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Suggest cases where a non-initialized DB may cause errors #356

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merged 1 commit into from
Feb 26, 2025

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dogversioning
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@dogversioning dogversioning commented Feb 26, 2025

In cases where an error :might: be related to a database not being initialized by the etl, we'll point out the documentation. Addresses #354

Checklist

  • Consider if documentation in docs/ needs to be updated
    • If you've changed the structure of a table, you may need to run generate-md
    • If you've added/removed core study fields that not in US Core, update our list of those in core-study-details.md
  • Consider if tests should be added
  • Update template repo if there are changes to study configuration in manifest.toml

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github-actions bot commented Feb 26, 2025

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines Covered Coverage Threshold Status
2448 2448 100% 100% 🟢

New Files

No new covered files...

Modified Files

File Coverage Status
cumulus_library/actions/builder.py 100% 🟢
cumulus_library/databases/athena.py 100% 🟢
cumulus_library/databases/base.py 100% 🟢
cumulus_library/databases/duckdb.py 100% 🟢
TOTAL 100% 🟢

updated for commit: c55bc47 by action🐍

if any(init_error in exit_message for init_error in config.db.init_errors()):
rich.print(
"Have you initialized your database?\n"
"https://docs.smarthealthit.org/cumulus/etl/setup/initialization.html"
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In our docs about our docs: https://github.com/smart-on-fhir/cumulus/blob/main/CONTRIBUTING.md
We suggest (well I suggest since I think I wrote that) that cross-repo doc links should only link to the top level, to reduce chances of having broken links when one repo reorganizes things.

I buy that in general, but I know it’s helpful here… is it bad to point at the top level and say “look at the ETL docs for initializing” or something without directly pointing at it? Or do you want to ignore the guidance and deal with the risk of link rot?

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I think in this case I do want to take the risk in part because we've already seen instances of people not navigating the docs well. I do think that the changes in the structure make it a little easier to find this information, so you could talk me out of this, but I kind of just want to hit people over the head with the specific information we're asking them to read.

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Meant to approve, sorry

@dogversioning dogversioning merged commit edce1a9 into main Feb 26, 2025
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@dogversioning dogversioning deleted the mg/warn_init branch February 26, 2025 20:34
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2 participants