Page History
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Community-Contributed Features
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 Wake Forest | 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. |
Backend Features
SAML Authentication
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- Backup your existing data folder
- Copy all the folders from the extracted download data folder into your existing data Upgrade folder
Example: Downloads\2b2core-upgrade-1712a\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\. This will replace
existing Crcdata, Hivedata, Metadata, PMdata folders.
Alternative to above step, navigate to the edu.harvard.i2b2.data\Release_1-7\Upgrade\ directory of your extracted folder - Copy the db.properties files from your back up into the respective locations(namely Crcdata, Hivedata, Metadata, PMdata )
- Open the command prompt and navigate to cell folders and run the following upgrade ant commands on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql.
Alternative to above Step, you can run individual SQL scripts on your db instance in place of ant commands.
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 |
Changelog
Database Drivers
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 12.2.0.1 | PostgreSQL 42.2.5 | MS Sql Server 7.0.0 |
Supported Db Server versions
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 |
Supported software versions
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 |
i2b2 Database Changes
New db updates |
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i2b2 Server and Client Changes
New Features and Improvements
Webclient | Server-Side |
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Bug Fixes
Webclient | Server-Side |
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Notes for Developers
For Java 11 install, if you change xsd, then modify the gensource.
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