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timsbiomed / tims-ts

TIMS instance of HAPI FHIR.
http://20.119.216.32:8888/
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OWL on FHIR #1

Closed joeflack4 closed 1 year ago

joeflack4 commented 1 year ago

Major updates

OWL Conversion
- Add: Script to do the conversion
- Add: requirements*.txt files for managing dependencies.
- Add: Docs to README.md
- Add: robot.jar, a current, temporary dependency for the conversion.
ShahimEssaid commented 1 year ago

@joeflack4 I will review and use this asap but the general idea is that the python code/script will go into the "setup-servers" repository, wrapped in a Click cli command, etc. The bash scripts under /bin will invoke that functionality from "setup-servers" as needed. The robot Jar will be downloaded on demand by the "setup-servers" command and not be committed in the repo (just like how the Maven distribution is downloaded and used on demand)

joeflack4 commented 1 year ago

I don't disagree w/ that approach. I don't see any setup-servers repo though. Is this a directory that will be created by the scripts that build and run the server?

I don't mind robot.jar being downloaded, but it would be nice to have a way to convert OWL to FHIR in a standalone way. That's what I was trying to do here, out of the context/coupling of anything like OAK, the terminology server code, etc. And I could pre-convert stuff to simply be downloaded so that it doesn't need to be built by the server. Even though I'm griping, I realize there's a lot of different ways to do this, and I can be flexible.

joeflack4 commented 1 year ago

@ShahimEssaid I think I forgot to undraft this before. This has been ready to merge.

joeflack4 commented 1 year ago

@ShahimEssaid It looks like OWL-on-FHIR has been successfully refactored out, so I'm going to close this PR now.

It actually was working correctly by the time we all met last Monday the 20th. The next step is for me to merge my OAK PR, so until then, OWL-on-FHIR won't work as a package and will need to be cloned and used with a local clone of OAK. I'm going to try to get that down now during my current work session.