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Totalnum Scripts  have been updated to improve the Totalnum counter performance on both many ontology tables and very large(>1.5 million) ontologies  such as ACT medications. Debug messages have also been added for troubleshooting and profiling purposes

Totalnum Scripts Setup

  1. 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 
  2. Run the stored procedures on your database. This can be done in two ways:
    1. Run the ant command to execute the data_build.xml file with below specified target 
      POSTGRESQL : ant -f data_build.xml db_metadata_run_total_count_postgresql
      ORACLE : ant -f data_build.xml db_metadata_run_total_count_oracle
      SQL SERVER : ant -f data_build.xml db_metadata_run_total_count_sqlserver   
    2. If using multiple fact tables, the recommended approach is to create a fact table view as the union of all your fact tables. (This is essentially going back to a single fact table, but it is only used for totalnum counting. This is needed to correctly count patients that mention multiple fact tables within a hierarchy.)
          e.g., 
             create view observation_fact_view as
             select * from CONDITION_VIEW 
             union all
             select * from drug_view
          And then run the totalnum counter with the wildcard flag, to ignore multifact references in the ontology
            e.g., in SQL Server, exec RunTotalnum 'observation_fact_view','dbo','@','Y'
          Note this approach does not work if you have conflicting concept_cds across fact tables.
    3. Execute the RunTotalNum  stored procedure manually against your database in from a sql Client. This can take several hours.  Example Usage:    

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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


i2b2 Database Changes

New db updates 
  • DATA-7 QT_PATIENT_SET_ENC_COLLECTION should be a bigint (DONE)
  • DATA-5 Synthea i2b2 data (TO DO)
  • DATA-8 Synthea data load test from Github
files
  • files (TO DO)
  • DATA-6 improve i2b2 db upgrade
process
  • process (TO DO)
  • DATA-12  Stored procedure to update concept
dimension
  • dimension (DONE)
  • DATA-11 Age in years updater during demodata
install
  • install (TO DO)
  • DATA-9 ACT v4
ontology
totalnums
  • totalnums  (NEW)
  • CORE-400 Show totalnums in top level folders (RESOLVED)

i2b2 Server and Client Changes

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