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Issue: Website crashes upon addition of a counts matrix #226

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reductiveminded opened this issue Jun 20, 2024 · 2 comments
Closed

Issue: Website crashes upon addition of a counts matrix #226

reductiveminded opened this issue Jun 20, 2024 · 2 comments
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@reductiveminded
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Description:
My name is Matthew Marino. I am a CFDE GlyGEN summer intern working under Jeet Vora and Rene Ranzinger. I am currently trying to create multiomics workflows starting with transcriptomics and proteomics data.
Upon uploading a file to the node "Gene Count Matrix" I encounter the following error (screenshot below). Essentially the website crashes and I lose all progress on my workflow. I am also unable to perform any downstream data transformation (such as log2 transformation of the counts) because the matrix does not upload correctly.
I am using Brave browser on a windows operating system.

Image of Error:

Error_when_adding_counts_image

URL when error is displayed:
https://playbook-workflow-builder.cloud/graph/2ed94da4-7c2a-0ca0-d40e-71c0e76d4867/node/a25f7836-ebc0-526b-2552-7ec0e2b0ac05

Here is the counts matrix I have tried to upload it is from published dataset from my previous lab (https://doi.org/10.1021/acs.jproteome.3c00838). I used R studio to remove duplicates and 0 value reads and this is from bulk RNA Seq. The file size is 874 KB.

counts_filt_multi.txt

@u8sand
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u8sand commented Jun 20, 2024

Hi @reductiveminded -- thank you for reporting this issue.

The issue is that the data file is not in any obvious format. Please export it from R as a .tsv or a .csv and upload that (with the proper extension).

However, we definitely should not crash the page when this kind of error occurs but should report the error message to the user properly.

@u8sand u8sand added the bug Something isn't working label Jun 20, 2024
@reductiveminded
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Hello @u8sand -- thank you for your response.

I will try again with .csv format and let you know how it goes.

u8sand added a commit that referenced this issue Jun 24, 2024
@u8sand u8sand closed this as completed in ef0a805 Jun 24, 2024
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