When upgrading to the v1.7.13 webclient, you will notice that i2b2_config_data.js has been renamed to i2b2_config_data.json. Your old configuration will still work with this new file name, but you will need to:
There are also new optional parameters, documented below and in 1.4.2 Domain Configuration. |
Description | |
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SAML Authentication | |
User Account Registration Tool | |
ACT Ontology v4 | |
Improved patient counting scripts ("totalnum") | |
Synthea SyntheticMass dataset in i2b2 format | |
Simplified database upgrade method | |
log4J upgrade (to address security concerns) | |
Code changes to address security vulnerabilities | |
Bugfixes |
Contribution | Contributor | |
SAML Authentication | Kevin Bui | i2b2 now includes support for SAML-based enterprise authentication via an institutional Identity Provider. See more information below. |
Ability to specify user parameter defaults | Michael Horvath | This change is meant to allowing user params to take precedence over hive params. Currently, it's the other way around. |
LDAP UPN Support | Michael Horvath | Active Directory enables other methods of binding which are more flexible besides just using the distinguished name. https://docs.microsoft.com/en-us/openspecs/windows_protocols/ms-adts/6a5891b8-928e-4b75-a4a5-0e3b77eaca52. This change is to enable binding the the User Principle Name form, which is very convenient when the distinguished names for users is not easily available (OU by department, etc.). |
API to get all children of an ontology node | Kevin Bui | The metadata GetChildren API call, which returns information on the children of an ontology node, can now be configured to return multiple levels of children (e.g., children, children's children, etc.). This is done by specifying the numLevel parameters. By default, the function assumes numLevel = 1 and will return the direct descendants of the concept, which is one level of children. When the numLevel = -1 the function will return ALL descendants of the concept, otherwise the function will return up to and including the number of levels specified by numLevel (eg. numlevel=2 returns two levels of descendants, numLevel=4 returns four levels of descendants). |
Totalnum Counter Performance Improvements | Darren Henderson University of Kentucky | Performance enhancements on SQL Server totalnum counting to not unnecessarily recompute temp tables. |
ACT v4 Postgres bugfixes | Ambreen Zaver | Bugfixes in time interval calculation (for age and age-at-visit) in ACT v4 ontology for Postgres. |
TODO - Documentation draft is here - https://github.com/kvb2univpitt/i2b2-saml-demo/tree/main/doc/user_registration
There are two paths: SAML and local
registrationMethod | Y | String | NEW 1.7.13! Defines an information source for the new user registration tool. (If showRegistration is true, this parameter must be present.)
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i2b2 now includes support for SAML-based enterprise authentication via an institutional Identity Provider. To configure this, you need to do the following:
loginType = "federated" see 1.4.2 Domain Configuration
Create a user for each SAML-authenticating user with the user name set to the SAML EPPN. Create a pm_user_param setting authentication_method to SAML. Alternately, configure the user registration tool for federated mode, and it will allow users to create an i2b2 account if they have a valid SAML authentication. (Such users will still not have access to any projects until the administrator adds projects to his/her profile.)
Detailed documentation is in the install docs. See SAML setup. Note that this requires site-specific information from your institution's SAML Identity Provider. (DOCUMENTATION IS NOT CORRECTLY IMPORTED FROM KEVIN'S VERSION - https://github.com/kvb2univpitt/i2b2-saml-demo/tree/main/doc/saml_setup)
Totalnum Scripts (patient counting scripts) have been updated to improve the counter performance on both many 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.
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.
Oracle:
begin
RUNTOTALNUM('observation_fact','i2b2demodata');
end;
You can optionally include a table named 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:
exec RunTotalnum 'observation_fact','dbo','@'
Parameters are: 1) the observation table name (for multi-fact-table setups), 2) the schemaname, 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:
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 wel
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. Note that 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).
i2b2 users must have the DATA_AGG user permission to view the counts through the web client. |
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 date.
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.
Insert_Concept_FROMTableAccess is designed to populate concept_dimenison table using Table_access table records.
The stored procedure loops through the table_access and inserts values from corresponding c_table_name metadatatable which have
c_tablename column value as 'concept_dimension'
Example usage: exec Insert_Concept_FROMTableAccess
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:
create_synthea_table_<your dbServertype>.sql
in your project to create the Synthea tables.synthea_to_i2b2_<your dbServerType>.sql
to clean up the date formatting.synthea_to_i2b2_<your dbServertype>.sql
to convert synthea data into i2b2 tables (this will truncate your existing fact and dimension tables!)i2b2metadata.dbo
in the script. Use the database and schema where your ACT ontology tables are.Metadata scripts are now available to load the latest ACT Version-4 Ontology into your i2b2 db schema
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:
Loading concept_dimension: You can run Insert_Concept_FROMTableAccess stored procedure on your db located in edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/<db type>/ which will iterate through table_access and load concept_dimension with data corresponding to the c_table_name metadata table
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:
In data folder\Release_1-7\Upgrade\ run the ant commands under each individual cell subfolder as below. | |
Upgrade From Build | Upgrade to Latest build |
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1.7.09c | In the Crcdata folder run the following ant command: 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 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-09c upgrade_hive_tables_release_1-7-10 upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata 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_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-09c upgrade_pm_tables_release_1-7-10 upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12 |
1.7.10 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-10 upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-10 upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-10 upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12 |
1.7.11 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12 |
1.7.12 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-12 |
The JDBC drivers were updated to the following versions.
Driver | ojdbc8.jar | postgresql-42.2.5.jar | mssql-jdbc-7.0.0.jre8.jar |
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New Version | Oracle 21.5 | PostgreSQL 42.3.2 | MS Sql Server 9.2 |
Server Type | SQL Server | Oracle | Postgres |
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Supported Version/s | 2012+ (tested with up to 2019) | 12g+ and 21c | 9 to 14 |
Application Type | Java | Wildfly | Apache HTD | Apache Ant | Apache Axis2 | PHP |
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Supported Version/s | 8 or 11 | 17.0.0 | 2.4.17 or higher | 1.9.6 | 1.7.1 | 7.2.27 or higher |
Webclient | Core-server |
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Webclient | Core-server |
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Database updates |
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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.