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OpenMRS Interoperability and Integration Updates

OpenMRS Interoperability and Integration Updates

Focus on OpenMRS interoperability & integrations at facility-level

Mondays at 9 AM EST, 4 PM EAT - Link: meet.google.com/ksh-mdae-rtw

Represented organizations: UCSF, UgandaEMR, Palladium, Mekom, MSF/Madiro

Examples: Laboratory, billing, stock management, etc.

Objectives

  • Share knowledge and use cases about data exchange use cases

  • Align on practices, tools, and architectures

Deliverables

  • Map ecosystem of existing solutions and challenges to address them as a group

  • Framework for integration

  • Sets of routes

  • Documentation about how to integrate OpenMRS with other health systems

Calls and notes

Call cancelled, low attendance

Wei (UCL), Siddharth, Romain, Eudson, Michael

  • Orthanc integration

    • Flows:

      • Order made in OpenMRS (radiology order planned in next 2 months) to be sent to Orthanc

      • Periodic sync from Orthanc to OpenMRS

      • Orthanc ID to be added to OpenMRS for mapping

    • Questions:

      • How to map/merge patients coming from Orthanc to OpenMRS ID? → For now, direct 1:1 mapping between the 2 systems (No CR)

      • SSO for login and privilege integration - Orthanc authentication Documentation and repo

    • Priority:

      • Link to patient/study in Orthanc in OpenMRS patient file

      • Later on, we can imagine a preview or iframe in OpenMRS with imagery

    • Next:

Wei (UCL), Siddharth, Romain, Eudson, Michael

  • Orthanc integration

    • Flows:

      • Order made in OpenMRS (radiology order planned in next 2 months) to be sent to Orthanc

      • Periodic sync from Orthanc to OpenMRS

      • Orthanc ID to be added to OpenMRS for mapping

    • Questions:

      • How to map/merge patients coming from Orthanc to OpenMRS ID? → For now, direct 1:1 mapping between the 2 systems (No CR)

      • SSO for login and privilege integration - Orthanc authentication Documentation and repo

    • Priority:

      • Link to patient/study in Orthanc in OpenMRS patient file

      • Later on, we can imagine a preview or iframe in OpenMRS with imagery

    • Next:

  • Deployment of dev-his.openmrs.org

    • Done, needs to fix the app switcher config. Fixing in progress.

    • Update on the README to point to direct access to apps by URL.

    • Next:

      • Enable SSO.

      • Enable Ozone Analytics

  • Stock & Price visible in O3 upon ordering.

    • openmrs-module-fhirproxy is now done.

    • fhir-odoo API is now done.

    • Need to implement the FHIR endpoints in Billing & Inventory OpenMRS modules. @Amos Laboso to reach out to Mekom regarding coding those FHIR endpoints.

    • UI implementation is happening ( @Usama Idriss Kakumba assigned to https://openmrs.atlassian.net/browse/O3-4009 ).

    • Testing currently in progress: finding some issues: initial development of OpenMRS module FHIR proxy done against 2.4.x and appears not compatible with 2.6.x, currently being looked at.

  • LIMS integration

  • Deployment of dev-his.openmrs.org

    • Done, needs to fix the app switcher config.

      • @Emmanuel Nyachoke to fix it this week.

    • Demoed at the conference multiple times.

  • Stock & Price visible in O3 upon ordering.

    • openmrs-module-fhirproxy is now done.

    • fhir-odoo API is now done.

    • Need to implement the FHIR endpoints in Billing & Inventory OpenMRS modules. @Amos Laboso to reach out to Mekom regarding coding those FHIR endpoints.

    • UI implementation is happening ( @Usama Idriss Kakumba assigned to https://openmrs.atlassian.net/browse/O3-4009 ).

  • Ozone Analytics

  • LIMS integration

    • OEG integration work is halted until the missing features are implemented.

    • Will touch base weekly to assess the progress and resume work when a number of the features are fixed.

    • Enable SENAITE as the default LIMS option currently in progress (PR in review and a bug reported) https://openmrs.atlassian.net/browse/HIS-15

  • Deployment of dev-his.openmrs.org

    • Work necessary in Ozone to build bundled Docker images is now done and currently being deployed (on the Ozone side).

    • Deployment of OpenMRS Distro HIS should be done through a Bamboo job - done by today or tomorrow.

  • FHIR API for Odoo

    ERP FHIR facade (1).jpg

    • Work has started.

      • Odoo Java Client: we will be using the Odoo Java API project as a Java client for Odoo XML RPC API → https://mekomsolutions.atlassian.net/browse/OZ-688 is not necessary anymore.

      • OpenMRS module FHIR Proxy work is started. Will get more updates after the Ozone internal call.

      • HAPI FHIR server work started today. Will get more updates after the Ozone internal call.

  • MambaETL

  • Ozone Analytics

    • Open sourcing of Ozone Analytics will be started by @Kakumirizi Daud this week.

  • LIMS integration

    • OEG integration work is halted until the missing features are implemented.

    • Will touch base weekly to assess the progress and resume work when a number of the features are fixed.

    • Will enable SENAITE as the default LIMS option for now. https://openmrs.atlassian.net/browse/HIS-15

  • Deployment of dev-his.openmrs.org

    • Delayed few days: init. estimate on end of last week. Looking at mid this week now. (technical work is done so that child distributions can build those Docker-embedded images).

    • Unable to reach out to Rafal. Scott has not answered regarding if a Bamboo job already exists or not.

  • FHIR API for Odoo

    • Proposed architecture: https://miro.com/app/board/uXjVKv4-SII=/?share_link_id=473611286361

    • ERP FHIR facade (1).jpg

    • Work has started.

  • MambaETL

    • Technical architecture call on Thursday

      • Simplicity of deployment (OMODs and/or SQL script)

      • Ability to dynamically flatten encounters and transpose questions as columns

      • Concerns over:

        • Change Data Capture done through monitoring some specific database fields (date_changed, date_voided…) instead of default mechanisms (binlog…)

        • Performance concerns (due to a lot of indexing) for 10M records databases.

        • Little to no testing.

  • Ozone Analytics

    • Open sourcing of Ozone Analytics will be started by @Kakumirizi Daud this week.

  • OEG integration

    • Project updates shared by Suruchi: integration work is being delayed (+1 week already) by low responsiveness from OEG devs. Attempting to setup weekly calls.

    • Eudson advises to not implement any workaround and rather wait for OEG folks to answer.

  • Deployment of dev-his.openmrs.org

    • Development work needed to deploy embedded distro Docker images is well advanced. Est. done by mid-week.

    • Then reaching out to Rafal in OpenMRS community to deploy via Bamboo.

    • Q: @Emmanuel Nyachoke where to deploy the OpenMRS Distro HIS-embedded Docker images?

  • FHIR API for ERPNext (or Odoo)

    • From Slack message Odoo might be a better fit for the default ERP system in Ozone and OpenMRS distro HIS.

    • Work needed to have ERPNext expose a FHIR API still needs to be documented as an example. Current work could be pushed and documented so to be picked up and resumed by other group.

    • ChargeItemDefinition and InventoryItem exposed in Billing & Pharmacy modules needs to start. Mekom will provide guidance. Need to use the https://github.com/ozone-his/fhir-structures-backport-r4/ library.

  • MambaETL + Oz Analytics

    • Plan a call this week between UCSF and Mekom to look at Mamba ETL in terms of incremental updates.

  • DHIS2 / DHIS Tracker integration:

    • Integration with Tracker. Advises to look at the Ethiori REDCap integration.

    • Integration DHIS2 (analytics). Advises to look at the Ozone Analytics when integrated data analytics.

OEG integration:

  • OpenMRS patient and Lab test order is synced in OpenELIS

  • Results from OpenELIS are synced in OpenMRS

  • Modification of lab order cancels the existing lab order in OpenELIS and creates a new lab order

  • Discontinue lab order in OpenMRS cancels the Incoming Order in OpenELIS

 

Deployment of dev-his.openmrs.org.

FHIR API for ERPNext:

  • Architecture still in progress. Leaning towards running HAPI FHIR to transform and expose FHIR objects from the ERPNext database.

    • Architecture will be defined this week and implementation started the week after.

 

  • Analytics in OpenMRS Distro HIS: Ozone Analytics + Mamba ETL

  • OEG integration in progress:

  • Deployment of dev-his.openmrs.org server:

    • Will be looked at tomorrow.

  • FHIR specs for ERP Processes completed. Link: https://docs.google.com/document/d/1uvJwYCGZg_wnt5eMCFLBIJoWU4CQaUWSKENvHrR-MEg/edit?usp=sharing

    • Designs for Price + Stock upon ordering will be added in Zeplin today.

      • Need some architecture call with Wyclif regarding exposing the FHIR API of the ERP (and authenticating to it)

  • SSO: Should be configurable to be enabled by implementers.

  • Custom systems integration:

    • Ethiori being integrated with a custom LIMS. → good progress done in Ethiori hackathon.

    • Used as an example to add more integrations.

  • Enabling SENAITE in OpenMRS distro HIS:

    • @Stephen Senkomago Musoke starting evaluation of SENAITE integration.

      • Patients are synced

      • Lab orders not tested as unable create orders with admin users. Reached out on the #ozone channel.

      • Mekom reported some issues with the Lab order basket (unable to revise order).

  • DHIS2 integration by @Michael Bontyes . Interested in looking UgandaEMR existing DHIS2 integration.

    • MSF scope: Initialize a new OpenMRS instance with DHIS2 patients (w/ DHIS2 ID + demographics)

      • Using OpenFn to send the new patients and data points.

      • Business logic available on GitHub.

  • OEG integration in progress: Define exact extent of the work needed. Mekom to outline a timeline and project manage.

  • Testing of OpenMRS Distro HIS in progress.

    • ERPNext processes confirmed to be working.

    • Documenting how Implementers can adopt OpenMRS Distro HIS-> to be reviewed by @Stephen Senkomago Musoke

      • Investigate how OpenMRS Distro HIS can be adopted

        • Direct inheritance from Ozone.

        • Inheritance of OpenMRS Distro HIS.

          • @Stephen Senkomago Musoke to try both options.

  • Deployment of dev-his.openmrs.org server in progress: Mekom and OpenMRS devops to meet tomorrow.

  • FHIR specs for ERP processes progressed. Almost ready to be shared.

  • @Stephen Senkomago Musoke is looking into trying Superset within Ozone.

    • Mamba ETL flattened encounters tables must be forwarded to the PostgreSQL analytics table (from Ozone Analytics) as to be available as 1 single datasource in Superset.

      • Not so straightforward as the table columns is dynamic.

      • Need to find a way to identify a source data model and create the corresponding target database

      • → Set to the agenda next week. Invite @Wyclif Luyima @Emmanuel Nyachoke @Arthur D. Mugume @Laureen Omare .

  • OEG integration in progress: See Slack conversation between Mekom and UW.

  • Testing of OpenMRS Distro HIS in progress.

    • No demo patients created when running start-demo.sh. Further testing needed. Might need some documentation improvement → @Stephen Senkomago Musoke confirms that demo patient are created.

    • Testing of the actual integration between OpenMRS and ERPNext in progress. Should be done by mid-week by @Stephen Senkomago Musoke .

      • Create patient in OpenMRS

      • Create an order for that patient

      • See the patient in ERPNext

      • See the quotation opened in ERPNext

    • Documenting how Implementers can adopt OpenMRS Distro HIS → redirect to Ozone docs here: https://docs.ozone-his.com/create-distro/

  • Deployment of dev-his.openmrs.org server in progress: host is ready on OpenMRS infrastructure. Next step is to actually deploy OpenMRS Distro HIS (need to identify how can do so).

  • No progress on FHIR specs for ERP processes. @Romain Buisson will provide updates in next call.

  • @Stephen Senkomago Musoke is looking into trying Superset within Ozone.

    • Discuss how we could leverage on Mamba ETL flattening in Ozone Analytics.

    • Superset alone (in Ozone FOSS) is decommissioned for now in favor of running it with Ozone Analytics.