Contribution | Contributor | |
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:
Metadata scripts are now available to load the latest ACT Version-4 Ontology into your i2b2 db schema
ACT4 dataload process:
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+ |
Oracle | 12g+ |
Postgres | 9 |
Application | Version |
Java | 8 |
java | 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
For Java 11 install, if you change xsd, then modify the gensource.