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nf-osi / NF_data_curator

Data Ingest Shiny App
https://sagebio.shinyapps.io/NF_data_curator/
Apache License 2.0
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Shiny deploy fails with new configuration expectations #144

Closed anngvu closed 2 years ago

anngvu commented 2 years ago

Describe the bug It looks like shiny deploy is expecting different config parameters and now fails. We reference the model via model.input.download_url, not model.input.repo.

config <- yaml::yaml.load_file("schematic_config.yml");
system(sprintf("echo MODEL_REPO=%s >> $GITHUB_ENV", config$model$input$repo));
Error in system(sprintf("echo MODEL_REPO=%s >> $GITHUB_ENV", config$model$input$repo)) : 
  non-empty character argument expected
Execution halted
Error: Process completed with exit code 1.

@allaway Is it safe to try to update this line to repo to use the new shiny deploy workflow?

allaway commented 2 years ago

I'm on my phone at the moment but it looks like this is just the develop branch, right? If so, I am waiting for an upstream change that is backwards compatible with the older config files. I'll take a closer look when I get home!

anngvu commented 2 years ago

Yes, this is just for develop. Was just looking at this file change: https://github.com/nf-osi/NF_data_curator/commit/605c82469d2bdc440fa3d53f35bc438d83639ee8#diff-5c0719296c8d398fa56ddc451d923ab39844d3ca179e8eb4c5d7debf8101d5b7

anngvu commented 2 years ago

I think this is another one of those instances where backwards-compatibility should have been prioritized...

allaway commented 2 years ago

Yeah, I think the DCA and schematic releases are slightly out of sync. The next DCA release to main should include changes that will make this backwards compatible.

allaway commented 2 years ago

Actually, I just checked and it seems like the PR (https://github.com/Sage-Bionetworks/data_curator/pull/411) has made it into main (https://github.com/Sage-Bionetworks/data_curator/pull/410)

anngvu commented 2 years ago

OK, looks like deployment works again. :tada: