Add new feature to change taxon tree type in tree viewer

[CarolineDenis]

Fixes #4829
Fixes #4978
Fixes #4979

Checklist

• Self-review the PR after opening it to make sure the changes look good
  and self-explanatory (or properly documented)
• Add relevant issue to release milestone

Testing instructions

==> you need to add a new taxon tree in your db to test this PR

Tree Viewer

• Open the taxon tree viewer
• If the db as only one taxon tree, verify that the header is a H2
• If the db as several taxon trees, verify that the header is a drop down
• Verify that the header drop down contain all the trees of the db
• Change the tree type
• Verify the tree has changed
• click on a node, add a child
• verify that the ranks in the drop down are from the correct tree

QB

• Open the a new Taxon query
• Verify it is the same case when doing: New CO query > Determination > Taxon
• Query on any rank from any tree
• Query on a rank present in 2 or more trees and verify all nodes are doing return

[melton-jason]

@acwhite211 @CarolineDenis

Here is a summary of the major changes I did

Commits:
https://github.com/specify/specify7/pull/5036/files/fc36e4c1b779e172f35010c63c5a9a1c5be11f76..dcc229a65f5af2f1797937136d8d52710c26ec70

Backend

I have gone ahead and implemented the endpoint I suggested in a520069#commitcomment-143518914.

The endpoint returns all of the tree-structure related information for every tree the user has read access to.
That is, for each type of tree (Taxon, Storage, Geography, Lithostrat, Geologictimeperiod), an array of all definitions (TreeDefs) as well as all ranks (TreeDefItems) for each definition sorted by rankid.

The frontend previously was doing a serious of requests to create an object similar to what this endpoint now returns.

specify7/specifyweb/frontend/js_src/lib/components/InitialContext/treeRanks.ts

Lines 58 to 104 in b893ef7

	export const treeRanksPromise = Promise.all([
	// Dynamic imports are used to prevent circular dependencies
	import('../Permissions/helpers'),
	import('../Permissions').then(async ({ fetchContext }) => fetchContext),
	import('../DataModel/tables').then(async ({ fetchContext }) => fetchContext),
	fetchDomain,
	])
	.then(async ([{ hasTreeAccess, hasTablePermission }]) =>
	hasTablePermission('Discipline', 'read')
	? getDomainResource('discipline')
	?.fetch()
	.then((discipline) => {
	if (!f.has(paleoDiscs, discipline?.get('type')))
	disciplineTrees = commonTrees;
	})
	.then(async () =>
	Promise.all(
	disciplineTrees
	.filter((treeName) => hasTreeAccess(treeName, 'read'))
	.map(async (treeName) =>
	getDomainResource(getTreeScope(treeName) as 'discipline')
	?.rgetPromise(
	`${unCapitalize(treeName) as 'geography'}TreeDef`
	)
	.then(async (treeDefinition) => ({
	definition: treeDefinition,
	ranks: await fetchRelated(
	serializeResource(treeDefinition),
	'treeDefItems',
	0
	).then(({ records }) =>
	Array.from(records).sort(
	sortFunction(({ rankId }) => rankId)
	)
	),
	}))
	.then((ranks) => [treeName, ranks] as const)
	)
	)
	)
	: []
	)
	.then((ranks) => {
	// @ts-expect-error
	treeDefinitions = Object.fromEntries(ranks.filter(Boolean));
	return treeDefinitions;
	});

Feel free to share what you think:

specify7/specifyweb/specify/tree_views.py

Lines 420 to 444 in c64b8b6

	def all_tree_information(request):
	def has_tree_read_permission(tree: TREE_TABLE) -> bool:
	return has_table_permission(
	request.specify_collection.id, request.specify_user.id, tree, 'read')
	is_paleo_discipline = request.specify_collection.discipline.is_paleo()
	accessible_trees = tuple(filter(
	has_tree_read_permission, ALL_TRESS if is_paleo_discipline else COMMON_TREES))
	result = {}
	for tree in accessible_trees:
	result[tree] = []
	treedef_model = getattr(models, f'{tree.lower().capitalize()}treedef')
	tree_defs = treedef_model.objects.all()
	for definition in tree_defs:
	ranks = definition.treedefitems.order_by('rankid')
	result[tree].append({
	'definition': obj_to_data(definition),
	'ranks': [obj_to_data(rank) for rank in ranks]
	})
	return HttpResponse(toJson(result), content_type='application/json')

Also did some other small refactoring where I saw fit: primarily improving typing.

Frontend

The frontend work consisted of using the newly defined endpoint, getting the cache for the definition names up and running, and changing the pre-existing code to be compatible with all of the changes we have done to treeRanksPromise (and to lay the foundations for other changes in this PR).

Instead of having a single object in the cache which keeps track of each Tree's definition the user was last using, now we are creating a separate cache entry for each tree. This should make it simpler and easier to both access and set.

https://github.com/specify/specify7/pull/5036/files/fc36e4c1b779e172f35010c63c5a9a1c5be11f76..dcc229a65f5af2f1797937136d8d52710c26ec70#diff-af2e7f4cf2d56aca1781676234d2c93967a908b230cc5a04eb37a1309815e2b2R83-R84

💡 Although I would like to use the definition ids rather than the name internally to keep track of the 'current' tree. If the names of the trees change, this would automatically handle the case.

The code is completely functional right now: if the user has more than one Tree of a specific type created, they can switch which tree they are using. in the TreeView.

Other places which used the treeDefinitions promise and object should now also be compatible with the changes. We will just need to touch these places up when we work out resolving the 'default' Tree (currently it uses the first tree in the array of all trees).

[CarolineDenis]

@melton-jason,
Thank you for these changes, the new API makes the frontend code so much simpler

Although I would like to use the definition ids rather than the name internally to keep track of the 'current' tree. If the names of the trees change, this would automatically handle the case.

Yes, I think that would be good

resolving the 'default' Tree (currently it uses the first tree in the array of all trees).

We'll have to define where we set this default

[realVinayak]

@emenslin , or I guess @specify/ux-testing, clear your cache out before testing

[realVinayak]

actually, this'll be in production too.....

[emenslin]

@emenslin , or I guess @specify/ux-testing, clear your cache out before testing

I did clear my cache and it's still happening

[emenslin]

Still not working, I get this error once logged into the db

Specify 7 Crash Report - 2024-07-31T15_12_25.055Z.txt

[realVinayak]

Sorry, I didn't get to test it locally before pushing. Resolved now.

[emenslin]

Testing instructions

==> you need to add a new taxon tree in your db to test this PR

Tree Viewer

• Open the taxon tree viewer
• If the db as only one taxon tree, verify that the header is a H2
• If the db as several taxon trees, verify that the header is a drop down
• Verify that the header drop down contain all the trees of the db
• Change the tree type
• Verify the tree has changed
• click on a node, add a child
• verify that the ranks in the drop down are from the correct tree

QB

• Open the a new Taxon query
• Verify it is the same case when doing: New CO query > Determination > Taxon
• Query on any rank from any tree
• Query on a rank present in 2 or more trees and verify all nodes are doing return

Everything looks good from what I can tell, did not run into any of the previous errors this time

[Areyes42]

Testing instructions

==> you need to add a new taxon tree in your db to test this PR

Tree Viewer

• Open the taxon tree viewer
• If the db as only one taxon tree, verify that the header is a H2
• If the db as several taxon trees, verify that the header is a drop down
• Verify that the header drop down contain all the trees of the db
• Change the tree type
• Verify the tree has changed
• click on a node, add a child
• verify that the ranks in the drop down are from the correct tree

QB

• Open the a new Taxon query
• Verify it is the same case when doing: New CO query > Determination > Taxon
• Query on any rank from any tree
• Query on a rank present in 2 or more trees and verify all nodes are doing return

---

Tree viewer and QB looks good across multiple different DBs that I tested with. Didn't come across any major issues 👍

[lexiclevenger]

Testing instructions

==> you need to add a new taxon tree in your db to test this PR

Tree Viewer

• Open the taxon tree viewer
• If the db as only one taxon tree, verify that the header is a H2
• If the db as several taxon trees, verify that the header is a drop down
• Verify that the header drop down contain all the trees of the db
• Change the tree type
• Verify the tree has changed
• click on a node, add a child
• verify that the ranks in the drop down are from the correct tree

QB

• Open the a new Taxon query
• Verify it is the same case when doing: New CO query > Determination > Taxon
• Query on any rank from any tree
• Query on a rank present in 2 or more trees and verify all nodes are doing return

---

Looks good, everything seems to be working as expected. 👍

reviewed

[realVinayak]

@acwhite211 could have at least tried to add unit tests 🤦

[specifysoftware]

This pull request has been mentioned on Specify Community Forum. There might be relevant details there:

https://discourse.specifysoftware.org/t/specify-7-9-7-release-announcement/1979/1