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Sage-Bionetworks / dccmonitor

Allows for monitoring of data uploaded via the dccvalidator application. Functions for getting information on the uploaded files, metadata validation status, and more.
https://sage-bionetworks.github.io/dccmonitor
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Unable to pull templates for validation #97

Closed Aryllen closed 3 years ago

Aryllen commented 3 years ago

Updated the dccmonitor on the shiny server to have the lastest changes from dccvalidator. Now dccmonitor won't pull templates from synapse. Says that it's either not logged in or that it's not a valid synID. Before my local vm died, I could see that dccmonitor was pulling the correct synID from the config file, but that dccvalidator::get_templates() was failing. I could also see that it logged in on startup of the app. However, when in debug mode, I could not use syn to do anything.

In an R session on the shiny server, I can log in and use syn to download the templates via dccvalidator::get_template(). I think something is wrong in how syn is being referenced in dccmonitor, but I don't see where that change that broke it happened.

Currently trying to set up an environment that I can debug in.

Aryllen commented 3 years ago

On a relevant side note, I need to check over the GH actions PR again, merge it (assuming it's all good to go), and follow best practice when updating dccmonitor (use renv to update version in lockfile, open PR to change, verify it works, and then update the shiny server). 😒

Aryllen commented 3 years ago

Found the problem: I completely forgot that we added check support for existing study specimen/individual IDs, which means needing the samples_table in the config and passing the study name into dccvalidator::check_all(). 🤦

Aryllen commented 3 years ago

And...didn't realize my new branch was on the other computer and committed on master. Nice. Good job, me. Way to go...

Aryllen commented 3 years ago

Fixed in 6fda2147035278176d8f2fc7eab2a16d79f41418