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OMOP/Impala/README.md

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Common-Data-Model / Impala

This folder contains the SQL scripts for Impala.

In order to create your instantiation of the Common Data Model, we recommend following these steps:

  1. Create an empty schema.
impala-shell -q 'CREATE DATABASE omop_cdm'
  1. Execute the script OMOP_CDM_ddl_Impala.sql to create the tables and fields.
impala-shell -d omop_cdm -f OMOP_CDM_ddl_Impala.sql
  1. Load your data into the schema.

a. Load the vocabulary tables.

First, download the data from http://www.ohdsi.org/web/athena/ and unzip into a cdmv5vocab directory, then run

hadoop fs -put cdmv5vocab cdmv5vocab
hadoop fs -chmod +w cdmv5vocab
impala-shell -d omop_cdm -f VocabImport/OMOP_CDM_vocabulary_load_Impala.sql --var=OMOP_VOCAB_PATH=/user/$USER/cdmv5vocab

b. Load the patient data.

For example, download the 1000 person sample of simulated CMS SynPUF patient data from http://www.ltscomputingllc.com/downloads/ and unzip into a synpuf directory, then run

hadoop fs -put synpuf synpuf
hadoop fs -chmod +w synpuf
impala-shell -d omop_cdm -f DataImport/OMOP_CDM_synpuf_load_Impala.sql --var=OMOP_SYNPUF_PATH=/user/$USER/synpuf
  1. Run simple queries to sanity check.
impala-shell -d omop_cdm -q 'SELECT COUNT(1) FROM concept'
impala-shell -d omop_cdm -q 'SELECT COUNT(1) FROM person'