Problems Adding Tags to Elements

usegalaxy.org support
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1

Hi all. I am trying to attach tags to some elements in a collection. Whenever I use the “edit dataset tags” function, the tag disappears after closing the collection. What could be the cause of this issue?

I don’t have this problem when adding tags to the whole collection or to datasets which aren’t part of a collection.

2

Hi @Iisa
thank you for bringing this issue to our attention! I’ve reproduced it.

@jennaj We need your expertise. The tag label icon is absent from individual datasets in a collection in new history view. It is present in legacy history view, but I cannot add tags. ‘tag elements’ tool creates a new collection with Tagged in the name, but tags are not visible, and DESeq2 does not see the tags, when I loosely followed tutorial Group tags for complex experimental designs
The same issue on both usegalaxy.org and Galaxy Australia. I have very little experience with tags in collections, but this option was used on Galaxy Australia some time ago. Maybe you can double check? It looks like a Galaxy issue…
Kind regards,
Igor

1 Like
3

Hi @Iisa & @igor

I think that most of this is working correctly, and maybe the items tested out below help more. Running through the tutorial is definitely possible. Adding/removing tags directly for general collection tags or element dataset “group” tags is error prone but also possible.

  • Adding in tags to a collection (top level):
    1. Expand the collection
    2. Click on the tag icon
    3. Type in the tag content
    4. Then, make sure to hit return after completing or the changes could be lost.
      → the tag itself will look different after: be in a distinct box with text and a color
    5. If using the legacy history view, the history needs to be refreshed to show the tag.
    6. The tag must start with a hash # if you want it display in the history view, otherwise it will only show up when the collection is expanded. Both versions will display for input lists on a tool form.
  • Adding in tags to any dataset
    1. Expand the dataset (found only under the Hidden tab of the new Beta history view if in a collection)
    2. Click on the tag icon
    3. Type in the tag content
    4. Then, make sure to hit return after completing or the changes could be lost.
    5. Tags that start with a hash # will propagate the tag to downstream outputs.
      → Many are annoyed by this content not automatically saving, and it also presents when adding tags to or renaming a History (the latter also requires an extra “save” button click). The entire “tag” UI/UX functionality will be adjusted in the next release, and the PR below already includes several of these “nicer” UI adjustments but those are not yet available at the public servers.
  • The Tag elements tool has what looks like a bug: doesn’t always remove tags and oddly seems to create duplicated tags but again, not always. I will mark this for testing in the upcoming release, and follow-up with a tool-level bug issue if still needed.
  • Importantly, those duplicated tags do not cause a technical or content error with DESeq2.

Tests

function beta view legacy view 23.0 PR 15225 will address?
Upload rule-based adding tags element tags not displayed or changeable in history view “active” tab + but are displayed and changeable in hidden tab element tags not displayed or changeable unless the dataset is expanded and tag-icon is clicked on N/A
Extract/Replace/Tag tools adding tags element tags not displayed or changeable in history view “active” tab + but are displayed and changeable in hidden tab element tags not displayed or changeable unless the dataset is expanded and tag-icon is clicked on N/A
Tag elements tool modifying tags: add + kept added + kept + will create duplicated tags + tag color default when duplicated same + tag color (warning?) red when duplicated pending release tests
Tag elements tool modifying tags: add + remove added + NOT (all) removed + will create duplicated tags + tag color default when duplicated same + tag color (warning?) red when duplicated pending release tests
Tag elements tool modifying tags: remove added + NOT (any) removed + will create duplicated tags + tag color default when duplicated same + tag color (warning?) red when duplicated pending release tests
DESeq2 Determines differentially expressed features from count tables (Galaxy Version 2.11.40.7+galaxy2) following Group tags for complex experimental designs proper tags duplicated tags
Collection from: Upload rule-based adding tags correct result correct result
Collection from: Extract/Replace/Tag tools adding tags correct result correct result

Hope that helps!