additional_info.Rmd not displaying on Ingest tab

ndcn / omicser

The NDCN omics browser app for browsing and sharing general omics data.

https://ndcn.github.io/omicser

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additional_info.Rmd not displaying on Ingest tab #154

Closed bnovotny closed 2 years ago

bnovotny commented 2 years ago

Describe the bug The default additional_info.Rmd from the omicser package does not display on the Ingest tab. Instead, the Rmd template from RStudio displays, see screenshot. Possible file path issue on Windows?

To Reproduce Steps to reproduce the behavior:

Run omicser (on Windows 10), click on Ingest tab

Expected behavior The contents of omicser/app/www/additional_info.Rmd should be displayed.

Screenshots

Desktop (please complete the following information):

OS: Windows 10
Browser: Chrome

ricoderks commented 2 years ago

I'll have a look at this. First need to setup a Windows 10 test environment.

ricoderks commented 2 years ago

I just setup a Windows 10 test environment and installed omicser, but I don't see your issue. Can you tell which files are in: omicser\app\www\ ? The omiser folder is the library folder of R, e.g. C:\R\R-4.0.2\library.

bnovotny commented 2 years ago

Hi @ricoderks, in the the omicser/app/www/ folder I see additional_info.Rmd, favicon.ico, info.Rmd, logo.svg, and welcome.Rmd. The file additional_info.Rmd starts with

## Database Information Document

> This is a PLACEHOLDER!! 

> WIP template

### This Information HAS NOT been curated

Which I think is the right file, but it's not being displayed in the browser. I will keep poking around and try to find if this is coming from my computer. Thanks!

bnovotny commented 2 years ago

Figured it out, I had another additional_info.Rmd in my database folder that was being read. I was thinking that the custom Rmd had to be in the omicser/app/www/ folder rather than the database folder, so I didn't realize this one was being displayed. All is well now, thank you!