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Relevant Documentation:
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1.8.2-beta Release Notes
i2b2 1.8.2-beta Release introduces functionality of user-created data table definition and data download of limited data sets (LDS). The data request Data Request Management tool enhances the capabilites of the Project manager enables project managers to manage the data file exports. In addition, there are enhancements to the UI Admin console and UI Query tool and few bug fixesminor improvements in the Query tool, improvements to the fast "totalnum" patient counting scripts, and some bug fixes.
Highlight of Features
Top New Features
| Description | ||||
|---|---|---|---|---|
| Create data table for Export Extension for i2b2 |
| The Create Data Table tool allows the i2b2 user to create their own data table definitions with ontology variables and then request data exports in the Run Query dialog. | ||
| Data Request Manager Extension for i2b2 |
| The Data Request Manager tool allows an i2b2 manager to manage and process the user data requests. NOTE: In this beta release, clicking Create File on a custom-table data request in a Postgres database does not actually generate the file. | ||
| Enhanced Data Exporter (v1.8.1) |
| v1.8.1-style data exports (pre-defined tables defined by domain) can now be run and managed using the new tools. Manager users can manage and generate these data file exports using the Data Request Manager Console | ||
UI Query tool improvements | The new webclient has minor updates to improve the user experience | Enhanced Admin Console and UI Query tool | The new webclient has been enhanced with new features such as faster term search, streamlined icons, and an administration console. | |
| Digital Twin Bundle (distributed separately) |
| Tools for computing loyalty cohorts and computational phenotypes in i2b2. | ||
Bug fixes |
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Community-Contributed Features
Contributor
Description
Detailed Documentation on New Features
Data Exporter extension for i2b2
i2b2 data exporter functionality is now enhanced the enable 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. users to create their own Data table definitions from ontology elements. The data table definitions are displayed as options that can be selected in the Run Query dialog. Users can submit multiple data requests for with a query. The Manager user can manage the data requests and generate data files using a Data Request Manager console. 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 creates Data table definition using the Create Data Table tool, using desired Ontology elements
- User runs a regular i2b2 query, checking the desired User-created Data request breakdown option option(s) 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 filesviews the data requests using the Data Request Manager Console.
- Manager user generates the data export files using the Data Request Manager Console.
- The generated export flat data 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).
Changelog
Database Drivers
The JDBC drivers were updated to the following versions.
Server Type | oracle | Postgresql | mssql |
|---|---|---|---|
Driver Version | ojdbc8.jar | postgresql-42.7.1.jar | mssql-jdbc-12.4.2.jre8.jar |
Supported Db Server versions
Server Type | SQL Server | Oracle | PostgresSQL |
|---|---|---|---|
Supported Version/s | 2012+ (tested with up to 2022) | 23.3 | 9 to 14 |
Supported software versions
Application Type | Java | Wildfly | Apache HTD | Apache Ant | Apache Axis2 | PHP | |
|---|---|---|---|---|---|---|---|
Supported Version/s | 8 or 11 | 17 | 3417.0.1Final | 2.0 (RHEL 6) and 2.2 ( RHEL 7) | 1.9.61.7.1 | 2 | 7.2.27 or higher |
Supported Operating Systems
Rocky linux 8 and 9, CentOS versions CentOS versions 7
Windows 2016 -2019
- There is a new 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
| Web client |
|---|
WEBCLIENT-368 1.8.2 Webclient update |
| Core-server |
CORE-456 Data Export: agg table CORE-455 Data Export: Request Management admin tool CORE-451 Enhanced Data Export - download file generation CORE-459 updrade to wildfly 34 with axis2 version2 CORE-460 Upgrade to JAVA 17 CORE-454 Upgrade Spring jar to version 6 CORE-447 Update JDBC drivers CORE-458 Software maintainence - drivers, libraries CORE-445 java code folder structure for 1.7 should be changed to refer to 1.8.2 |
i2b2 Database Changes
New Features and Improvements
Bug Fixes
| Core-server / Data | |
|---|---|
CORE-450 html injection in Queryname and workplace CORE-249 Search by code fails ungracefully |
Notes for Developers
For Java 11 install, if 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 1117.
Note about the beta release
In this beta release, clicking Create File on a custom-table data request in a Postgres database does not actually generate the file.
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