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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.
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Highlight of Features
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Oracle: | begin You can optionally include a table name if you only want to count one ontology table (this IS case sensitive): Note: If you get the error as: ERROR at line 1: ORA-01031: insufficient privilege, then run the command: |
SQL server: | 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: | 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 |
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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>.sql
in 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>.sql
to clean up the date formatting. - Run
synthea_to_i2b2_<your dbServertype>.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.
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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 scripts and stored procedures from data_build.xml files. Details are on the i2b2 Upgrade Page here.
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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
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Webclient | Core-server |
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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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