Species of Interest TaxaList Filter #777

mohamedelabbas1996 · 2025-03-13T14:25:57Z

Summary

This PR introduces a Taxa List filter for occurrences and taxa views, enabling filtering based on taxons in a Taxa List . The filter ensures that Occurrences and Taxa can be filtered by their presence in a Taxa List or if their ancestors belong to a specified Taxa List. Additionally, Taxa Lists can be managed from the admin dashboard, allowing users to Create new Taxa Lists, Add taxa to a Taxa List and Link Taxa Lists to projects.

List of Changes

Added OccurrenceTaxaListFilter: Enables filtering Occurrence objects where determination is in a TaxaList or has an ancestor in the list.
Added TaxonTaxaListFilter: Enables filtering Taxon objects where the taxon is in a TaxaList or has an ancestor in the list.
Added Taxa List filter UI for Occurrences and Taxa Pages:
Users can now filter occurrences and taxa by selecting a Taxa List from a dropdown.

Related Issues

#745

How to Test the Changes

Verify Taxa List Filtering in Occurrences and Taxa Pages
Navigate to the Occurrences Page.
Locate the Taxa List filter dropdown.
Select a TaxaList.
Verify that:
Only Occurrences with a determination in the selected TaxaList or its ancestors are displayed.
Changing the TaxaList filter updates the results accordingly.
Repeat the same steps on the Taxa Page.

Screenshots

Deployment Notes

No database migrations required.

Checklist

I have tested these changes appropriately.
I have added and/or modified relevant tests.
I updated relevant documentation or comments.
I have verified that this PR follows the project's coding standards.
Any dependent changes have already been merged to main.

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mihow · 2025-03-13T23:58:16Z

ami/main/api/views.py

+                logger.debug(f"Filtering by taxalist {taxalist_id} taxa_ids {taxa}")
+
+                # filter by the exact determination
+                query_filter = Q(determination__in=taxa)


Can you use a sub query instead? If you generate the list of taxa in python first and then pass it back, it may be too long. Some regional taxa lists will have over a few thousand items.

Example:

antenna/ami/main/models.py

Lines 2343 to 2346 in 1adb99d

Classification.objects.filter(detection__occurrence=self)

.filter(

score__in=models.Subquery(

Classification.objects.filter(detection__occurrence=self)

Actually I don't think a subquery is possible with our parents_json field. We can come back to that later. Also the first filter can occur on the Taxa view. Instead of the Occurrences view. Ideally both, but Taxa is the most important for the first demo.

mihow · 2025-03-13T23:59:51Z

config/api_router.py

 router.register(r"detections", views.DetectionViewSet)
 router.register(r"occurrences", views.OccurrenceViewSet)
 router.register(r"taxa", views.TaxonViewSet)
+router.register(r"taxalists", views.TaxaListViewSet)


Will you try mounting under /taxa? /taxa/lists? Like the ml prefix. We will eventually move all taxonomy related things into a taxa app. If it causes a headache then no worries.

mihow · 2025-03-14T00:06:36Z

ami/main/api/serializers.py



+class TaxaListSerializer(serializers.ModelSerializer):
+    taxa = serializers.PrimaryKeyRelatedField(queryset=Taxon.objects.all(), many=True)


I don't think the TaxaListSerializer needs to return the actual taxa in the list. Try adding a link to the filtered taxa view instead like this example in SourceImageCollectionSerializer which links to a filtered SourceImages view:

antenna/ami/main/api/serializers.py

Lines 1099 to 1108 in c18ff50

def get_source_images(self, obj) -> str:

"""

Return URL to the captures endpoint filtered by this collection.

"""

return reverse_with_params(

"sourceimage-list",

request=self.context.get("request"),

params={"collections": obj.pk},

)

Perhaps in the detail view, but I don't think the taxa list is necessary in either right now and it will be long!

mihow · 2025-03-14T00:08:32Z

ami/main/api/views.py

+    query_param = "taxalist"
+
+    def filter_queryset(self, request, queryset, view):
+        taxalist_id = request.query_params.get(self.query_param)


I'm glad you are using the IntegerField here for validating the query param! Here is how we are doing it in other filters. You don't need to check for the taxalist_id first if you set required to False.

antenna/ami/main/api/views.py

Lines 864 to 868 in c18ff50

def filter_queryset(self, request, queryset, view):

collection_id = IntegerField(required=False).clean(request.query_params.get(self.query_param))

if collection_id:

# Here the queryset is the Occurrence queryset

return queryset.filter(detections__source_image__collections=collection_id)

…RolnickLab/antenna into feat/species-of-interest-filter

mihow · 2025-03-17T21:40:07Z

ami/main/api/serializers.py

+        """
+        Return URL to the taxa endpoint filtered by this taxalist.
+        """
+        return reverse_with_params(


Thanks for finding this!

mihow · 2025-03-17T21:46:02Z

ami/main/api/views.py

        return super().list(request, *args, **kwargs)


+class TaxonTaxaListFilter(filters.BaseFilterBackend):


OccurrenceTaxaListFilter and TaxonTaxaListFilter are almost identical. If we can't reuse the filter, will you at least update the docstring in the filter classes to make it clear they are doing the same type of recursive search? Something like "Query for all taxa in the requested TaxaList, and any of their children that are in the the TaxaList, recursively"

Thank you!

mihow · 2025-03-17T21:53:03Z

It works!

mihow · 2025-03-17T22:01:53Z

@annavik will you review the frontend changes on this one?

We will likely have a Taxonomy section soon in the new Project sub-menus as well!

…stFilter

…RolnickLab/antenna into feat/species-of-interest-filter

mihow · 2025-03-19T01:39:45Z

@annavik I pushed one simple method of hiding the Taxa List filter if there are no lists configured for the current project. I couldn't see how to add a showFilter() method to the TaxaList type because we don't have the current project in that context.

If we do more of these, we could add a hideIfDisabled attribute to the FormControl component? Because the Taxa List filter component has already checked the data and disabled the form field.

Anyway, let us know what you think of the other changes. We can improve the lists feature over time.

annavik

So glad you could include some FE updates @mohamedelabbas1996 ! 👏

Just let me know if you want to have a chat about anything. The multi fetch problem I want to think about a bit more, I think no show stopper though!

ui/src/data-services/hooks/taxalists/useTaxalists.ts

ui/src/data-services/models/taxalist.ts

ui/src/utils/useFilters.ts

ui/src/data-services/models/taxalist.ts

ui/src/data-services/constants.ts

ui/src/pages/occurrences/occurrences.tsx

…fetch

annavik · 2025-03-21T14:38:49Z

Thanks for the fixes @mohamedelabbas1996, this looks good to me now! :) I pushed an update to make it possible to pass custom data to filter controls. Thanks to that we can now skip the multi fetching. See commit 7cd7738 if you are curious about the solution.

I will approve this now!

annavik · 2025-03-21T14:46:04Z

One detail: do you think we should exclude "id" from the filter key everywhere, to follow same pattern we use for other filters? No blocker though.

(Not just here, but overall)

mohamedelabbas1996 · 2025-03-24T10:00:42Z

One detail: do you think we should exclude "id" from the filter key everywhere, to follow same pattern we use for other filters? No blocker though.

Thanks for pointing that out, Anna! I was actually following the pattern discussed in issue #660, where we're aiming to use object_id to refer to the actual ID and object for the object itself (e.g., project_id vs. project). Not sure if we’re still aligning with that convention, happy to adjust if needed!

annavik · 2025-03-24T13:19:50Z

One detail: do you think we should exclude "id" from the filter key everywhere, to follow same pattern we use for other filters? No blocker though.

Thanks for pointing that out, Anna! I was actually following the pattern discussed in issue #660, where we're aiming to use object_id to refer to the actual ID and object for the object itself (e.g., project_id vs. project). Not sure if we’re still aligning with that convention, happy to adjust if needed!

I see, I understand it's a bit confusing since we have been a bit inconsistent here! I do like having id as part of the key, I think it's more clear :) I also like to keep the filter feature consistent though...

Let's keep this filter key as is, if the plan is to update other filter keys in a near future? :) @mihow any thoughts?

mihow · 2025-03-25T01:31:43Z

@annavik I'm glad you noticed this detail! And I am glad you like the _id version. This will help distinguish which properties are just IDs (or specific attributes) and which ones are nested json representations of related objects. For example:

project: { deployment_id: 2}
project: { deployment: {name: "Mothra", id: 2} }

I'm sorry we haven't updated them all at once! project => project_id was the first full-project change. And now taxa_list_id is the first new attribute it's being applied to.

mihow · 2025-03-25T01:34:21Z

Thanks for the fixes @mohamedelabbas1996, this looks good to me now! :) I pushed an update to make it possible to pass custom data to filter controls. Thanks to that we can now skip the multi fetching. See commit 7cd7738 if you are curious about the solution.

I will approve this now!

Thanks for sharing the fix. It seems like that approach opens the door for a lot of flexibility.

feat: Added TaxList Viewset and TaxaListOccurrence Filter

28fdd7b

mohamedelabbas1996 linked an issue Mar 13, 2025 that may be closed by this pull request

Add filtering options for Taxa Lists #745

Closed

Merge branch 'main' into feat/species-of-interest-filter

76d7044

mohamedelabbas1996 self-assigned this Mar 13, 2025

mohamedelabbas1996 marked this pull request as draft March 13, 2025 14:28

mohamedelabbas1996 changed the title ~~Species of Interest TaxaList Filter~~ [Draft] Species of Interest TaxaList Filter Mar 13, 2025

mohamedelabbas1996 requested a review from mihow March 13, 2025 14:28

mihow reviewed Mar 13, 2025

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mihow reviewed Mar 14, 2025

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mohamedelabbas1996 added 3 commits March 14, 2025 20:32

feat: Added Taxa List filter to the TaxonViewSet

33b42ac

feat: Added Taxa List filter to occurrences and species pages

c108111

Merge branch 'main' into feat/species-of-interest-filter

59eb1c1

mohamedelabbas1996 changed the title ~~[Draft] Species of Interest TaxaList Filter~~ Species of Interest TaxaList Filter Mar 15, 2025

mohamedelabbas1996 marked this pull request as ready for review March 15, 2025 00:59

mohamedelabbas1996 added 4 commits March 14, 2025 22:11

fix: Fixed formatting

afc9e45

Merge branch 'feat/species-of-interest-filter' of https://github.com/…

60bff4e

…RolnickLab/antenna into feat/species-of-interest-filter

chore: renamed taxalists folder to taxa-lists

0111ef7

Merge branch 'main' into feat/species-of-interest-filter

bfe5784

mihow reviewed Mar 17, 2025

View reviewed changes

feat: use autocomplete field for taxa in taxlist admin

d9744c9

mihow requested a review from annavik March 17, 2025 21:59

mohamedelabbas1996 and others added 3 commits March 18, 2025 11:24

chore: Updated docstring for TaxonTaxaListFilter and OccurrenceTaxaLi…

c127a62

…stFilter

Merge branch 'feat/species-of-interest-filter' of https://github.com/…

c6e2fb8

…RolnickLab/antenna into feat/species-of-interest-filter

feat: hide the Taxa List filter if no lists for current project

aa552a0

annavik requested changes Mar 19, 2025

View reviewed changes

mohamedelabbas1996 and others added 6 commits March 20, 2025 07:10

Merge branch 'main' into feat/species-of-interest-filter

5695c3c

chore: rafactored TaxaList model to inherit from the Entity

36e9783

fix: Added missing model

d0116a2

fix: make it possible to pass data to filter controls and skip extra …

7cd7738

…fetch

chore: rename file "taxalist-filter.tsx" -> "taxa-list-filter.tsx"

b1a8203

chore: format code

51c7b05

annavik approved these changes Mar 21, 2025

View reviewed changes

mihow merged commit 815f952 into main Mar 25, 2025
6 checks passed

mihow deleted the feat/species-of-interest-filter branch March 25, 2025 01:34

mihow mentioned this pull request Apr 3, 2025

Support for "geo-fencing" approach to improve prediction accuracy for regional species list #797

Open

annavik mentioned this pull request May 2, 2025

Make it possible to add tags to taxa #825

Closed

	Classification.objects.filter(detection__occurrence=self)
	.filter(
	score__in=models.Subquery(
	Classification.objects.filter(detection__occurrence=self)



		class TaxaListSerializer(serializers.ModelSerializer):
		taxa = serializers.PrimaryKeyRelatedField(queryset=Taxon.objects.all(), many=True)

	def get_source_images(self, obj) -> str:
	"""
	Return URL to the captures endpoint filtered by this collection.
	"""

	return reverse_with_params(
	"sourceimage-list",
	request=self.context.get("request"),
	params={"collections": obj.pk},
	)

	def filter_queryset(self, request, queryset, view):
	collection_id = IntegerField(required=False).clean(request.query_params.get(self.query_param))
	if collection_id:
	# Here the queryset is the Occurrence queryset
	return queryset.filter(detections__source_image__collections=collection_id)

		return super().list(request, args, *kwargs)


		class TaxonTaxaListFilter(filters.BaseFilterBackend):

Species of Interest TaxaList Filter #777

Species of Interest TaxaList Filter #777

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Summary

List of Changes

Related Issues

How to Test the Changes

Screenshots

Deployment Notes

Checklist

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