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Gravitate-Health / fhir-connector

FHIR connector example
Apache License 2.0
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[ePI] Adapt connector to retrieve resources from IG #15

Closed gmej closed 7 months ago

gmej commented 8 months ago

https://build.fhir.org/ig/joofio/test-epi-composition/toc.html

gmej commented 8 months ago

@joofio I have a question, is there an endpoint in the previous link that gives all the bundles or references to them in order to retrieve them from FOSPS so they are available for us?

gmej commented 8 months ago

OR are those bundles uploaded anywhere?

joofio commented 8 months ago

http://sandbox.hl7europe.eu/gravitate/fhir/Bundle

gmej commented 8 months ago

thanks

gmej commented 8 months ago

I have generalized the fhir-connector so it can be fully configured via environment variables in https://github.com/Gravitate-Health/fhir-connector/commit/b3299e7a643f30cd02957e9a5c303847913c727b. Different working modes are being developed. I just refactored the connector to make it generic and scalable. Now it pulls fsh files from github as before, next step is to pull from a FHIR server, and next one is acting as a proxy for FHIR servers.

gmej commented 8 months ago

@joofio you have a problem with your HAPI FHIR deployment. Pagination is broken.

When requesting a GET to /bundle, the "next" page is missing part of the path. The next url is constructed like this (missing "/fhir/" in path): 

http://sandbox.hl7europe.eu/gravitate?_getpages=fc1cc8c0-39a2-4d3b-b59e-6b90b3ad7e30&_getpagesoffset=10&_count=10&_pretty=true&_bundletype=searchset

When it should be like (with "/fhir" in path):

http://sandbox.hl7europe.eu/gravitate/fhir?_getpages=fc1cc8c0-39a2-4d3b-b59e-6b90b3ad7e30&_getpagesoffset=10&_count=10&_pretty=true&_bundletype=searchset

I think you are missing the "SERVER_SERVLET_CONTEXT_PATH" environment variable to configure the deployment of HAPI FHIR server under a different path.

Please tell me when it is solved so I can execute the connector (it is ready but waiting for the pagination to work)

image

gmej commented 8 months ago

Well indeed I don't think it's beacause of "SERVER_SERVLET_CONTEXT_PATH" as that is the part of the path behind "/fhir", @jkiddo any idea? We need this for the review

joofio commented 8 months ago

Why do you need that for the review ?

gmej commented 8 months ago

Alejandro commented us that you wanted those ePIs to be shown in the review

joofio commented 8 months ago

There is no need for that. The need for the epis is the ig which is done. However, this should be done of course.

gmej commented 8 months ago

OK then. I'll do it but not necessary for the review ok. Anyway for us to develop this connector we should solve this issue, not urgent as you say.

joofio commented 8 months ago

by the looks of it, it seems like a bug. but more analysis is required

jkiddo commented 8 months ago
image
jkiddo commented 8 months ago

seems to work fine to me

gmej commented 8 months ago

then it might not be a bug but a misconfiguration?

joofio commented 8 months ago

can you show me your config @jkiddo ?

jkiddo commented 8 months ago 
server:
  port : 8080
  servlet:
    context-path: /example/path
joofio commented 8 months ago

i think i found the issue. i will update after the midterm

joofio commented 8 months ago

should be solved

gmej commented 7 months ago

URL changed to http://sandbox.hl7europe.eu/gravitate-health/fhir/

joofio commented 7 months ago

@gmej to test and close if done

gmej commented 7 months ago

@joofio I was about to finish this task, but the server looks like it has no ePIs. https://sandbox.hl7europe.eu/gravitate-health/fhir/Bundle returns 0 results.

joofio commented 7 months ago

check now

gmej commented 7 months ago

Done. Now we have 1290 ePIs in dev.

Close this issue when you want. Next step we will generate provenance for all of them in #17