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onc-healthit / onc-certification-g10-test-kit

ONC Certification (g)(10) Standardized API Tests
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Problems building terminology (macOS) #68

Closed dwebe003 closed 2 years ago

dwebe003 commented 2 years ago

Issue: Terminology not loaded after following the steps in the instructions.

Steps followed: 1) Cloned repo 2) Ran sudo ./setup.sh 3) Ran sudo docker-compose -f terminology_compose.yml build (Took about 7mins) 4) Added api_key to .env (UMLS_API_KEY=my_api_key and CLEANUP=true) 5) Ran sudo docker-compose -f terminology_compose.yml up

Clearly something happened with building and running the terminology_compose, but I can't figure it out. Is there a configuration or a vital step that I'm missing? Could it be a Mac issue?

Any help would be appreciated! Thanks.

Jammjammjamm commented 2 years ago

Thank you for bringing that tmp folder issue to our attention. That is something we definitely need to address.

The inferno development team uses macs, so it isn't a mac issue. I don't use sudo for anything inferno related, so it's possible that could cause issues at some point.

It looks like your build is failing because your api key is incorrect. You should see output like this:

g10-certification-test-kit-terminology_builder-1  | Getting Ticket Granting Ticket
g10-certification-test-kit-terminology_builder-1  | Getting ticket
g10-certification-test-kit-terminology_builder-1  | Downloading
g10-certification-test-kit-terminology_builder-1  | text/html; charset=iso-8859-1
g10-certification-test-kit-terminology_builder-1  | application/zip
g10-certification-test-kit-terminology_builder-1  | 1% complete
g10-certification-test-kit-terminology_builder-1  | 2% complete
...
dwebe003 commented 2 years ago

@Jammjammjamm Thank you for such a quick response! Glad I could help identify the tmp folder thing.

As for my issue, you are completely correct. I was using a colleague's API key because my UMLS access had not been approved yet. But my account just got approved and now, using my API key, the terminology up is currently processing as it should be.

Jammjammjamm commented 2 years ago

Great, please let us know if you encounter any more problems. The terminology build process takes a lot of resources and a lot of time. As long as you're not in one of the downloading parts of the process (which you can tell from the % complete messages), it's fine if you need to put your computer to sleep. I've done it plenty of times and it picks right back up when you wake it.

dwebe003 commented 2 years ago

Screen Shot 2022-04-05 at 1 22 23 PM

It seems that my download process had a hiccup around the 32% mark. It may have very well been my internet connection though. I'm going to attempt it again.

Thank you for the help by the way!

dwebe003 commented 2 years ago

My download process keeps ending prematurely (like in the above screenshot). I have gotten as far as 75% on one attempt and then it stops. Is this a timeout issue or something?

dwebe003 commented 2 years ago

@Jammjammjamm Would it be possible to simply download the ZIP from my browser and put it in this directory manually? Unless you know what's going on with my situation.

Jammjammjamm commented 2 years ago

If you're able to download it via your browser, that would absolutely work. Three different version get downloaded, 2019, 2020, and 2021.

dwebe003 commented 2 years ago

https://www.nlm.nih.gov/research/umls/licensedcontent/umlsarchives04.html#2019AA Is this what I would want? The 2019 AA full release?

And for the 2020 and 2021 versions, can I assume their own folders get created like such:

Jammjammjamm commented 2 years ago

Yes, the filenames are like that. We're using the 2019AB, 2020AB and 2021AA releases. You can see the exact urls we're using here: https://github.com/onc-healthit/onc-certification-g10-test-kit/blob/main/lib/inferno/terminology/tasks/download_umls.rb#L12

yunwwang commented 2 years ago

@dwebe003

I close this issue since no activity in the last three month. If you are still experiencing the same problem, you can either create a new issue or reopen this one.

Thank you.