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Note |
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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:
- Download the newinstall zip package from https://www.i2b2.org/software/download.html?d=452
- Extract the metadata\act folder from the downloaded zip folder
- Replace edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act folder with extracted new act folder
- Edit the db.properties file in your metadata folder to update the project properties to 'ACT' ; db.project=ACT
- 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
- 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
- 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
- i2b2 has been made more secure by addressing parameterization and other potential vulnerabilities according to a Veracode scan.
- Log4J has been upgraded to the latest version. Following jars are updated in lib/axis2.war/WEB-INF/lib folder
- log4j-api-2.17.1.jar
- log4j-core-2.17.1.jar
- log4j-jcl-2.17.1.jar
Improved db Upgrade Process
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Steps to Perform db upgrade:
- Backup your existing data folder
- 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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- Example: Downloads\i2b2core-upgrade-1713\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\.
- 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 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 Build | Upgrade to Latest build 1.7.13 |
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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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