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AlexsLemonade / OpenScPCA-analysis

An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal
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Update data download script: symlink treatment #530

Open sjspielman opened 1 week ago

sjspielman commented 1 week ago

Related to #523

We'd like to update the download-data.py script to have an option where users can swap symlinks between test and release without having to re-download all the data.

To implement this, we discussed an argument --update-symlinks <test/current/a given release date> to toggle the symlink. This argument should check to see if the data of interest exists locally and give some kind of informative message about the swap, but should not attempt to download fresh. We should write a small function to do the symlink toggling.

jashapiro commented 1 week ago

Just noting that the relevant current code is at https://github.com/AlexsLemonade/OpenScPCA-analysis/blob/36314e4dd8730dca4820c1502c8d18898f687d48/download-data.py#L245C1-L252C69

You will probably want to refactor this out into the function as described above that can be called either in its current location or when using the --update-symlinks function.