Summary

InterSystems FHIR Client Get Resources information from FHIR Server. Command Line utility and Web interface.

Application Layout

Online Demo

https://medicaldatasets.demo.community.intersystems.com/csp/datasets/index.csp by using SuperUser | SYS

Datasets List

• 1 - Synthetic Medical Data : Synthetic medical record data for Introduction to Biomedical Data Science. LICENCE:Public Domain
• 2 - Health Care Analytics - 1 : Part of Janatahack Hackathon in Analytics Vidhya LICENCE:Public Domain

Features

• Retrieve all the resource list
• Retrieve already defined resources
• List Resource details
• List Resource details from command prompt and from web interface
• Patient and Observation resource CRUD operations
• Interoperability PEX
• Programatically add any open source FHIR Web server
• Smart on FHIR application details

Recommendation

• Read related documentations LOAD DATA (SQL).

How to Run

To start coding with this repo, you do the following:

1. Clone/git pull the repo into any local directory

git clone https://github.com/mwaseem75/DataSetProj.git

2. Open the terminal in this directory and run:

docker-compose build

3. Run the IRIS container with your project:

docker-compose up -d

Installation with ZPM

zpm "install dataset-medical"

Repo Contents

• Dockerfile, docker-compose.yml, and Installer.cls to create container
• iris.script, contains script to execute during container initialization
• /src with source files
• /.vscode/settings.json for automatic server connections when opened in VS Code.

Requirements:

• Docker desktop
• Get the latest InterSystems IRIS for Health image for use in the Dockerfile: https://hub.docker.com/_/intersystems-iris-for-health

Getting Started

Importing DataSet from Terminal

Connect to IRIS Terminal

docker-compose exec iris iris session iris

Change Namespace to DATASETS

ZN "DATASETS"

Run below command to import Synthetic Medical Data dataset by passing dataset ID(1)

do ##class(dc.data.medical.utility).ImportDS(1)

11 Tables are created, 83,341 Records Loaded successfully, 140 errors Reported

Use of %SQL_Diag.Result and %SQL_Diag.Message to check errors

As you noticed previous LOAD DATA returns 140 errors. To check the error details we will use %SQL_Diag.Result and %SQL_Diag.Message tables. We need diag ID to check detail which in our case is 5 (Last column in previous snapshot)

We will use Management Portal SQL to check the details

Open Management Portal SQL and type below SQL command to check details in %SQL_Diag.Result table against Diag ID

SELECT * FROM %SQL_Diag.Result WHERE ID = 5

and to check the details of 140 errors type below SQL command

SELECT * FROM %SQL_Diag.Message WHERE severity = 'error' and diagResult = 5

System is displaying details of 140 errors. Please note that we are passing same %SQL_Diag.Result ID to diagResulg column

Importing DataSet from Web Application

Navigate to http://localhost:52773/csp/datasets/index.csp and press Install DataSet button

Dataset is imported successfully

View Data from Web Application

Navigate to http://localhost:52773/csp/datasets/index.csp and click any table from sidebar

Export Data from Web Application

Navigate to View Datasets and select particular dataset, click Excel,CSV or PDF button to export data

Removing DataSet from Terminal

Run below command to Remove Synthetic Medical Data dataset by passing dataset ID(1)

do ##class(dc.data.medical.utility).RemoveDS(1)

Removing DataSet from Web Application

Navigate to http://localhost:52773/csp/datasets/index.csp and press Remove DataSet button

Dataset is removed successfully

Importing all DataSets at once

Run below command to Import all datasets by passing ID 999

do ##class(dc.data.medical.utility).ImportDS(999)

Removing all DataSets at once

Run below command to Remove all datasets by passing ID 999

do ##class(dc.data.medical.utility).RemoveDS(999)

Check Status of DataSet

Run below command to check the status of particular DataSet by passing DataSet ID,

do ##class(dc.data.medical.utility).GetStatusDS(1)

Run below command to check the status of all Datasets

do ##class(dc.data.medical.utility).GetStatusDS(999)

Other information

Template used in web application is from Bootstrap 4 Admin Dashboard and it is free to use to develop non-commercial applications.

Thanks