15 Apr

An Opinionated Approach to OpenMRS Concept Management

Posted by ssmusoke in eHealth, openmrs, opensource, software delivery, software development lifecycle, tips and tricks. Tagged: , , .

One of the key strengths of the OpenMRS platform is the concept dictionary, which allows for the mapping of real world health care data needs into concepts that provide the questions and answers.

The concept dictionary provides ability to map real life concepts to specializations across health care domains such as: SNOMED CT (clinical healthcare terminology), LOINC (laboratory observations), ICD-10/11 (disease classifications), RxNORM (normalized names for clinical drugs), CVX (vaccination codes) in addition to leaders in certain medical fields such as Partners In Health and AMPATH (HIV Care and treatment).

However with great power comes great responsibility, the concept dictionary coding can easily get out of hand, with duplicate concepts leading to inability to extract data for reporting and improving the efficiency clinical care that are key goals of health informatics activities.

This guide is based on my personal experience from working across multiple diverse implementations and the fact that Open Concept Lab (OCL) is not yet in widespread production usage which would alleviate most of the pains, which includes:

  1. Supporting the upgrade, evolution and rollout of UgandaEMR in Uganda from 350 sites in 2016 to over 1000 sites (December 2019) including implementation of 2 major revisions of national Health Management Information Systems tools
  2. Migration of 2 custom OpenMRS implementations in Uganda to align to and build on top of UgandaEMR
  3. Namibia PTracker PMTCT program
  4. Enhancements of the Reference Application

The key principles to this approach are as follows:

  1. CIEL dictionary is the official source of concepts, and first place to check for concepts
  2. Custom concepts must be setup in such a way that updates to CIEL or other custom modules used do not overwrite the customizations

Concept Server Setup

The setup involves using the following OpenMRS instances:

  1. CIEL dictionary server running the latest reference application version – contains the latest version of the CIEL dictionary and helps for data export when needed. The complete concept dictionary however is not recommended to be loaded for an implementation due to slowdowns in concept lookup, as sample concept numbers are:
    • Reference Application 2.9.0 – 446 concepts
    • UgandaEMR – 5,500 concepts
    • CIEL dictionary – 54,000 concepts
  2. Custom Concepts Server – this one contains the custom concepts and CIEL concepts that exist, is the single source of truth for the project concepts. This needs to run similar modules to what the implementation is running. I would recommend the following additional steps:
    • Set the autoincrement value of the concept table to 5,000,000. This ensure that the concepts created will never be overwritten by CIEL concepts, the last numeric ID as of April 2020 is 165900 due to retired concepts etc
    • Set the auto increment values of the rest of the concept* tables to 10,000,000 (there are usually more values than so these tables grow)
    • Create a custom mapping for your project or implementation, and use that to reference the custom and CIEL concepts that you use in your forms and reports. This adds a layer of redirection and consistency for access
  3. Implementation Development, Staging and Demo Servers – as needed

Moving Concepts Across Servers

There are multiple options for moving concepts from the CIEL to the Custom Concepts Server and finally to the implementation servers

Approach Description Notes
Use of Metadata sharing and metadata deploy modules to build of metadata packages (zip files)
  • Manually downloaded from the servers and uploaded where needed – faces the challenges of manual processes
  • Provide a dedicated url from source servers that clients can subscribe to get updates as the deploy packages are updated following the pub-sub model
  • The creation of the metadata packages is manual
  • The metadata packages are zip files which are difficult to debug
Download the concept data into CSV or DB Unit compliant XML The concept files are then loaded into the implementation using either Initializer or Data Exchange modules
  • This requires developers to extract the concept data from the different tables, without making mistakes.
  • This is still a manual and error prone process
Open Concept Lab (OCL) Allows creation of custom dictionaries and extraction of data through an online web interface This tool is not yet production ready but would provide the automation that solves all issues

Data Export Tools

The following additional tools can be leveraged for this purpose

  1. Dbunit XML data export plugin for Data Grip – https://ssmusoke.com/2017/04/17/techtip-dbunit-export-from-jetbrains-datagrip/

 

 

19 Feb

Perspective: User Requirements for Technology Projects

Posted by ssmusoke in enterprenur, frugal innovation, software delivery, tips and tricks. Tagged: , , , , .

I was asked to talk about the handling of user requirements, how to link them to implementation within technology projects, by The Medical Concierge Group (TMCG) a digital ehealth service provider.

The key principles are being able to respond to change (agile), keep learning, and how to capture business/customer outcomes as well as improving communication across different departments and external stakeholders.

17 Feb

TechTip: Secure Access to S3 Folder

Posted by ssmusoke in aws, devops, tips and tricks. Tagged: .

This is more a reminder to myself, so that I do not always have to struggle. Amazon S3 is probably the cheapest cloud storage service, that exists, and in these days of multi-tenant architecutures, provides a great way of accessing data from multiple instances.

However in some cases, you need to store files in S3 that are not viewable to anyone in the world, only to your app. I am hoping that this guide will help with that, and I will keep improving it with feedback and additional learning

The steps are as follows:

  1. Optional: Create an IAM group for users to help in user management
  2. Create an IAM user for each app environment with programmatic access to provide isolation from all other users who share the AWS account, I recommend creating separate users for dev, qa and production environment
  3. Generate access keys for each user which will be used to configure the app
  4. Create an access policy for each environment to restrict access to a bucket or a collection of buckets like below for restricting access to only the dev bucket
    {
  "Version": "2012-10-17",
  "Statement": [
    {
      "Sid": "VisualEditor1",
      "Effect": "Allow",
      "Action": [
        "s3:ListBucket"
      ],
      "Resource": [
        "arn:aws:s3:::project-dev"
      ]
    },
    {
      "Sid": "VisualEditor0",
      "Effect": "Allow",
      "Action": "s3:*",
      "Resource": [
        "arn:aws:s3:::project-dev/*"
      ]
    }
  ]
}
  5. Create S3 buckets with no public access, but with the names matching what is defined in the policies
  6. Test adding files to S3 using the credentials to confirm access (I tend to use the AWS cli with profiles for this case)
    

    aws s3 ls s3://project-dev –profile project-dev
    

    7. 



UPDATE 1 – February 24, 2019: Added a poilicy for being able to read the bucket which is different from the bucket contents, see Sid: VisualEditor1.


			




	
		


	

		26
		Oct
	

	
Agile Software Development for Ugandan Context 2019 Edition

	

	Posted by ssmusoke in APIs, opensource, software delivery, software development lifecycle, tips and tricks.	Tagged: .	

	

		
Excited to share my thoughts and experiences in agile software delivery for use within Uganda at the Google Dev Fest in Kampala, on October 26, 2019



 


 


			




	
		


	

		18
		Oct
	

	
My OpenSource Journey

	

	Posted by ssmusoke in opensource, software development lifecycle, tips and tricks.	Tagged: .	

	

		
I am having a great time sharing my experiences with new developers as part of giving back to the community hoping to encourage them on their own journeys…



			




	
		

			
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