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- 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 form from the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act folder to create the new ACT4 Ontology tablesand loads the corresponding metadata. \scripts\<db type> folder and create and load ACT4 Ontology metadata tables
- You can now verify the new Ontology by logging into the webclient.
The following command will load the corresponding concept_dimension data of the Onbtology tables that will enable you to run queries in the webclient
From a sql Client>select 'insert into concept_dimension select c_dimcode AS concept_path, c_basecode AS concept_cd, c_name AS name_char, null AS concept_blob, update_date AS update_date, download_date as download_date, import_date as import_date, sourcesystem_cd as sourcesystem_cd, 1 as upload_id from '
+c_table_name+' where m_applied_path=''@'' and c_tablename=''CONCEPT_DIMENSION'' and c_columnname=''concept_path'' and c_visualattributes not like ''%I%'' and (c_columndatatype=''T'' or c_columndatatype=''N'') and c_synonym_cd = ''N'' and (m_exclusion_cd is null or m_exclusion_cd='''') and c_basecode is not null and c_basecode!='''''
from <your_dbschema>.dbo.TABLE_ACCESS where c_visualattributes like '%A%'
Loading concept_dimension: You can run Insert_Concept_FROMTableAccess stored procedure on your db located in edu.harvard.i2b2.data/Release_1-7/NewInstall/Crcdata/scripts/procedures/<db type>/ which will iterate through table_access and load concept_dimension with data corresponding to the c_table_name metadata table
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.
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