Contents
- Overview
- Required Software
- Definitions
- Installation
- Running the ETL to extract from your database or file
- Scrubbing Protected Health Identifiers from Free Text
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Overview
The ETL program Extracts patient information from existing systems, Transforms the results into standard HIPAA safe medical vocabularies, and Loads the results into a locally controlled Peer node.
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Definitions
ETL: (1) Extract (2) Transform (3) Load
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Required Software:
Java 1.5 or later
MySQL 4.1 or later
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Installation
(1) Unzip the ETL zip archive to a directory of your choice
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# Extractor for the VSL pipeline #
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\[DB\] Database Connection |
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\[XML\] XML Formatted File |
[DB] Database Connection
[XML] XML Formatted File
[CUSTOM] Wiki Markup
Extractor for the VSL pipeline=DB
The wizard will then ask which type of DB extractor to use:
# Database Extractors #
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\[STANDARD\] Standard Pathology LIMS |
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\[MGH\] MGH Frozen Tissue Repository |
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\[BWH\] BWH Frozen Tissue Repository |
[STANDARD] Standard Pathology LIMS
[MGH] MGH Frozen Tissue Repository
[BWH] BWH Frozen Tissue Repository
[CRIMSON] Crimson Biomaterials Collection Wiki Markup
Database Extractors=STANDARD
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Done.
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Running the ETL Program
Running ETL on Demand
Syntax:
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ETLRunner myConfig.xml hours 1 MM-DD-YYYY HH:mm:ss
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SCRUBBER
The SCRUBBER can be setup to de-identify text "on the fly" before it is loaded into the peer database.
We recommend using the 2.8 scrubber because it has numerous upgrades. For more information, contact us.