Posts Tagged ‘software design’

An Opinionated Approach to OpenMRS Concept Management

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/

 

 

Software Delivery Skills Plan 2018

If you fail to plan, you are planning to fail! ~Benjamin Franklin

A new year is upon me, and looking over the horizon I am looking to do the following work streams to help better my development skills

1. Work with a new age Javascript framework – vue.js seems the rage, this is also working with webpack and new Javascript build tools

2. Make docker part of my development workflow – this will be project based

3. Distributed ledger proof of concept – the distributed ledger is the rage now, but what can be achieved to prove its capability

4. API First project – this is a separatation of the backend REST APIs from the front end, may be combined with the vue.js to deliver a working project. I will also look to leverage the OpenAPI

5. Write a paper for a scientific journal leveraging the health informatics work I have been doing over the last 3 years and present it at a conference.

Tech Tip: Websites on Github with Jekyll

We have been facing a challenge on how to manage the Styx Technology Group corporate website without having dedicated resources to host, deal with security, updates and maintenance. Having been in the website business for over a decade at the turn of Y2K,  having an easily maintainable solution was key for the long haul.

Enter GitHub pages (https://help.github.com/categories/github-pages-basics/), of course any decent software developer and team are using some form of version control, but the beauty is that it allows projects, users and organisations to have self hosted sites that are managed through a repository.  That in combination with Jekyll (http://jekyllrb.com/) supports content management without a database.

To further speed up our development process, we leveraged existing themes for the website look and feel that were close to our need, while keeping the site design very simple so that we focused on solving the problem at hand.

It was suddenly music to our ears as the team did not have to leave their IDEs (random plug for Jetbrains IDE tool suite that we have standardized upon)  in order to make updates to the website. Just create a new markdown document, verify and push … And bam!! the updates are done, version controlled and all, no more hassles with database configurations …

Need help getting your website up and running in such a fashion do shoot us an email at consulting at styxtechgroup dot com and we shall be happy to help and engage…. Have a great weekend

OpenMRS Module Development Learnings – 102

Update November 2018: This blog post has been superseded by the OpenMRS SDK (https://wiki.openmrs.org/display/docs/OpenMRS+SDK)
My team mates and I are completing a number of OpenMRS workshops focused on improving our module development capability. This blog post captures the unwritten lessons that we have picked up as a way of giving back our lessons to help others in the community (and will be moved to the OpenMRS Wiki once the lessons have been internalized and consolidated, as that is its natural home).
The approach is based on the following OpenMRS community articles:
  1. Creating Modules – https://wiki.openmrs.org/display/docs/Creating+Modules
  2. Creating your First Module – https://wiki.openmrs.org/display/docs/Creating+Your+First+Module
As you develop the module it is important to keep testing and verifying whatever you do especially when the module involves user interface components, extending the OpenMRS UI. The process we ended up using was as follows:
  1. Setup a module using the module creation command line utility
  2. Downloaded Spring Loaded from its maven repository http://mvnrepository.com/artifact/org.springframework/springloaded
  3. Downloaded and setup OpenMRS standalone from http://openmrs.org/download/ picking a version greater than 1.11.x which supports debugging options
  4. Once the standalone version is installed, open the openmrs-standalone-runtime.properties and add the following variables to the vm_arguments: (should all be one line – separated here for clarity)
    • -Xdebug -Xnoagent -Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8000
    • -Dmodule.development.directory={absolute path to root folder of the module}
    • -javaagent:{absolute path to spring loaded jar}
    • -noverify -Dspringloaded=inclusions=org.openmrs.module.modulepackage..* (note the two trailing dots before the *)
  5. Setup newly the module into an IDE (tested with IntelliJ & Eclipse)
  6. Installed a FileSync utility, RemoteSynchronizer for IntelliJ & FileSync (http://andrei.gmxhome.de/filesync/) for Eclipse
  7. Setup sync for the omod webapp folder into the standalone webapp folder located at WEB-INF/view/module/{modulename}
Our development workflow is smoothened out since any changes to Java classes & JSPs are automatically applied & reflected in the standalone app.
Additional Tips and Tricks
  1. Tomcat – Change the following init params in web.xml:
    • modificationTestInterval from 4 to 0, so that JSPs are automatically recompiled
    • development is true (this is the default)
  2. Intellij – the Java classes are not automatically recompiled on saving changes so there is need to run mvn package -DskipTests
  3. Follow the OpenMRS conventions as much as possible by cloning openmrs-core to see how the design of the interfaces, service layers is done. This will help get access to lots of the magic that happens behind the scenes.
  4. Java 8 will give you trouble, stick to 1. 7 as we did not try 1.6 anywhere.

 

Bringing Security to the heart of Uganda Consumer Applications 

A very welcome addition to Uganda technology scene are the multiple consumer facing apps, from banks, to telecommunication companies to support mobile money services, to parastatals getting closer to their customers. The newest apps that I am aware of include (in no particular order):
  1. Airtel Money
  2. My MTN
  3. NWSC Mobile
  4. NSSF Go
  5. Stanbic Bank Mobile Banking
  6. DFCU Mobile Banking
  7. Bank of Africa Mobile Wallet (BMW)
  8. Ask URA
On one hand, this is a very welcome addition to address the increasing sophistication of the Ugandan urban consumer who demands more from the corporations. However a worrying trend which needs to be addressed is the security of these applications, in collecting and managing user information. I have taken to social media to ask for more information on the security setup for these apps, but have never gotten a response.
This is hoping to the regulators, Bank of Uganda, Uganda Communications Commission and NITAU (at the moment) to provide a united front to ensure that the following areas are addressed:
  1. Excess permissions, one app wanted to access my contacts, SMS messages, WIFI, phone identity yet was not a banking app
  2. Encryption of data stored on the phone to ensure that if the phone is separated from the owner the data is safe
  3. Secure connections for communication with external servers – via HTTPS and SSL
  4. Security audits of back end infrastructure following ISO and COBIT standards (http://www.isaca.org/Journal/archives/2002/Volume-6/Pages/A-Survey-of-Application-Security-in-Current-International-Standards.aspx)
  5. Penetration, stress and load testing to ensure that aside from
  6. Software development practices that include OWASP top 10 Proactive Controls for software developers https://www.owasp.org/index.php/OWASP_Proactive_Controls
What else do you see being done to improve the security of our consumer facing applications
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