https://github.com/teleivo/import-radlex-openmrs

Helper scripts to import RadLex into OpenMRS
https://github.com/teleivo/import-radlex-openmrs

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Helper scripts to import RadLex into OpenMRS

• Host: GitHub
• URL: https://github.com/teleivo/import-radlex-openmrs
• Owner: teleivo
• License: mit
• Created: 2016-09-07T12:02:17.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2016-09-07T14:21:13.000Z (over 8 years ago)
• Last Synced: 2024-11-08T18:52:59.150Z (about 2 months ago)
• Language: Shell
• Size: 4.88 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        
# Import Radlex to OpenMRS

## Overview

This guide shows how you can import the Radlex Playbook into OpenMRS concept

reference terms.

ATTENTION: I only tested this on linux!

## Background

Search the OpenMRS wiki for some backround information about concepts/concept

sources, like:

https://wiki.openmrs.org/display/docs/Standard+and+Non-standard+Terminology+Mapping

## Howto

### Get Radlex

You need to download it yourself since you need to accept their license terms

http://www.rsna.org/radlexdownloads/

### Import into OpenMRS

_Create Concept Source Radlex_

You first need to create Radlex as an OpenMRS concept source.

You can directly execute this sql statement in your database:

```sql

INSERT concept_reference_source (concept_source_id,name,description,creator,date_created,uuid) VALUES

(1,"RADLEX","RadLex Playbook is a project of the Radiological Society of North America (RSNA)",1,"2016-08-01 09:00:00","616a9691-a1bf-4426-85a6-21a60c558265");

```

_Create Concept Reference Terms for Radlex terms_

We need to generate UUIDs for every concept reference term.

I am doing this with [uuidgen command](http://man7.org/linux/man-pages/man1/uuidgen.1.html) on linux.

Execute the following to create sql insert statements for Radlex terms as

OpenMRS concept reference terms.

```bash

#!/bin/bash

[ -f import-radlex.sql ] && rm import-radlex.sql

awk -vFPAT='[^,]*|"[^"]*"'']"' '{if (NR!=1) {print "\42" sq $1 "\42," $3 sq ","sq $4 sq ");" }}' core-playbook-2_1 > radlex-columns.csv

while read; do

    echo "INSERT concept_reference_term

    (concept_source_id,version,creator,date_created,uuid,code,name,description)

    VALUES (1,\"2.1\",1,\"2016-08-01 12:00:00\",\"$(uuidgen)\",${REPLY}" >>

import-radlex.sql done < radlex-columns.csv

```

NOTE: if you use a different Radlex version adjust it in the command, if you

dont agree with the Radlex columns I use to populate the reference terms just

adjust them ;)

If you have suggestions/improvements please share!!

## Limitations

ATTENTION: still having issues with the complete radlex, guess there is a

special character getting in the way of the awk/scripting magic. First to find

it gets a :beer: ;)