1.8.1a Release Notes

i2b2 1.8.1a Release builds on the rewritten web interface introduced in 1.8 with new features and new administration tools, it introduces a powerful new data export module, and it adds core support for the OMOP data model on Postgres databases (adding to MSSQL and Oracle databases in 1.8). 

This release includes fix for breakdown queuing for SQL and Postgres queries when the SQL breakdowns take a long time to finish after the patientset completes - references CORE-443

Highlight of Features

Top New Features

Community-Contributed Features

Detailed Documentation on New Features

Data Exporter extension for i2b2

i2b2 can now export patient data for a patient set. The workflow involves breakdowns in the webclient, which allow users to request exports and data managers to generate exports. The export types and options are fully configurable in the database. Detailed documentation on set up can be found here: Data Exporter Set-up

The below steps describe the overall process:

• User logs into i2b2 webclient and runs a regular i2b2 query, checking the desired Data request breakdown option when running the query.
• E-mail is sent to the data manager and the User, informing them that the user's data request has been made.
• The manager logs in and reruns the user query with the Data Export breakdown selection to generate the export flat files.
• The generated export flat file is stored in a configurable location on the i2b2 server.
• An e-mail is sent to the manager confirming the file extract and how to access the files (which can be shared with the requester).

Steps to upgrade:

First, install the new war file. Next, upgrade the database. Because the upgrade requires loading some new content from the NewInstall, we have created an ant target to upgrade the data tables: upgrade_tables_release_1-8-0 This should be run from Upgrade/CrcData, e.g., ant f data_build.xml upgrade_tables_1 8-0 

Detailed upgrade instructions can be found here: Upgrade to version 1.8.1

ACT - V4.1 Ontology

The V4.1 Ontology includes  19 ontologies- 3 new and 11 updated and 5 unchanged

Metadata and CRC zip files are provided to load the latest ENACT Version-4.1 ontology into your db schema using ANT scripts.

The CPT4 ontology table is not included with i2b2 due to AMA restrictions on redistribution of CPT code information. Contact the ENACT team to get a copy if your institution is an AMA member.

ACT V4.1 data load process

1. Download and extract the newinstall zip package from "Download Binary Distribution" in the top section of https://www.i2b2.org/software
2. Edit the  edu.harvard.i2b2.data\Release_1-8\NewInstall\Metadata\db.properties file to update the project properties to 'ACT' ; db.project=ACT
3. From the edu.harvard.i2b2.data\Release_1-8\NewInstall\Metadata folder, run the ant command: ant -f data_build.xml db_metadata_load_data. This will execute the SQL scripts from the edu.harvard.i2b2.data\Release_1-8NewInstall\Metadata\act\scripts\<db type> folder to create and load the metadata tables 
4. From the edu.harvard.i2b2.data\Release_1-8\NewInstall\crcdata folder, run the ant command: ant -f data_build.xml db_demodata_load_data. This will execute the SQL scripts from the edu.harvard.i2b2.data\Release_1-8NewInstall\crcdata\act\scripts\<db type> folder to create and load the concept_dimension 
5.  Run the scripts from the edu.harvard.i2b2.data\Release_1-8\NewInstall\Metadata \<dbtype>\scripts folder to load the Schemes, Table_access tables
6. You can now verify the new Ontology by logging into the webclient

Additional details on the ontology are available at this link.

ACT i2b2 on OMOP for Postgres database

ACT i2b2 on OMOP functionality uses ACT Ontology in the front-end and enables the i2b2 Software to run against Postgres database that uses the OMOP CDM architecture. 

For enabling use of an OMOP database with i2b2, follow the instructions in the install guide for a new install of i2b2 using the i2b2-OMOP install option. The documentation here will guide you through this process. i2b2-on-OMOP With ENACT-OMOP Ontology v4.1

For historical reference on old 2018 OMOP installation , refer to OMOP Home on i2b2 Community Wiki

Changelog

Database Drivers

The JDBC drivers were updated to the following versions.

Supported Db Server versions

Supported software versions

Supported Operating Systems

 Rocky linux 8 and 9, CentOS versions  7

Windows 2016 -2019

• There is a new PHP install process for IIS in the i2b2 install guide: 2.5.3.2 PHP for Windows
  

Unofficially, MacOS and other flavors of Linux are likely to work.

i2b2 Server and Client Changes

New Features and Improvements

i2b2 Database Changes

New Features and Improvements

Bug Fixes

Notes for Developers

• For Java 11 install, if you change the xsd (REST API message definitions), then you will need to regenerate gensrc via JAXB in Java 8. In the i2b2-core cell directory for which you're regenerating the XSD-Java, run the ant target "jaxb_gen" on Java 8 and then build as usual using Java 11.
• For developers that need to recompile the new admin tool in the webclient, remove the package-lock.json file from i2b2-webclient/plugins/edu/harvard/catalyst/admin-tool/ before compiling. This will ensure you have the latest non-breaking changes for all third-party libraries used in building the tool, including security fixes.