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@alesan99 alesan99 commented Jan 23, 2026

Fixes #7641

Speeds up default tree creation significantly.

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
  • Add pr to documentation list
  • Add automated tests
  • Add a reverse migration if a migration is present in the PR

Testing instructions

  • Test with the setup page
    • Use a blank database
    • Pre-load all the trees you can and complete the setup
    • Make sure the trees were pre-loaded correctly.
  • Test in the taxon tree viewer
    • Add a new taxon tree and choose to import a populated one.
    • Make sure the tree was created correctly. An easy way to check is to compare it with the same tree created before the speed ups.

Testing instructions from the issue-7593 PR to check:

  • Guided Setup on a blank database
  • Use a blank DB to test this PR.
  • Configure ranks for the geography.
  • Test the new pre-load tree check box for geography and taxon trees.
  • The pre-load checkbox for taxon trees should only be enabled if your discipline has a default tree (EX: Mammalogy has one, Geology doesn't).
  • After the setup, make sure the default tree creation process started for the trees you selected to pre-load. (You will see notifications)
    • If you chose a paleo/geo database then a chronostrat tree should also be imported automatically.
  • If you chose not to pre-load the taxon tree, the tree that was created should not have a root node.
  • After the setup, check all the new trees, make sure the ranks respect your configuration.
  • Pre-loaded trees should have had full names generated. You can check the full name preview on a taxon record for example.
  • Configuration tool and existing trees
  • Creating a new discipline with the configuration tool should create an empty taxon tree.
  • An empty taxon tree should have an import button
  • Make sure you can import a taxon tree into the existing empty tree
  • Make sure you can still create a new populated tree

@github-project-automation github-project-automation bot moved this to 📋Back Log in General Tester Board Jan 23, 2026
@alesan99 alesan99 changed the base branch from main to issue-7593 January 23, 2026 14:05
@alesan99 alesan99 marked this pull request as ready for review January 23, 2026 15:51
@CarolineDenis
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CarolineDenis commented Jan 23, 2026

Storage Tree:

  • Change separator from to ,
  • Building, Collection, Room, Aisle need to have full name checked

Taxon Tree:

  • Subspecies check Is full name needs to be removed
  • Preload tree is back, normal? (It works)
  • Ranks added in the setup but not included by default (i.e Subphylum) are not included in the generated tree (Which makes sense when we think about it)
  • Ranks cannot be deleted ('cannot delete root level tree definition item')
    ==> Notes: The above issues will not have to be addressed. We are going to simplify the implementation. See section simplification below.

Geography Tree:

  • County, State and Country need to have full name checked

Working:

  • Geography tree is loaded and respects the configuration made during the setup
  • Storage tree is created and respects the configuration made during the setup
  • Ranks removed in the setup that were included by default (i.e Genus) are not included in the generated tree, changes are reflected
  • Taxon tree is loaded with the correct taxon tree
  • Creating an empty tree in the tree viewer works and respects the rank config
  • Loading a tree in the tree viewer works and respects the ranks
  • Creating a new discipline with a collection in the system config creates a default empty tree
  • Loading the tree creating during the creation of the new discipline in system config works

Simplifications:

For the taxon tree configuration in the setup, some simplifications will be introduced.
The updated flow will be as follows:

  • The user selects the discipline type and name.
  • The user chooses whether or not to load a taxon tree (via a simple checkbox).
  • All taxon tree customization options are removed from the setup process.
  • Once in Specify 7, the user can access the Tree Viewer to make any desired configuration changes or remove ranks as needed.

@alesan99
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The simplifications have been implemented, ready to test again 👍

@alesan99 alesan99 requested review from a team January 23, 2026 20:01
@alesan99 alesan99 changed the title [Guided Setup] Optimize default tree creation fix [Guided Setup] Optimize default tree creation (fixed) Jan 23, 2026
@alesan99 alesan99 merged commit f4783f5 into issue-7593 Jan 26, 2026
13 checks passed
@github-project-automation github-project-automation bot moved this from 📋Back Log to ✅Done in General Tester Board Jan 26, 2026
@alesan99 alesan99 deleted the issue-7641-1 branch January 26, 2026 20:32
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[Guided Setup] : Speed up default tree creation

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