1.7.13 Release Notes

Highlight of Features

Frontend Features

LOTS OF TABS!

P2

Community-Contributed Features

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.

a. Run the ant command to execute the data_build.xml file with below specified target 

• 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   

b. Execute the RunTotalNum  stored procedure manully against your database in from a sql Client. 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
                                               

1. 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:

1. Create db Schema with name labeled synthea
2. 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.

1. Download latest stored procedures from github
2. Execute the stored procedures on your database to create the patientnum and encounternumbers
3. Download SyntheticMass Data, Version 2 (24 May, 2017)
4. Set up an i2b2 project with the ACT ontology.
5. Run create_synthea_table_sqlserver.sql in your project to create the Synthea tables.
6. Import the Synthea data you downloaded in step one into the Synthea tables in your project.
7. Load the i2b2-to-SNOMED table in this repository into your project. https://www.nlm.nih.gov/healthit/snomedct/us_edition.html
8. Run synthea_to_i2b2_sqlserver.sql to convert synthea data into i2b2 tables (this will truncate your existing fact and dimension tables!)
   • Replace references to i2b2metadata.dbo in the script. Use the database and schema where your ACT ontology tables are.

ACT Version-4 Ontology data load

Metadata scripts are now available to load the latest ACT Version-4  Ontology into your i2b2 db schema

ACT4 dataload process:

• Download the newinstall  zip package from https://www.i2b2.org/software/download.html?d=452
• Extract the  metadata\act folder from the downloaded zip folder
• Replace edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act  folder with extracted new act folder
• Edit the  db.properties file in your metadata folder  to update the project properties to 'ACT'db.project=ACT
• From the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata folder, run the ant command: ant -f data_build.xml db_metadata_load_data
• This will execute the  SQL scripts form the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act folder  to create the new ACT4 Ontology tables
• and loads the corresponding metadata. 
• You can now verify the new Ontology  by logging into the webclient.

The following command will load the corresponding concept_dimension data of the Onbtology tables  that will enable you to run queries in the webclient

From a sql Client>select 'insert into concept_dimension select c_dimcode AS concept_path, c_basecode AS concept_cd, c_name AS name_char, null AS concept_blob, update_date AS update_date, download_date as download_date, import_date as import_date, sourcesystem_cd as sourcesystem_cd, 1 as upload_id from '
+c_table_name+' where m_applied_path=''@'' and c_tablename=''CONCEPT_DIMENSION'' and c_columnname=''concept_path'' and c_visualattributes not like ''%I%'' and (c_columndatatype=''T'' or c_columndatatype=''N'') and c_synonym_cd = ''N'' and (m_exclusion_cd is null or m_exclusion_cd='''') and c_basecode is not null and c_basecode!='''''
from <your_dbschema>.dbo.TABLE_ACCESS where c_visualattributes like '%A%'

Improved db Upgrade Process

Currently i2b2 db upgrade is a multi-step process of running upgrade scripts and stored procedures. This release provides a set of upgrade scripts which will perform the complete db upgrade.

based on your current build version.

For example: Following Ant command will upgrade your db instance from 1.7.09c to latest version.

>ant -f data_build.xml upgrade_table_release_1-7-09c upgrade_table_release_1-7-10 upgrade_table_release_1-7-11 upgrade_table_release_1-7-12

Steps to Perform db upgrade:

• Backup your existing data folder
• Copy all the folders from the extracted download data folder   into your existing  data Upgrade folder
             Example:  Downloads\2b2core-upgrade-1712a\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\. This will replace
             existing Crcdata, Hivedata, Metadata, PMdata folders.
   Alternative to above step, navigate to the edu.harvard.i2b2.data\Release_1-7\Upgrade\   directory of your extracted folder
• Copy the db.properties files from your back up into the respective locations(namely Crcdata, Hivedata, Metadata, PMdata )
• Open the command prompt and navigate to  cell folders and run the following upgrade ant commands on your i2b2 database instance, where {db}      can  be Oracle, sqlserver or postgresql.
  Alternative to above Step, you can run individual SQL scripts on your db instance in place of  ant commands.

Changelog

Database Drivers

The JDBC drivers were updated to the following versions.

Supported Db Server versions

Supported software versions

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 improve 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.