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Note

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.


ACT4 data load process:

  1. Download the newinstall  zip package from https://www.i2b2.org/software/download.html?d=452
  2. Extract the  metadata\act folder from the downloaded zip folder
  3. Replace edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act  folder with extracted new act folder
  4. Edit the  db.properties file in your metadata folder  to update the project properties to 'ACT' ; db.project=ACT
  5. From the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata folder, run the ant command: ant -f data_build.xml db_metadata_load_data
  6. This will execute the  SQL scripts from the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act\scripts\<db type> folder and create and load ACT4 Ontology metadata tables  
  7. You can now verify the new Ontology  by logging into the webclient.

Loading concept_dimension: You can run  run the stored procedure on your db to update concept_dimension table.This will iterate through table_access and load concept_dimension with data corresponding to the  c_table_name metadata tables.

  • Location of Insert_Concept_FROMTableAccess

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  • .sql:  edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/<db type>/

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Security Enhancements

  1. i2b2 has been made more secure by addressing parameterization and other potential vulnerabilities according to a Veracode scan.
  2. Log4J has been upgraded to the latest version. Following jars are updated in lib/axis2.war/WEB-INF/lib folder
    1. log4j-api-2.17.1.jar
    2. log4j-core-2.17.1.jar
    3. log4j-jcl-2.17.1.jar

Improved db Upgrade Process

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Steps to Perform db upgrade:

  1. Backup your existing data folder
  2. Copy all the folders from the extracted latest version download data folder   into your existing  data Upgrade folder. This will replace existing Crcdata, Hivedata, Metadata, PMdata folders.

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  1.  Example:  Downloads\i2b2core-upgrade-1713\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\.
  2. Copy the db.properties files from your back up into the respective locations (namely Crcdata, Hivedata, Metadata, PMdata )
  3. Open the command prompt and navigate  to each cell folder 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 folder as below.

Upgrade From BuildUpgrade to Latest build 1.7.13

1.7.09c

In the Crcdata 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_1-7-12a

In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10  upgrade_tables_release_1-7-12a

1.7.10

In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a

In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-12a

1.7.11


In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11  upgrade_table_release_1-7-12a

In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

1.7.12a

In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a

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