Issue 8124 8126 fix 7660 7682 2 6266 after review

[melton-jason]

Taken from #8142 (comment) by @CarolineDenis:

Fixes #8124
Fixes #8126
Fixes #8101
Fixes #8065

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
• Add migration function to

  specify7/specifyweb/specify/management/commands/run_key_migration_functions.py

  Line 50 in ea04665

  def fix_schema_config(stdout: WriteToStdOut | None = None):

Testing instructions

Summary by CodeRabbit

• Bug Fixes

  • Corrected schema configuration references in data migrations
  • Fixed discipline and tree definition linking issues
  • Improved admin and permission initialization logic
  • Enhanced query logging controls based on debug settings

• Refactor

  • Streamlined migration utilities for improved efficiency
  • Simplified multi-database routing during migrations
  • Optimized permission seeding with per-user checks
  • Restructured role assignment logic using set-based operations

• Chores

  • Removed legacy debugging code and unused migration helpers
  • Updated function signatures to remove unnecessary parameters

[grantfitzsimmons]

This review was kind of a mess so I reformatted using Gemini.

Good news is that it works!

Databases tested:

Database	Discipline
aumnh_fish_2026_06_26	Ichthyology
alfmuseum_2026_06_26	Multi
aumnh_herbarium_2026_06_26	Botany
aumnh_inverts_2026_06_26	Invertebrate
bohart_entomology_2026_06_26	Entomology
calvertmarinemuseum_2026_06_26	Multi

Forward Migrations PASS ✅

Every database tested shows "No migrations to apply", the branch's migrations are already present.

Reverse Migrations, Core Apps Pass, Permissions Fail 🔴

App	Status	Notes
workbench (8 migrations)	✅ PASS	All reverse cleanly
setup_tool (1)	✅ PASS	All reverse cleanly
businessrules (9)	✅ PASS	All reverse cleanly
specify (44)	✅ PASS	All reverse cleanly (0023→0044)
patches (8)	✅ PASS	All reverse cleanly
notifications (6)	✅ PASS	All reverse cleanly
accounts (3)	✅ PASS	All reverse cleanly
attachment_gw (1)	✅ PASS	All reverse cleanly
permissions (8)	❌ FAIL	Not reversible — 0008 crashes

Permission reverse failure is expected and was pre-acknowledged by @melton-jason

Schema Config (splocale*)

From the 0023_update_schema_config_text migration logs, the revert function properly processes Schema Config items per table:

CollectionObjectGroup:     17 items reverted
CollectionObjectGroupJoin: 10 items reverted
AbsoluteAge:               12 items reverted
RelativeAge:               14 items reverted
TectonicUnit:              7 items reverted
TectonicUnitTreeDefItem:   5 items reverted
CollectionObject:          4 items reverted
TectonicUnitTreeDef:       2 items reverted
CollectionObjectType:      4 items reverted
CollectionObjectGroupType: 1 item reverted
AbsoluteAgeCitation:       1 item reverted
RelativeAgeCitation:       1 item reverted

All re-applied cleanly on forward migration with matching item counts.

TectonicUnit Trees ✅

Migration 0009_tectonic_ranks creates:

• 6 ranks per tree (Root, Superstructure, Tectonic Domain, Tectonic Subdomain, Tectonic Unit, Tectonic Subunit)
• Root nodes where missing (with nodenumber=1, isaccepted=1)
• Trees for Disciplines that lack them

Reverse deletes all trees (nodes → ranks → defs → discipline associations). This is a data-loss operation but the trees are reconstructed on re-apply with identical structure (just new primary keys).

Uniqueness Rules ✅

businessrules.0006 and 0007 successfully create rules on apply:

• Storage.uniqueIdentifier → Global scope
• Deaccession.deaccessionNumber → Global
• Disposal.disposalNumber → Global
• ExchangeOut.exchangeOutNumber → Division scope (Global)
• AccessionAuthorization.permit → scoped to accession/repositoryAgreement (per discipline)
• CollectingEventAuthorization.permit → scoped to collectingEvent (per discipline)
• CollectingTripAuthorization.permit → scoped to collectingTrip (per discipline)

Some notes

We might want to put a warning for the 0009 migration since it deletes TectonicUnit trees on reverse? I imagine if you are reversing you know the risks. There are also some model changes in the specify app that we should resolve.