.2 CRC Installation Overview
10.10 Next Steps
10.1 Prerequisites
1.6 Next Steps
1.5 Verify Web Client Installation
1.4.2 Domain Configuration
1.4.1.2 Configure Web Client to Connect to Proxy
1.4.1.1 Security Configuration in PHP Proxy
1.4.1 Proxy Configuration
1.4 Configuration
1.3 Install Web Client on Web Server
1.2.2 Directory Structure and Working Directories
1.2.1 Extract Source Code
1.2 Web Client Installation Overview
1.1 Prerequisites
1. i2b2 Web Client Install
1. Deployment
1. Configure cell properties
Documentation Introduction
Getting Started
.bookmarks
1.1 About this Guide
1.2 Installation Process
1.3 Next Steps
2.1 Chapter Overview

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Installation Guide