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Deploying a shiny app

#1

Hello,

I’d like to deploy the IBD characterization + diagnostics apps; is https://github.com/OHDSI/ShinyDeploy the right place? Who can grant permissions to put it there?

Also, seems that many (perhaps most) apps in ShinyDeploy use a database to store the results. When is it preferred over PreMerged.RData? And how do I upload results into that db (permissions, code)?

Thanks.

#2

@cyanover If you upload your shiny application to that github repo then it will automatically be deployed to the public data.ohdsi.org data server. I’m not sure who within OHDSI maintains permissions to write to that GitHub repo. Maybe @Patrick_Ryan can provide a contact for you.

The decision point on whether to use a PreMerged.RData file or a database depends on the size of the dataset. There isn’t a hard limit but if the dataset is perhaps > 256MB then switching to using a database will help with the performance of the shiny app (and the shiny application server).

The data.ohdsi.org shiny server uses a postgresql database so I’d recommend that you test the shiny application with a local postgresql database prior to deploying it on the OHDSI shiny server.

If you are approved to upload your shiny app to the ShinyDeploy server then send me a direct message with your contact information and I can setup the OHDSI shiny server database permissions and connection details if database access is needed.

#3

Thanks a lot, @admin, that’s very helpful.

Is there an example code that shows how to upload the results to a postgresql database?

#4

@admin, a follow-up question: the size of my PreMerged.RData file is approx. 140MB. However, when I’m trying to commit it, I get the following warning:

The following files are over 100MB. If you commit these files, you will no longer be able to push this repository to GitHub.com. We recommend you avoid committing these files or use Git LFS to store large files on GitHub

Does this actually mean I have to switch to DB?

#5

@cyanover That is a limitation of GitHub. Previously, I uploaded my files to GitHub by Git LFS, but the uploaded files were not opened. So I don’t want to recommend Git LFS. The easiest way would be splitting the files…

#6

Thanks for the advice, @SCYou. The IBD Characterization shiny app is finally up and running!

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