Page History
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ACT V41OMOP metadata and CRC scripts along with OMOP views are now available for load into 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.
Ontology tables load process.
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Ontologies derived from visit_dimension or patient_dimension top folders will not have counts because of the way these terms are defined and cannot be rolled up. |
SAML Authentication
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ACT OMOP Totalnum Scripts
Totalnum Scripts (patient counting scripts) have been updated to improve the counter's performance on both 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.
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i2b2 users must have the DATA_AGG user permission to view the counts through the web client. |
Additional New
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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 the ontologies listed in table_access table records.
The stored procedure loops through the table_access 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
- Set up an i2b2 project with the ACT ontology.
- 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
- 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.
- Set up an i2b2 project with the ACT ontology.
- Download the scripts from https://github.com/i2b2/i2b2-synthea
- Run
create_synthea_table_<your dbServertype>.sqlin your project to create the Synthea tables. - Import the Synthea data you downloaded in step one into the Synthea tables in your project.
- Load the i2b2-to-SNOMED table in this repository into your project. https://www.nlm.nih.gov/healthit/snomedct/us_edition.html
- Click on the "Download SNOMED-CT to ICD-10-CM Mapping Resources" link to download. (You will need a UMLS account.)
- Unzip the file
- Import the TSV file into a table called SNOMED_to_ICD10 in your database.
- In Postgres and Oracle, follow the additional instructions in the comments at the top of
synthea_to_i2b2_<your dbServerType>.sqlto clean up the date formatting. - Run
synthea_to_i2b2_<your dbServertype>.sqlto convert Synthea data into i2b2 tables (this will truncate your existing fact and dimension tables!) - Replace references to
i2b2metadata.dboin 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.
| Note |
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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
- Download and extract the newinstall zip package from "Download Binary Distribution" in the top section of https://www.i2b2.org/software
- Edit the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\db.properties file 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 from the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act\scripts\<db type> folder and create and load ACT4 Ontology metadata tables
- You can now verify the new Ontology by logging into the webclient.
Security Enhancements
- i2b2 has been made more secure by addressing parameterization and other potential vulnerabilities found in an internal a Veracode scan.
- 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
Previously, i2b2 db upgrade 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 files. Details are on the i2b2 Upgrade Page here.
Changelog
Database Drivers
The JDBC drivers were updated to the following versions.
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Driver
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ojdbc8.jar
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postgresql-42.2.14.jar
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mssql-jdbc-9.2.0.jre8.jar
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New Version
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Oracle 21.5
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PostgreSQL 42.3.2
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MS Sql Server 9.2
Supported Db Server versions
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Server Type
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SQL Server
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Oracle
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Postgres
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Supported Version/s
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2012+ (tested with up to 2019)
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12g+ and 21c
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9 to 14
Supported software versions
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Application Type
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Java
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Wildfly
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Apache HTD
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Apache Ant
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Apache Axis2
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PHP
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Supported Version/s
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8 or 11
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17.0.1Final
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2.0 (RHEL 6) and 2.2 ( RHEL 7)
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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
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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
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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
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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
ACT Version-4 Ontology data load
Metadata scripts are now available to load the latest ACT Version-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
- Download and extract the newinstall zip package from "Download Binary Distribution" in the top section of https://www.i2b2.org/software
- Edit the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\db.properties file 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 from the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act\scripts\<db type> folder and create and load ACT4 Ontology metadata tables
- You can now verify the new Ontology by logging into the webclient.
Security Enhancements
- i2b2 has been made more secure by addressing parameterization and other potential vulnerabilities found in an internal a Veracode scan.
- 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
Previously, i2b2 db upgrade 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 files. Details are on the i2b2 Upgrade Page here.
Changelog
Database Drivers
The JDBC drivers were updated to the following versions.
Driver | ojdbc8.jar | postgresql-42.2.14.jar | mssql-jdbc-9.2.0.jre8.jar |
|---|---|---|---|
New Version | Oracle 21.5 | PostgreSQL 42.3.2 | MS Sql Server 9.2 |
Supported Db Server versions
Server Type | SQL Server | Oracle | Postgres |
|---|---|---|---|
Supported Version/s | 2012+ (tested with up to 2019) | 12g+ and 21c | 9 to 14 |
Supported software versions
Application Type | Java | Wildfly | Apache HTD | Apache Ant | Apache Axis2 | PHP |
|---|---|---|---|---|---|---|
Supported Version/s | 8 or 11 | 17.0.1Final | 2.0 (RHEL 6) and 2.2 ( RHEL 7) | 1.9.6 | 1.7.1 | 7.2.27 or higher |
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
| Web client |
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WEBCLIENT-359: packaging, old webclient default configuration admin-only |
| Core-server |
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i2b2 Database Changes
New Features and Improvements
DATA-16 I2b2 on OMOP Support for multiple crc zip file extraction using databuld.xml DATA-23 Support for multiple crc zip file extraction using databuld.xml DATA-18 Move OMOP totalnum counters to main branch in Github |
Bug Fixes
| Webclient | Core-server |
|---|
Bug Fixes
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| Webclient | Core-server |
|---|---|
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 |
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