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[ENH] Datasets: Add domain field; respect "Unlisted" #6920

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merged 9 commits into from
Nov 11, 2024

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janezd
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@janezd janezd commented Oct 18, 2024

Issue
  • When reimplementing the repository of data sets, we added a field "Domain". Its current values are "core" and "sc", but the plan was to add (a very limited) number of others, such as "Education", and to allow the user to select a domain in the Data sets widget. Domains were not meant to be like tags but rather to allow the user select a single specific domain.

  • With the new repository, the Datasets widget started showing single-cell data sets that were previously (if I remember correctly) accessible only in the single cell's widget. This PR reverts the behaviour to the more sensible original: by default, it only shows "core" data sets.

  • With @BlazZupan we discussed that it would be handy if a data set could be unlisted - shown only if the user types the first five characters of the dataset's name into the filter. This would not be used to prevent the user from seeing the data set, but just to avoid polluting the list with data sets used at occasional workshops. The functionality has been implemented and deployed in the data sets editor (https://github.com/biolab/orada/commit/ccd980e5f05131a80ac33031d6d87009d80a2b21).

Description of changes
  • Add a combo for selection of domains.
  • Show the "core" domain as "(general)". It is the default and does not include sc data sets.
  • Don't show data sets whose visibility is set as "unlisted" unless the user types the first five character into the filter.

To test the latter, try typing luxem.

Includes
  • Code changes
  • Tests
  • Documentation

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codecov bot commented Oct 18, 2024

Codecov Report

Attention: Patch coverage is 87.65432% with 10 lines in your changes missing coverage. Please review.

Project coverage is 88.39%. Comparing base (52df166) to head (300a753).
Report is 15 commits behind head on master.

Additional details and impacted files
@@            Coverage Diff             @@
##           master    #6920      +/-   ##
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+ Coverage   88.37%   88.39%   +0.01%     
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  Files         329      329              
  Lines       72447    72544      +97     
==========================================
+ Hits        64028    64125      +97     
  Misses       8419     8419              

@borondics
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Would it be possible to make it so that if there is a specific addon installed which has datasetes available on the servers then this domain is also added automatically? Basically the addon would register the domain in the datasets widget...?

@janezd
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janezd commented Oct 18, 2024

This is not "domain" in the sense of internet domain. It's more like a field, a category ... The genesis of "domains" is that we have too many data sets that we need for teaching, so we want to separate them from other data sets. We also have data sets for the single-cell add-on, which are probably not useful for the majority of users.

The widget still shows only data sets served from a single server. If you have some data sets to add - from a specific domain -, we can upload them.

But your question is probably rather about adding other servers? We could let the user (or an add-on) add servers, but servers need to provide a json file in a particular not-so-well-documented format. I doubt many would set it up; if only the "official" add-ons would do so, it's simpler to put their corresponding data on the existing server. I think.

@borondics
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borondics commented Oct 18, 2024

I think I understood "domain" the way you originally meant it for the this PR.

We have some orange-spectroscopy datasets on the biolab server and they might be excluded with this new PR so I was wondering if we could enable the orange-spectroscopy addon (or any other) to include those files ("domain") if it is installed.

However, adding new servers sounds interesting too...

@janezd janezd changed the title Datasets: Add domain field Datasets: Add domain field; respect "Unlisted" Oct 20, 2024
@janezd janezd force-pushed the datasets-add-domain branch 2 times, most recently from 860d45e to 993b552 Compare October 20, 2024 16:35
@markotoplak markotoplak changed the title Datasets: Add domain field; respect "Unlisted" [ENH] Datasets: Add domain field; respect "Unlisted" Oct 21, 2024
@markotoplak markotoplak added this to the 3.38.0 milestone Oct 21, 2024
@markotoplak
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We are going to move datasets between domains. Thus, it is critical that, as we just discussed, output the saved selected data set even if it was moved. And yes, we are both aware that this is going to be cumbersome.

@markotoplak markotoplak merged commit 747b3b2 into biolab:master Nov 11, 2024
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3 participants