FHIR Intermediate - How To Set Up Your Own FHIR Server With HAPI FHIR

Hello developers! I am doing a code along with me webinar on 26th June. We will be building a SMART on FHIR 🔥 patient app on Epic in just 60 minutes. Are you up for the challenge? Sign up here: link.medblocks.com/fhir-62bfc9
🛠 Resources:
HAPI FHIR Documentation: hapifhir.io/hapi-fhir/docs/
Docker & Docker Compose Installation Guide: docs.docker.com/compose/install/
Insomnia REST Client: insomnia.rest/
Clone Repo for Simplified Server Setup: github.com/hapifhir/hapi-fhir...
Chapters:
0:00 - Introduction: Setting Up Your Own FHIR Server
0:07 - Choosing HAPI FHIR for Setting Up the Server
0:24 - Overview of the JPA Server and Its Components
0:58 - Getting Started with HAPI FHIR JPA Server Setup
1:13 - Cloning the Repository for Easier Setup
1:28 - Running the Repository Using Docker
1:57 - Explanation of Docker Compose Up Command Benefits
2:26 - Verifying the Jetty Server Launch on Localhost
2:33 - Testing the Server with Insomnia
2:53 - Validating the Server's Capability Statement
3:16 - Custom Changes Made for Easier Use and Validation
4:03 - Alternative Setup for Users Without Docker
4:39 - Initial Setup Download Times
4:58 - Conclusion
Welcome to this comprehensive tutorial on setting up your personal FHIR server using the HAPI FHIR framework, the most popular open-source implementation of FHIR standards in Java. This video is your step-by-step guide to getting your FHIR server running seamlessly using Docker, including tweaks made to simplify your setup experience.
🔥 What You Will Learn:
- The basics and importance of using HAPI FHIR as your FHIR server framework.
- An overview of the JPA server in HAPI FHIR and its architecture.
- How to clone and set up a pre-configured HAPI FHIR repository to fast-track your server setup.
- A straightforward method to run your HAPI FHIR server using Docker and Docker Compose.
- Testing your server's capability statement using Insomnia REST client.
- Adjustments made to the repository for a smoother setup, including validation of resources and simplified server URL.
- Alternative setup method for Windows Home Edition users or those preferring not to use Docker.
💡 Troubleshooting Tips:
Ensure Docker and Docker Compose are correctly installed and updated.
Verify your internet connection for first-time setup, as downloads can be extensive.
For Windows Home users, consider upgrading or exploring alternative setup methods as discussed.
📬 Do you have specific topics on HAPI FHIR you’d like explored further? Drop your questions and topic requests in the comments section below. Your feedback drives our content!
👍 Liked this video? Hit the 'Like' button, subscribe to our channel for more health informatics tutorials, and share this video with colleagues who might find it helpful.
Thank you for watching, and stay tuned for more insightful tutorials on leveraging FHIR for healthcare data interoperability.
#fhir #hl7 #healthinformatics #docker #healthcareinteroperability #tutorial #dockercompose #insomnia #restapi #repository

[@medblocks]

Hello developers! I am doing a code along with me webinar on 26th June. We will be building a SMART on FHIR 🔥 patient app on Epic in just 60 minutes. Are you up for the challenge? Sign up here: link.medblocks.com/fhir-adf6ed

[@jeanniehuang9117]

Hapi to help....what a kneeslapper! xD Thanks for the video Siddharth

[@tiagotele1]

Very useful!

[@karthickthiyagarajan8520]

Bro.. I couldn't believe you are a doctor by profession! Amazed to see your technical skills! Your videos are my motivation to learn fhir.. thanks for all the videos!

[@esparda07]

Doctors are so cheap they don't even activate Windows. xD

[@Kanishka6619]

Hi Siddharth, thanks for this vedio , I wanted to know where I can get the logic implemented for accommodating different databases

[@tonythadee9969]

Would it be safe to deploy this to production (let's say once you've added things like authentication and perhaps a customized front end)? Or are there steps to make this more production ready?

[@bushrakshaikh595]

Hi ramesh thanks for such awsome informative videos, could please make video where we will be able to understand how fhir is integrating with multiple his system or ehr/emr. I meant for mu how the request from client would come and how we can get started on it. Again thank you so much Awaiting your reply

[@sarankumar4198]

Hi Siddharth, Could you please make a video to deploy hapi server with authentication?

[@nikhilranka9660]

Thanks for the fork. Worked seamlessly.

[@FarhanAli-fo5tw]

Hey Nikil. Can you please tell me the process how you have run it ? Using docker or jetty? Because I tried and I'm not able to do so.

[@nikhilranka9660]

@@FarhanAli-fo5tw Sure. I used Siddharth's repo to get the docker up and running. With that HAPI server was working

[@sandeep-4433]

Hi Nikhil, do u know how to work with MONGODB in case of FHIR server

[@nikunjsoni8336]

Sidharth thanks for sharing FHIR information, I am not able to access your git repo.

[@damodarNaidu]

Hi Sidhart. How can I configure Authentication and Authorization in HAPI server?

[@ashwinipatil6688]

Thanks for the video

[@nedu47]

Hello Sidharth, thank you for this videos as always. Please, do you have a video on how to configure a locally maintained dictionary to work with hapi server?

[@nedu47]

@@medblocks I mean configuring Hapi Server to work with dictionary of ontology systems such as SNOMED CT, HPO, ICD10, etc coding schemes locally within the server system. for example: { "system": "loinc.org", "code": "LA25391-6", "display": "Normal metabolizer" }

[@vinodkalpaka]

Very good tutorial to learn the HPI FHIR server. I could set the customised IG prtofile/structure definition Uri to the validate function. Is it possible to put our own IF profile to the capability statement as we can do it in validation. And what is the possibility of setting this custom profile to the entire methods like create, search , validate , metadata(capability statement) ?

[@medblocks]

The HAPI FHIR server does support this kind of validation of custom profiles! You just need to ensure the meta.profile attribute of the resource is populated correctly and all StructureDefinition artefacts of the profile are uploaded to the FHIR Server!

[@khanhtran9547]

Hi Sidharth, I tried to install using docker-compose up but it's showing "command line is not found". Can you help me guild how to install docker-compose on Mac OS instead?

[@helentsai4518]

thank you for the video. it helps a lot. can you talk more about the server part. like how to create other resource types besides patients, and how they link to the patient profile?

[@lemhar7]

On the docker image i get 404 not found for endpoint "/metadata"

[@sureshkg1]

Hi Sidharth, your videos are very good, easy to follow, I have only one improvement, the quality of video seems low, the screen seems blurry, you can test that and see - compare to other videos may be.

[@sandeep-4433]

Hi... do u know how to load package in hapi fhir server???

[@sppsghosh]

I tried to follow your video but here is what I'm getting when I issue docker-compose up command after cloning the git repository : Traceback (most recent call last): File "site-packages\docker\api\client.py", line 205, in _retrieve_server_version File "site-packages\docker\api\daemon.py", line 181, in version File "site-packages\docker\utils\decorators.py", line 46, in inner File "site-packages\docker\api\client.py", line 228, in _get File "site-packages equests\sessions.py", line 543, in get File "site-packages equests\sessions.py", line 530, in request File "site-packages equests\sessions.py", line 643, in send File "site-packages equests\adapters.py", line 449, in send File "site-packages\urllib3\connectionpool.py", line 677, in urlopen File "site-packages\urllib3\connectionpool.py", line 392, in _make_request File "http\client.py", line 1244, in request File "http\client.py", line 1290, in _send_request File "http\client.py", line 1239, in endheaders File "http\client.py", line 1026, in _send_output File "http\client.py", line 966, in send File "site-packages\docker\transport pipeconn.py", line 32, in connect File "site-packages\docker\transport pipesocket.py", line 23, in wrapped File "site-packages\docker\transport pipesocket.py", line 72, in connect File "site-packages\docker\transport pipesocket.py", line 59, in connect pywintypes.error: (2, 'CreateFile', 'The system cannot find the file specified.') During handling of the above exception, another exception occurred: Traceback (most recent call last): File "docker-compose", line 3, in File "compose\cli\main.py", line 67, in main File "compose\cli\main.py", line 123, in perform_command File "compose\cli\command.py", line 69, in project_from_options File "compose\cli\command.py", line 132, in get_project File "compose\cli\docker_client.py", line 43, in get_client File "compose\cli\docker_client.py", line 170, in docker_client File "site-packages\docker\api\client.py", line 188, in __init__ File "site-packages\docker\api\client.py", line 213, in _retrieve_server_version docker.errors.DockerException: Error while fetching server API version: (2, 'CreateFile', 'The system cannot find the file specified.') [13528] Failed to execute script docker-compose

[@ramarora3168]

I get below error when I run docker-compose up: Step 1/8 : FROM maven:3.6.3-jdk-11-slim 3.6.3-jdk-11-slim: Pulling from library/maven ERROR: Service 'server' failed to build: no matching manifest for unknown in the manifest list entries I am using Windows OS. Any ideas? Thanks.

[@ramarora3168]

@@medblocks I see all the files from your github. Line breaks in which file? I didn't understand your Linux point, I am doing this on Windows.

[@user-nd7ee6wh6e]

Is it possible to connect custom tables, instead . My existing FHIR resources are in a JSON format inside a table column. I need to use the capability of FHIR server for searching the content?

[@medblocks]

Yeah. Using the Plain Server of HAPI

[@user-nd7ee6wh6e]

@@medblocks Thank, it is working.

[@bennyhammerperezvasquez6004]

Do you know if is it possible to implement consent interceptors on hapi-fhir-jpaserver-starter?

[@bennyhammerperezvasquez6004]

Thanks@@medblocks

[@icoding3982]

Hi Sidharth, i trying to use Azure FHIR, i don't know if u can help me, but the profiles validation not working. I did the registration for patient definition for us core profile, using /StructureDefinition endpoint on my service, and return 201 created. but when i post a json patient and remove the identifier that it's a required information, the resource is created anyway, so the validation is not working...... any suggestion? Regards.

[@icoding3982]

@@medblocks I found a FHIRValidator in a github repo support from microsoft to deal with us core profile validation. link for more detail => github.com/microsoft/health-architectures/tree/master/FHIR/FHIRValidator

[@lalithkumar9925]

when i run Docker-compose up, i am getting an error, Below is the error 'docker-compose' is not recognized as an internal or external command, operable program or batch file.

[@lalithkumar9925]

@@medblocks Hi Sidharth, i am using Windows 7, and i am getting an error while installing Docker, is there any other way to run the repository, This is the error i get Could not find Windows Runtime type 'Windows.Data.Json.JsonObject'. at CommunityInstaller.Manifest.FromJson(ILogManager logManager, String json, Boolean skipPrerequisites, IList`1 args) at CommunityInstaller.ExtractManifestStep.d__36.MoveNext() --- End of stack trace from previous location where exception was thrown --- at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw() at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) at CommunityInstaller.InstallWorkflow.d__32.MoveNext() --- End of stack trace from previous location where exception was thrown --- at System.Runtime.ExceptionServices.ExceptionDispatchInfo.Throw() at System.Runtime.CompilerServices.TaskAwaiter.HandleNonSuccessAndDebuggerNotification(Task task) at CommunityInstaller.InstallWorkflow.d__27.MoveNext()

[@saisrivatsa1092]

Hello there, your video helps us leaning a lot. thanks for posting useful videos for beginners. I need to setup a hapi fhir R5 server in my local, I tried in multiple ways but I couldn't do it. could you please help me in setup?

[@medblocks]

I believe we have helped you over email with the required docker compose files

[@saisrivatsa1092]

@@medblocks hello! I haven’t received any email. Could you please send it again to me.

[@mystery5868]

Can you make it with firely server.

[@medblocks]

The Firely Server is unfortunately not free and open-source. However, I'll see if I can ask for a collaboration to make a video on it.

[@user-nd7ee6wh6e]

Is it possible to connect custom tables, instead . My existing FHIR resources are in a JSON format inside a table column. I need to use the capability of FHIR server for searching the content? Either using Plain Server or JPA server ?

[@medblocks]

You are looking for a FHIR facade. The Plain Server is what you want to use here.

[@user-nd7ee6wh6e]

@cks yes, now search is working the plain server? Is there any option to work with JPA server instead of plain ? Because , as you know, JPA server can leverage the database's indexing and query optimization features, resulting in faster and more efficient searches compared to a plain server

[@medblocks]

@@user-nd7ee6wh6eYes, you can choose to just use the JPA server - here's the repo - github.com/hapifhir/hapi-fhir-jpaserver-starter

[@user-nd7ee6wh6e]

@@medblocks 👍

[@sanjayahuja22]

Where does it store the resources..I couldn't see you changing any connection string for the backend

[@sanjayahuja22]

@@medblocks thanks..Can you make one video on Azure Fhir server and using Smart on fhir?

[@sanjayahuja22]

@@medblocks Thanks Sidharth..Is there a way to bulk import the data for all the patients from FHIR server for analytics purpose?

[@juangabriel2559]

W

[@FarhanAli-fo5tw]

Hi Sidharth. I tried cloning your code and running it using both docker and mvn command but still i'm not bale to run it. it's showing me error on step 5 saying ERROR: Service 'hapi-fhir-jpaserver-start' failed to build: The command '/bin/sh -c mvn -ntp dependency:go-offline' returned a non-zero code: 1. MojoExecutinexception. Can you please help me with that. I'm using java 1.8 and Maven 3.6.3 version. Any help would be appreciated.

[@FarhanAli-fo5tw]

@@medblocks Yes. I have checked Internet is working inside my docker. Any other reasons?

[@FarhanAli-fo5tw]

@@medblocks Hi ! I tried it fresh again but this time I first tried it using jetty command and now it's running fine. Thank You so much ! Can you make video related to HAPI FHIR client Side too? And yes please keep posting more videos on Hapi FHIR. It helps a lot. :)

[@FarhanAli-fo5tw]

Can you please make a video on FHIR Facade ?

[@sayomakinwa7898]

Hi Siddharth, it appears you deleted your starter repo cos the link no longer works, and I couldn't find the repo on your github.

[@medblocks]

Sorry about that. I've updated it to the HAPI FHIR's official starter repo.

[@sayomakinwa7898]

@@medblocks Thanks! So I tried the starter server, but it would not validate against profiles, even after setting 'enable_repository_validating_interceptor' to true. Couldn't find much help online. Do you have any suggestions?

[@joostholslag8766]

There's been some changes in HAPI (docker compose.yml and application.yml moved and renamed), your video @@medblocks was still very helpful to get started. As was the readme on the repo you linked.

[@humairnoor3381]

Hi, Excellent video series on FHIR, i am running it in docker with mysql by cloning repository from above link, it works perfect. But when I try to check tables in "hapi" database, cannot find any: I am doing following on docker cli: # mysql -u admin -p Enter password: Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 11 Server version: 8.0.29 MySQL Community Server - GPL Copyright (c) 2000, 2022, Oracle and/or its affiliates. Oracle is a registered trademark of Oracle Corporation and/or its affiliates. Other names may be trademarks of their respective owners. Type 'help;' or '\h' for help. Type '\c' to clear the current input statement. mysql> use hapi; Database changed mysql> show tables; Empty set (0.00 sec) mysql> show databases; +--------------------+ | Database | +--------------------+ | hapi | | information_schema | +--------------------+ 2 rows in set (0.04 sec)

[@Tournesol143]

The urls are blurred. Hopefully this will help someone else: HAPI FHIR JPA Server: hapifhir.io/hapi-fhir/docs/server_jpa/get_started.html