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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 BuildUpgrade 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


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

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

17.0.0

2.4.17 or higher

1.9.61.7.17.2.27 or higher

Supported Operating Systems

TODO LIST THIS

i2b2

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  • DATA-7 QT_PATIENT_SET_ENC_COLLECTION should be a bigint (DONE)
  • DATA-14 Synthea i2b2 data (READY TO TEST)
  • DATA-8 Synthea data load test from Github files (DONE)
  • DATA-6 improve i2b2 db upgrade process (READY TO TEST)
  • DATA-12  Stored procedure to update concept dimension (DONE)
  • DATA-11 Age in years updater during demodata install (RESOLVED)
  • DATA-9 ACT v4 ontology (RESOLVED)
  • DATA-13 Postgres time interval corrections in ACT v4 demographics ontology (RESOLVED)
  • CORE-389 Totalnum performance improvements (RESOLVED)
  • CORE-394 Obfuscated totalnum reporting tables (RESOLVED)
  • CORE-398 Multifact support for totalnums  (READY TO TEST)
  • CORE-400 Show totalnums in top level folders (RESOLVED)

i2b2 Server and Client Changes

New Features and Improvements

Webclient Core-server
  • WEBCLIENT-334 Provide tabs for major plugins and temporal query (READY TO TEST)
  • WEBCLIENT-344 Cleanup Analysis Tools list of Plugins to only Supported Items (READY TO TEST) 
  • WEBCLIENT-325 Wayne's improvements to hierarchical find-by-name (READY TO TEST)
  • WEBCLIENT-343 Veracode security issues in web client(OPEN) ← STILL NEED TO DO
  • WEBCLIENT-353 SAML (client side) (READY TO TEST) 
  • CORE-399 Oracle index hints must use the table alias (RESOLVED)
  • CORE-382 Username / password errors should not specify which had the problem (READY TO TEST)
  • CORE-402 Fix Veracode identified Security flaws in i2b2 Server-Side Code (RESOLVED)
  • CORE-404 Adding support for JDK 11. Now including the gensrc due to jaxb has been removed. (RESOLVED)
  • CORE-413 FetchAllChildren (RESOLVED)
  • CORE-414 SAML (server side) (READY TO TEST)
  • CORE-415 Log4j upgraded to v2  (RESOLVED)
  • CORE-416 User parameter precedence change (contributed by Michael Horvath) (RESOLVED)
  • CORE-417 LDAP UPN support (contributed by Michael Horvath) (RESOLVED)

Bug Fixes

Webclient Core-server
  • WEBCLIENT-351 Obfuscated User Not Showing Graph (RESOLVED)
  • WEBCLIENT-342 switch response status check from "OK" to 200 to handle lab value pop up in http/2 protocols  (READY TO TEST)
  • WEBCLIENT-335 temporal query in webclient with no anchoring events not running (RESOLVED)
  • WEBCLIENT-350  Unable to drag items in workplace (READY TO TEST)
  • WEBCLIENT-325 Wayne's improvements to hierarchical find-by-name  (READY TO TEST)
  • WEBCLIENT-319 FindTerms- exceeding more than 200(default) return count - displaying server error (READY TO TEST)
  • WEBCLIENT-294 Webclient Reports "QUERY CANCELLED" While Query Is Still Running (CLOSED)
  • CORE-418 Local timestamps in sessions on Oracle - appserver /db server in diff time zones (READY TO TEST)
  • CORE-282 Error returned when obfuscated user is locked out (READY TO TEST)
  • CORE-281 Query continues to run after user receives lockout message (READY TO TEST)
  • CORE-412 Disable login to agg service account  (RESOLVED)
  • CORE-405 Upgrade JDBC Drivers (RESOLVED)
  • CORE-399 use alias for index hint  (RESOLVED)

i2b2 Database Changes

New Features and Improvements

Database updates
  • DATA-7 QT_PATIENT_SET_ENC_COLLECTION should be a bigint (DONE)
  • DATA-14 Synthea i2b2 data (READY TO TEST)
  • DATA-8 Synthea data load test from Github files (DONE)
  • DATA-6 improve i2b2 db upgrade process (READY TO TEST)
  • DATA-12  Stored procedure to update concept dimension (DONE)
  • DATA-11 Age in years updater during demodata install (RESOLVED)
  • DATA-9 ACT v4 ontology (RESOLVED)
  • DATA-13 Postgres time interval corrections in ACT v4 demographics ontology (RESOLVED)
  • CORE-389 Totalnum performance improvements (RESOLVED)
  • CORE-394 Obfuscated totalnum reporting tables (RESOLVED)
  • CORE-398 Multifact support for totalnums  (READY TO TEST)
  • CORE-400 Show totalnums in top level folders (RESOLVED)

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 "jaxb_gen" on Java 8 and then build as usual using Java 11.

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