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Info Box
titleImportant links

Downloads:

Documentation:


Warning
titleIssue Loading CRC Stored Procedures on MSSQL

Note that we have discovered an issue loading the CRC Stored Procedures on SQL Server and have found a workaround. Please be sure to read the updated content of Step 3.4.4 Create Crcdata Stored Procedures before performing this step.

1.7.13 Release Notes

i2b2 1.7.13 offers support for SAML federated login, enhanced security due to improvements found via an internal Veracode scan, a client-based user registration tool, support for Synthea synthetic data for testing, and a variety of other bugfixes and performance improvements. i2b2 1.7.13 has been tested with SHRINE 3.2.1.  

UI Button
colorred
sizesmall
iconstar
titleSHRINE Approved
urlhttps://open.med.harvard.edu/wiki/display/SHRINE/SHRINE-i2b2+Compatibility+Matrix

Table of Contents

Highlight of Features

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There is a new user registration tool that can be enabled in the webclient. It allows users to request an i2b2 account that can then be activated by an administrator. It supports manual entry of user information through the form shown below, or automatic population of user information through SAML.

Documentation on this new feature is here: 6.5a i2b2 Webclient User Registration

local registration

SAML Authentication

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i2b2 now includes support for SAML-based enterprise authentication via an institutional Identity Provider.

Detailed setup instructions are in Chapter 8 of the Installation Guide.

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Improved Totalnum Scripts

Totalnum Scripts (patient counting scripts) have been updated to improve the counter's performance on both many multiple ontology tables and very large(>1.5 million) ontologies  such as ACT medications. Debug messages have also been added for troubleshooting and profiling purposes. Support for multiple fact tables has been added and bugfixes have been made.

Totalnum Scripts Setup

  1. If upgrading, create the totalnum and totalnum_report tables. In Release_1-7/Upgrade/Metadata, run the ant upgrade script.
    ant -f data_build.xml upgrade_tables_release_1-7-12a
  2. In  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 
  3. Set privileges: If using multiple schemas, the stored procedure should be run from the metadata schema. Make sure the stored procedure can read the tables in the crcdata schema (observation_fact, visit_dimension, patient_dimension) and can both read an update ontology tables in the metadata schema (including table_access). 
  4. If using multiple fact tables, the recommended approach is to create a fact table view as the union of all your fact tables. (This is essentially going back to a single fact table, but it is only used for totalnum counting. This is needed to correctly count patients that mention multiple fact tables within a hierarchy.)
        e.g., 
       create view observation_fact_view as
       select * from CONDITION_VIEW 
       union all
       select * from drug_view
    
If running the counting script in SQL Server, add the wildcard flag, to ignore multifact references in the ontology:
      e.g. exec RunTotalnum 'observation_fact_view','dbo','@','Y'
    This is automatically accounted for in the other database platforms.
Note this approach does not work if you have conflicting concept_cds across fact tables.
  5. Run the stored procedures on your database. This can be done in two ways:
    • 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   
    • Execute the RunTotalNum  stored procedure manually against your database from a SQL Client. This can take several hours for large databases or large ontologies.  Examples are below.
     

Running the totalnum stored procedure directly


Oracle:     

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begin
    RUNTOTALNUM('observation_fact','i2b2demodata');
end; 

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You can optionally include a table name if you only want to count one ontology table (this IS case sensitive):
begin
  runtotalnum('observation_fact','i2b2demodata','I2B2');
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: 

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exec RunTotalnum 'observation_fact','dbo','@'
Parameters are: 1) the observation table name (for multi-fact-table setups), 2) the schema name, 3) a single table name to run on a single ontology table or '@' to run on all, and 4) and a wildcard flag that will ignore multifact references in the ontology if 'Y'
PostgreSQL: 

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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

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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.

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Parent folders will get counts (of all patients with facts in the leaves) except for ontology folders derived from visit_dimension or patient_dimension. These cannot be rolled up because of the way these terms are defined in the ontology. They will have no count at all (not a zero).

Info

i2b2 users must have the DATA_AGG user permission to view the counts through the web client.

Additional New Stored Procedures

Age In Years Updater

When the CRC data is installed via ant, a new SQL script updates the age_in_years_num in the patient dimension based on the birth dates of the sample patients. As a reminder, this load process can be triggered with ant -f data_build.xml db_demodata_load_data in the CRC directory of NewInstall.

Concept Dimension Updater

Insert_Concept_FROMTableAccess  is designed to populate concept_dimenison table using Tablethe ontologies listed in table_access table records.
The stored procedure loops through the table_access  and  and inserts values from each metadata table (specified in the c_table_name column), when
c_dimtablename is set to 'concept_dimension'
Example usage: exec Insert_Concept_FROMTableAccess

I2b2-Synthea data Load

Synthetic patient data generated by Synthea can be loaded into i2b2. The Synthea SyntheticMass sample files have been converted to i2b2-ACT format, and scripts to load Synthea data from scratch are available here: https://github.com/i2b2/i2b2-synthea

Synthea Load Process

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  1. Set up an i2b2 project with the ACT ontology.
  2. Either download the SyntheticMass 63k sample in i2b2 format from https://github.com/i2b2/i2b2-synthea/blob/main/syntheamass_63K_sample.zip, or follow the instructions below to load any Synthea dataset from scratch. This information can also be found on the Synthea-i2b2 Community Project page.

Loading Synthea data from scratch
  1. Download SyntheticMass Data, Version 2 (24 May, 2017) 
    • All data sets (1k, COVID 10k, COVID 100k) have been verified to work EXCEPT the 100k patients in the large SyntheticMass Version 2 download. 
    • The 100k patients in the large SyntheticMass Version 2 download needs an extra step to delete invalid records before import. In this case, download synthea_cleanup.pl to your disk, and then run "synthea_cleanup <directory-for-synthea-csv-files>" The fixed csv files will be in <directory-for-synthea-csv-files>/fixcsv.2.
  2. Set up an i2b2 an i2b2 project with the ACT ontology.
  3. Download the scripts from https://github.com/i2b2/i2b2-synthea)
  4. Run create_synthea_table_<your dbServertype>.sql in your project to create the Synthea tables.
  5. Import the Synthea data you downloaded in step one into the Synthea tables in your project.
  6. Load the i2b2-to-SNOMED table in this repository into your project. https://www.nlm.nih.gov/healthit/snomedct/us_edition.html
  7. Click on the "Download SNOMED-CT to ICD-10-CM Mapping Resources" link to download. (You will need a UMLS account.)
  8. Unzip the file
  9. Import the TSV file into a table called SNOMED_to_ICD10 in your database.
  10. In Postgres and Oracle, follow the additional instructions in the comments at the top of synthea_to_i2b2_<your dbServerType>.sql to clean up the date formatting.
  11. Run synthea_to_i2b2_<your dbServertype>.sql to convert synthea Synthea data into i2b2 tables (this will truncate your existing fact and dimension tables!)
  12. 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 4 ontology into your i2b2 db schema.

Note

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

ACT4 data load process

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  1. Download and extract the newinstall  newinstall zip package from "Download Binary Distribution" in the top section of https://www.i2b2.org/software/download.html?d=452
  2. Extract the  metadata\act folder from the downloaded zip folder
  3. Replace
  4. Edit the  edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act  folder with extracted new act folderEdit the  db.properties file in your metadata folder  file  to update the project properties to 'ACT' ; db.project=ACT
  5. 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
    1. This will execute the  SQL scripts from the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act\scripts\<db type> folder and create and load ACT4 Ontology metadata
    tables  
    1. tables 
  6. You can now verify the new Ontology  by logging into the webclient.

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  1. i2b2 has been made more secure by addressing parameterization and other potential vulnerabilities found in an internal a Veracode scan.
  2. Log4J has been upgraded to the latest version. The following jars are updated in lib/axis2.war/WEB-INF/lib the folder:
    • log4j-api-2.17.1.jar
    • log4j-core-2.17.1.jar
    • log4j-jcl-2.17.1.jar

Improved db Upgrade Process

Currently Previously, i2b2 db upgrade is was a multi-step process of running upgrade SQL scripts and stored procedures individually on the db instance. This release simplifies the process of running the table upgrade SQL scripts and stored procedures from data_build.xml .

Steps to Perform db upgrade:

  1. Backup your existing data folder
  2. Copy all the folders created by extracting the latest version into your existing  data Upgrade folder. This will replace existing Crcdata, Hivedata, Metadata, PMdata folders. Example:  Downloads\i2b2core-upgrade-1713\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\.
  3. Copy the db.properties files from your back up into the respective locations (namely Crcdata, Hivedata, Metadata, PMdata )
  4. Open the command prompt and navigate to each cell folder 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.
  5. In datafolder\Release_1-7\Upgrade\  run the ant commands under each individual cell folder as below

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1.7.09c

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In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-09c upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a

In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10  upgrade_tables_release_1-7-12a

In the Pmdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-09c  

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1.7.10

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In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a

In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-12a

1.7.11

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In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11  upgrade_table_release_1-7-12a

In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

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In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

Finally,  upgrade your db instance with stored procedures. Details are here

files. Details are on the i2b2 Upgrade Page here.

Changelog

Database Drivers

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Driver

ojdbc8.jar

postgresql-42.2.14.jar

mssql-jdbc-89.2.20.jre8.jar

New Version

Oracle 21.5

PostgreSQL 42.3.2

MS Sql Server 9.2

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Supported Operating Systems

CentOS versions 6 (deprecated) or 7 (highly recommended) 

Windows 7-2019

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

i2b2 Server and Client Changes

New Features and Improvements

Core-serverwebclient 

CORE-399 Oracle index hints must use the table alias 

CORE-382 Username / password errors should not specify which had the problem

CORE-402 Fix Veracode identified Security flaws in i2b2 Server-Side Code

CORE-404 Adding support for JDK 11. Now including the gensrc due to jaxb has been removed. 

CORE-413 FetchAllChildren 

CORE-414 SAML (server side)

CORE-415 Log4j upgraded to v2

CORE-416 User parameter precedence change (contributed by Michael Horvath)

CORE-417 LDAP UPN support (contributed by Michael Horvath)

CORE-405 Upgrade JDBC Drivers 

CORE-412 Disable login to agg service account

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-353 SAML and user registration tool (client side) 

i2b2 Database Changes

New Features and Improvements

DATA-7 QT_PATIENT_SET_ENC_COLLECTION should be a bigint

DATA-14 Synthea i2b2 data 

DATA-6 improve i2b2 db upgrade process

DATA-12  Stored procedure to update concept dimension

DATA-11 Age in years updater during demodata install

DATA-9 ACT v4 ontology

DATA-13 Postgres time interval corrections in ACT v4 demographics ontology

CORE-389 Totalnum performance improvements 

CORE-394 Obfuscated totalnum reporting table

CORE-398 Multifact support for totalnums  

CORE-400 Show totalnums in top level folders 

Bug Fixes

Webclient Core-server

WEBCLIENT-351 Obfuscated User Not Showing Graph

WEBCLIENT-342 switch response status check from "OK" to 200 to handle lab value pop up in http/2 protocols

WEBCLIENT-335 temporal query in webclient with no anchoring events not running

WEBCLIENT-350  Unable to drag items in workplace 

WEBCLIENT-294 Webclient Reports "QUERY CANCELLED" While Query Is Still Running 

WEBCLIENT-354 Removed broken context menu in Find Previous Queries

CORE-418 Local timestamps in sessions on Oracle - appserver /db server in diff time zones 

CORE-282 Error returned when obfuscated user is locked out 

CORE-281 Query continues to run after user receives lockout message 

CORE-399 use alias for index hint  

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 target "jaxb_gen" on Java 8 and then build as usual using Java 11.

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