Bug report: duplicate entities appearing in sets
Adding entities to sets doesn't check if those entities are already present, leading to duplicate entities. For example, say I create a set "set1" with entities "sample1", "sample2", "sample3". If I repeat the same command, I will end up with "set1" having 6 entities, with each of the original entities appearing twice. This should not be possible; either the set should be entirely replaced (so entities previously in the set but not in the new set will be removed), or the result should be the union of the previous set entities and new set entities.
Comments
10 comments
Hi Stephanie Gogarten,
Thanks for writing in about this and I apologize that this is impacting usability for you. I have sent this request to our development team and will follow up if it gets built!
Kind regards,
Pamela
Hey Stephanie Gogarten,
Thanks again for writing in about this issue. I wanted to follow up about it since I wasn't able to replicate this situation. When I tried to create another set of the same name I got an error from Terra that the set already exists.
Can you give us more details for how you are adding additional entities to the set that already exists? Are you uploading a table TSV?
Kind regards,
Jason
I was using the Bioconductor AnVIL R package, function `avtable_import_set`
Hi Stephanie,
Thanks for the information! Allow me to answer for Jason. I'll be testing that package for you and see if I can replicate the results. If I can, I'll determine if that bug only exists within that package, as we may need to open a request to have the Bioconductor AnVIL team take a look.
I'll try to test this as soon as I can and I'll provide any updates.
Please let me know if you have any questions.
Best,
Josh
Hi Stephanie,
I was able to replicate the issue you're currently seeing. As I stated earlier, it looks like this bug is with the Bioconductor AnVIL package, and I have already opened an issue for this on their GitHub page. I'll let you know if this gets resolved. Thanks again for bringing this to our attention.
Please let me know if you have any questions.
Best,
Josh
See the comments from the Bioconductor package maintainer here reporting they were able to reproduce this problem in the Terra UI.
Hi Stephanie,
Thanks for the reply! We're doing to testing with the UI now, and I'll let you know once we have any updates.
Please let me know if you have any questions.
Best,
Josh
Hi Stephanie,
I wanted to give you an update on this ticket. As it turns out, we were able to determine that there is a bug in the Terra UI that the Bioconductor package interfaces with to cause the behavior you've reported. We've already reported this bug to our engineering teams, and we'll let you know once this has been resolved.
Please let me know if you have any questions.
Best,
Josh
Hi Terra Support,
Our team has encountered similar issues. We received data for secondary analysis and observed that the sample_set contained duplicated samples. It appears that Terra recognizes the presence of duplicates in the sample_set when I am about to launch the workflow. However, I am confuded as to why the sample_set allows for sample duplication in the first place.
Thanks,
Gao
Hi Gao,
Thank you for your comment. I've added your screenshot and description to the existing bug ticket for this issue to help our engineers prioritize it. I can follow up here when there are any updates on it.
Kind regards,
Pamela
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