This tool will generate Entity Files that can be used to load into Datasources.
Author: Thomas DeSain
This example was validated on a Mac and AMI Linux terminals.
To see it in action follow here to load the NHANES dataset
- Open bash connection to your ETL Client Docker
docker exec -e COLUMNS="`tput cols`" -e LINES="`tput lines`" -ti etl-client bash
- use git to clone this project to a dir of your choosing.
git clone https://github.com/hms-dbmi/ETLToolSuite-EntityGenerator
- Navigate to root directory:
- Make a directory to store your data:
- Make a directory to store your mapping file:
- Make a directory to store your processed data files:
- Copy the data file and mapping file generated from the MappingGenerator Example
( The BASE_DIR will be the location of the MappingGenerator git project you cloned in the Mapping generator example ) :
cp ../ETLToolSuite-MappingGenerator/example/Asthma_Misior_GSE13168.txt data/
cp ../ETLToolSuite-MappingGenerator/example/mapping.csv mappings/mapping.csv
cp ../ETLToolSuite-MappingGenerator/example/mapping.csv.patient mappings/PatientMapping.csv
- execute following code block to generate your I2B2 entities:
java -jar EntityGenerator.jar -jobtype CSVToI2b2TM
- Navigate to completed directory
- list the directory's contents.
- Once the job has completed processing this folder will contain the following files:
- If your data files exist you can now move on to loading the entity files into your database by following the readme here.