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Name tags seem to not be displaying on collections on 23.0 / .org #15878

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hexylena opened this issue Mar 31, 2023 · 4 comments
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Name tags seem to not be displaying on collections on 23.0 / .org #15878

hexylena opened this issue Mar 31, 2023 · 4 comments

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@hexylena
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I have not reproduced this anywhere else yet since EU was having issues but here's the problem. I created a collection with the rule builder, and from the dataset information we see multiple name tags applied

request_json | {"targets": [{"destination": {"type": "hdca",  "object_id": 2006930}, "collection_type": "list:paired", "name":  "PRJNA128733", "elements": [{"name": "SRR057629", "collection_type":  "paired", "elements": [{"name": "forward", "dbkey": "hg38", "ext":  "auto", "tags": ["name:carcinoma_C02", "name:GSM554076"], "src": "url",  "url":  "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR057/SRR057629/SRR057629_1.fastq.gz",  "hashes": [], "in_place": false, "purge_source": false}, {"name":  "reverse", "dbkey": "hg38", "ext": "auto", "tags":  ["name:carcinoma_C02", "name:GSM554076"], "src": "url", "url":  "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR057/SRR057629/SRR057629_2.fastq.gz",  "hashes": [], "in_place": false, "purge_source": false}]},

which looks great. But they're not rendered in most useful views:

list doesn't show them paired doesn't show them individual elements also don't but show hidden shows everything
image image image image
@hexylena hexylena added this to the 23.0 milestone Mar 31, 2023
mvdbeek added a commit to mvdbeek/galaxy that referenced this issue Mar 31, 2023
Fixes galaxyproject#15878.
I don't love it, but the endpoint is paginated, and if we want
to show tags in the summary view I think we have to do this.
@mvdbeek
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mvdbeek commented Mar 31, 2023

list doesn't show them

it shouldn't, right ? If you tag the actual collection (like in the old history, click on the collection, then the pencil icon) it shows.

individual elements also don't

that'll be fixed by #15883

paired doesn't show them

I guess it probably shouldn't if those tags are applied to the leaf elements ?

mvdbeek added a commit to mvdbeek/galaxy that referenced this issue Mar 31, 2023
Fixes galaxyproject#15878.
I don't love it, but the endpoint is paginated, and if we want
to show tags in the summary view I think we have to do this.
@hexylena
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hexylena commented Apr 3, 2023

I could have sworn the old implementation tags 'bubbled' up to be present on the top level element, meaning tagging leafs would still result in the base element showing them, but there's a chance I'm mis-remembering that and not worth spinning up an environment to check. If that was how it worked, it was 'wrong' especially if you can tag a parent element of a collection, but I think I used it for get a feeling for which datasets were inside without having to browse it.

But ok, thanks for #15883, let's say that solves this.

@hexylena hexylena closed this as completed Apr 3, 2023
@mvdbeek
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mvdbeek commented Apr 3, 2023

I don't remember exactly how it all worked in the old history. There are still cases where tags can bubble up, which is when you reduce child elements. All the tags of the children should appear on the reduced output (in the tumor/normal setting with the funky side-effect of tumor and normal tags when you mask background mutations ... ). We could also do what you describe, but there's a cost to doing arbitrary depth lookups for tags in the summary view that the history requests, I'm not sure which way to go there.

@hexylena
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hexylena commented Apr 3, 2023

It makes sense, the abritrary depth lookups are not ideal, especially for large collections I'm not sure it'd be useful. And you'd probably want a way to distinguish parent from child tags at that point which is extra UI we don't want or need as it's already complex enough.

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