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
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ACT
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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
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Version
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ACT Version-4 Ontology data load
Metadata scripts are now available to load the latest ACT Version-4 ontology into your i2b2 db schema.
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New Features and Improvements
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)
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WEBCLIENT-359: packaging, old webclient default configuration admin-only |
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i2b2 Database Changes
New Features and Improvements
| 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 folders16 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
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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 |
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