1.7.13 Release Notes
Highlight of Features
Frontend Features
LOTS OF TABS!
P2
Community-Contributed Features
Contribution | Contributor | |
Backend Features
Improved Totalnum Scripts
Totalnum Scripts for Postgres and MSSQL have been updated to improve the Totalnum counter performance on very large(>1.5 million) ontology elements such as ACT medications, Debug messages have also been added for troubleshoot purposes
Totalnum Scripts Setup
- In the Release_1-7/NewInstall/Metadata/ run the ant script to create the stored procedures. ant -f data_build.xml create_metadata_procedures_release_1-7
- Run the stored procedures on your database. This can be done in two ways.
- POSTGRESQL : ant -f data_build.xml db_metadata_run_total_count_postgresql
- ORACLE : ant -f data_build.xml db_metadata_run_total_count_oracle
- SQL SERVER : ant -f data_build.xml db_metadata_run_total_count_sqlserver
- Execute the RunTotalNum stored procedure on your database. This can take several hours. Example Usage:
Oracle:
begin
RUNTOTALNUM('observation_fact','i2b2demodata');
end;
Note: If you get the error as: ERROR at line 1: ORA-01031: insufficient privilege, then run the command:
grant create table to (DB USER)
SQL server:
exec RUNTOTALNUM
PostgreSQL:
select RUNTOTALNUM('observation_fact','public')
– (replace 'public' by the schema name for the fact table)
– If using a schema other than public for metadata, you might need to run "set search_path to 'i2b2metadata','public' " first as well
- When finished, verify it is complete by checking that c_totalnum columns in your ontology tables contain numbers (not nulls).
These total counts will be visible in the ontology browser in the web client.
I2b2-Synthea data Load
A new option is now available for loading Synthea data files into i2b2. Synthetic patient data generated by Synthea is hosted on SyntheticMass..The Synthea sample files have been converted to i2b2-ACT format. The zipped data files can be downloaded from https://github.com/i2b2/i2b2-synthea
Synthea Load Process:
- Create db Schema with name labeled synthea
- Load Synthea data from the sample data files provided
- Download the zipped flat files and extract to them to a local directory
- Using SSMS, import the sample obs file into obvseration_fact table
- Import the sample obs-pat file into patient dimension table.
- Download latest stored procedures from github
- Execute the stored procedures on your database to create the patientnum and encounternumbers.
Improved db Upgrade Process
Currently i2b2 db upgrade process is tedious involving multiple manual steps of running upgrade scripts and stored procedures. This release provides a single upgrade script which will perform the complete db upgrade.
Changelog
Database Drivers
The JDBC drivers were updated to the following versions.
Driver | New Version |
ojdbc8.jar | Oracle 12.2.0.1 |
postgresql-42.2.5.jar | PostgreSQL 42.2.5 |
mssql-jdbc-7.0.0.jre8.jar | MS Sql Server 7.0.0 |
Supported Db Server versions
Type | Version |
SQL Server | 2012+ |
Oracle | 12g+ |
Postgres | 9 |
Supported software versions
Application | Version |
Java | 8 |
java | 11 |
Wildfly | 17.0.0 |
Apache HTD | 2.4.17 or higher |
Apache Ant | 1.9.6 |
Apache Axis2 | 1.7.1 |
PHP | 7.2.27 or higher |
i2b2 Database Changes
New db updates include
- DATA-7 QT_PATIENT_SET_ENC_COLLECTION should be a bigint
- DATA-5 Synthea i2b2 data
- DATA-8 Synthea data load test from Github files
- DATA-6 i mprove i2b2 db upgrade process
i2b2 Server and Client Changes
New Features and Improvements
- CORE-389 Totalnum performance improvements
- CORE-399 Oracle index hints must use the table alias
- CORE-400 CORE-389 Show totalnums in top-level folders
- CORE-382 Username / password errors should not specify which had the problem
- WEBCLIENT-334 Provide tabs for major plugins and temporal query
- WEBCLIENT-344 Cleanup Analysis Tools list of Plugins to only Supported Items
- WEBCLIENT-325 Wayne's improvements to hierarchical find-by-name
- WEBCLIENT-320 Provide REFRESH ALL context menu in FindTerms panel
- WEBCLIENT-307 Drag and drop in term info panel
- WEBCLIENT-306 Beth Israel contribution: commas in counts, query option infrastructure
- WEBCLIENT-342 switch response status check from "OK" to 200 to handle lab value pop up in http/2 protocols
- CORE-402 Fix Veracode identified Security flaws in i2b2 Server-Side Code
- WEBCLIENT-343 Fix Veracode identified Security flaws in i2b2Webclient Code
- CORE-404 Adding support for JDK 11. Now including the gensrc due to jaxb has been removed.
Bug Fixes
- WEBCLIENT-341 Toggle between <and > group panel buttons resulting in blank QueryResults view
- WEBCLIENT-319 FindTerms- exceeding more than 200(default) return count - displaying server error
- WEBCLIENT-316 Admin tool unresponsive in IE11
- WEBCLIENT-305 Occasionally items in Find Terms by name are not draggable
- WEBCLIENT-304 Hierarchical levels in Find Terms might not work in ontologies that have extra backslashes
- WEBCLIENT-294 Webclient Reports "QUERY CANCELLED" While Query Is Still Running
- WEBCLIENT-291 Date constraints popup OK button disabled, maintains new date if canceled
- WEBCLIENT-196 Temporal query more than 2 events is not populating query name in the query name textbox and displaying new event added msg
- WEBCLIENT-156 switching from events grouppanel view to 'same financial encounter' selection is not switching to original concept group panel view
- CORE-282 Error returned when obfuscated user is locked out
- CORE-281 Query continues to run after user receives lockout message
Notes for Developers
For Java 11 install, if you change xsd, then modify the gensource.