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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Re-upload underlying figure data to Zenodo #1744

Closed jaclyn-taroni closed 1 year ago

jaclyn-taroni commented 1 year ago

Because: https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1743

sjspielman commented 1 year ago

I checked that all other CSV files are properly delimited, and #1743 appears to be the only thing to fix.

sjspielman commented 1 year ago

And https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1751.

I checked that all other CSV files are properly delimited,

I did this by reading everything all the CSVs in with readr::read_csv(), and I've since learned that was not the right approach. readr has no problem figuring out extra \n in the middle of lines (is this a bug or a feature? i'm on the fence!), but other platforms likely will not like this! I've now manually looked over every CSV and feel much more convinced that this additional fix in #1751 takes care of the the only other problematic file, but if someone else wants to peek around I will not argue...

jashapiro commented 1 year ago

And #1751.

I checked that all other CSV files are properly delimited,

I did this by reading everything all the CSVs in with readr::read_csv(), and I've since learned that was not the right approach. readr has no problem figuring out extra \n in the middle of lines (is this a bug or a feature? i'm on the fence!), but other platforms likely will not like this! I've now manually looked over every CSV and feel much more convinced that this additional fix in #1751 takes care of the the only other problematic file, but if someone else wants to peek around I will not argue...

I think removing newlines is good and fine, but having a newline in a CSV is pretty common, and I would expect most readers to handle it just fine (as long as the line is quoted). https://stackoverflow.com/questions/566052/can-you-encode-cr-lf-in-into-csv-files

jaclyn-taroni commented 1 year ago

DOI: 10.5281/zenodo.7877739