Contribution | Contributor | |
Ability to specify user parameter defaults | Michael Horvath Wake Forest | This change is meant to allowing user params to take precedence over hive params. Currently, it's the other way around. |
i2b2 now includes support for SAML-based enterprise authentication via an institutional Identity Provider. To configure this, you need to configure SimpleSAMLPHP (now included with i2b2) to talk to your institution's Identity Provider. Follow these guides:
1) Setting up Apache and simplesamlphp: https://simplesamlphp.org/docs/latest/simplesamlphp-install.html
2) Configure the service provider and add an identity provider: https://simplesamlphp.org/docs/latest/simplesamlphp-sp.html
Totalnum Scripts for Postgres and MSSQL have been updated to improve the Totalnum counter performance on very large(>1.5 million) ontology elements such as ACT medications, Debug messages have also been added for troubleshoot purposes
Totalnum Scripts Setup
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
Run the stored procedures on your database. This can be done in two ways.
a. Run the ant command to execute the data_build.xml file with below specified target
b. Execute the RunTotalNum stored procedure manully against your database in from a sql Client. This can take several hours. Example Usage:
Oracle:
begin
RUNTOTALNUM('observation_fact','i2b2demodata');
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
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
These total counts will be visible in the ontology browser in the web client.
A new option is now available for loading Synthea data files into i2b2. Synthetic patient data generated by Synthea is hosted on SyntheticMass..The Synthea sample files have been converted to i2b2-ACT format. The zipped data files can be downloaded from https://github.com/i2b2/i2b2-synthea
Synthea Load Process:
create_synthea_table_sqlserver.sql
in your project to create the Synthea tables.synthea_to_i2b2_sqlserver.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
ACT4 dataload process:
The following command will load the corresponding concept_dimension data of the Onbtology tables that will enable you to run queries in the webclient
From a sql Client>select 'insert into concept_dimension select c_dimcode AS concept_path, c_basecode AS concept_cd, c_name AS name_char, null AS concept_blob, update_date AS update_date, download_date as download_date, import_date as import_date, sourcesystem_cd as sourcesystem_cd, 1 as upload_id from '
+c_table_name+' where m_applied_path=''@'' and c_tablename=''CONCEPT_DIMENSION'' and c_columnname=''concept_path'' and c_visualattributes not like ''%I%'' and (c_columndatatype=''T'' or c_columndatatype=''N'') and c_synonym_cd = ''N'' and (m_exclusion_cd is null or m_exclusion_cd='''') and c_basecode is not null and c_basecode!='''''
from <your_dbschema>.dbo.TABLE_ACCESS where c_visualattributes like '%A%'
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 |
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 | New Version |
ojdbc8.jar | Oracle 12.2.0.1 |
postgresql-42.2.5.jar | PostgreSQL 42.2.5 |
mssql-jdbc-7.0.0.jre8.jar | MS Sql Server 7.0.0 |
Type | Version |
SQL Server | 2012+ (tested with up to 2019) |
Oracle | 12g+ and 21c |
Postgres | 9 to 14 |
Application | Version |
Java | 8 or 11 |
Wildfly | 17.0.0 |
Apache HTD | 2.4.17 or higher |
Apache Ant | 1.9.6 |
Apache Axis2 | 1.7.1 |
PHP | 7.2.27 or higher |
New db updates include
8/21 - If Oracle has different timezone settings than the i2b2 application server, i2b2 sessions used to match the Oracle server. Now they will match i2b2.
CORE-399 use alias for index hint
For Java 11 install, if you change xsd, then modify the gensource.