Fix: Add a new custom delete for parent field in taxontreedefitem by CarolineDenis · Pull Request #8375 · specify/specify7

CarolineDenis · 2026-07-29T12:22:12Z

Fixes #8310

Warning

This PR affects database migrations. See migration testing instructions.

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

Verify you can delete unused ranks
Verify you cannot delete used ranks
Verify you can delete non default trees
Proceed with various testing creating - deleting - editing tree ranks and add new nodes in the tree

Summary by CodeRabbit

Bug Fixes
- Updated taxonomic hierarchy deletion behavior: deleting an individual rank now preserves related child records, while deleting an entire taxonomy still removes the associated hierarchy.
- Improved database consistency for parent relationships in the taxonomic structure by adjusting the foreign key delete policy.

coderabbitai · 2026-07-29T12:22:32Z

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Run ID: ce7e8f6c-c0a9-41a9-b620-c745c518be04

📥 Commits

Reviewing files that changed from the base of the PR and between 09cbf24 and f07bdcb.

📒 Files selected for processing (3)

specifyweb/backend/businessrules/migrations/0002_default_unique_rules.py
specifyweb/backend/businessrules/tests/test_taxontreedefitem.py
specifyweb/specify/models.py

📝 Walkthrough

Walkthrough

Changes

The PR adds context-aware deletion handling for TaxonTreeDefItem.parent and makes a non-functional brace adjustment in the geolocation component.

Context-aware taxon deletion

Layer / File(s)	Summary
Context-aware parent deletion `specifyweb/specify/models.py`, `specifyweb/specify/migrations/0047_taxontreedefitem_parent_context_delete.py`	The custom handler selects `CASCADE` for full-tree deletion and `DO_NOTHING` for individual-rank deletion; migration `0047` records the foreign-key change.

Geolocation formatting

Layer / File(s)	Summary
File-ending adjustment `specifyweb/frontend/js_src/lib/components/WbToolkit/GeoLocate.tsx`	The closing brace of `getGeoLocateData` is adjusted without functional or API changes.

Sequence Diagram(s)

sequenceDiagram
  participant DjangoCollector
  participant DeleteHandler
  participant TaxonTreeDefItem
  DjangoCollector->>DeleteHandler: provide deletion context
  DeleteHandler->>TaxonTreeDefItem: inspect tree deletion state
  DeleteHandler-->>DjangoCollector: return CASCADE or DO_NOTHING

🚥 Pre-merge checks | ✅ 3 | ❌ 3

❌ Failed checks (2 warnings, 1 inconclusive)

Check name	Status	Explanation	Resolution
Out of Scope Changes check	⚠️ Warning	The GeoLocate.tsx whitespace-only edit is unrelated to the taxontreedefitem delete-handler changes.	Remove the unrelated frontend formatting change unless it is part of a separate documented task.
Automatic Tests	⚠️ Warning	No tests exercise the new delete handler’s CASCADE/DO_NOTHING branches; existing taxon tests don’t cover it.	Add backend tests for deleting a whole tree vs. a rank, plus reparenting and blocked-deletion cases, and include migration coverage.
Linked Issues check	❓ Inconclusive	Core CASCADE/DO_NOTHING behavior is added, but the summary doesn't confirm the required unused-rank check or child reparenting.	Add or verify rank-usage checks and child reparenting logic for rank deletions, or point to the reused implementation.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Testing Instructions	✅ Passed	The testing notes match the changed deletion behavior: unused ranks, used ranks, and non-default trees.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly matches the main change: adding a custom delete handler for TaxonTreeDefItem.parent.

✨ Finishing Touches

🧪 Generate unit tests (beta)

Create PR with unit tests
Commit unit tests in branch issue-8310

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github-actions · 2026-07-29T12:22:33Z

Warning

One or more dependencies are approaching or past End-of-Life.
Please plan upgrades accordingly.

STATUS=OK
NODE_VERSION=24
NODE_CYCLE=24
EOL_DATE=2028-04-30
DAYS_REMAINING=613

--- Node.js ---
Version: 24
EOL: 2028-04-30
Status: OK

STATUS=OK
PYTHON_VERSION=3.12
PYTHON_CYCLE=3.12
EOL_DATE=2028-10-31
DAYS_REMAINING=797

--- Python ---
Version: 3.12
EOL: 2028-10-31
Status: OK

STATUS=WARNING
DJANGO_VERSION=4.2
DJANGO_CYCLE=4.2
EOL_DATE=2026-04-07
DAYS_REMAINING=-141

--- Django ---
Version: 4.2
EOL: 2026-04-07
Status: WARNING

coderabbitai

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@specifyweb/frontend/js_src/lib/components/WbToolkit/GeoLocate.tsx`:
- Around line 281-284: Update the points construction to distinguish coordinate
parse failures from valid zero values: use a parse-aware helper near the
existing formatCoordinate logic that returns undefined for unparseable latitude
or longitude, then set points only when both parsed coordinates are defined.
Preserve formatting for valid coordinates, including zero, and leave points
undefined for blank or malformed values.

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Create a new PR with the fixes

ℹ️ Review info

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Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: f492c1ce-856d-4c92-b81b-0d4c2f2b2937

📥 Commits

Reviewing files that changed from the base of the PR and between 01f1a2d and 5a439c4.

📒 Files selected for processing (3)

specifyweb/frontend/js_src/lib/components/WbToolkit/GeoLocate.tsx
specifyweb/specify/migrations/0047_taxontreedefitem_parent_context_delete.py
specifyweb/specify/models.py

CarolineDenis · 2026-07-29T12:57:41Z

@CodeRabbit full review

coderabbitai · 2026-07-29T12:57:48Z

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CarolineDenis · 2026-07-29T13:23:11Z

@CodeRabbit full review

coderabbitai · 2026-07-29T13:23:17Z

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Full review finished.

coderabbitai

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@specifyweb/specify/models.py`:
- Around line 20-32: Update delete_taxon_rank_parent_with_context for
individual-rank deletion to validate that the rank is unused and reparent any
child treedefitems before deletion, preventing dangling
DefinitionID/DefinitionItemID references; do not return models.DO_NOTHING for
this path. Preserve the existing models.CASCADE behavior when is_tree_delete
detects a full TaxonTreeDef deletion.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

Push a commit to this branch (recommended)
Create a new PR with the fixes

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: b5a6521c-878d-4de4-9e93-9ef2dd5e56ca

📥 Commits

Reviewing files that changed from the base of the PR and between 01f1a2d and 09cbf24.

📒 Files selected for processing (3)

specifyweb/frontend/js_src/lib/components/WbToolkit/GeoLocate.tsx
specifyweb/specify/migrations/0047_taxontreedefitem_parent_context_delete.py
specifyweb/specify/models.py

…ed with implicit (fall through) returns' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>

emenslin

Verify you can delete unused ranks
Verify you cannot delete used ranks
Verify you can delete non default trees

Looks good, I didn't run into any new issues.

kwhuber

Verify you can delete unused ranks
Verify you cannot delete used ranks
Verify you can delete non default trees

Caroline Denis added 2 commits July 29, 2026 10:32

Fix: Pull existing locality values from WB dataset

dea5af2

Fix: Add a new custom delete for parent field in taxontreedefitem

5a439c4

CarolineDenis added this to the 7.12.2 milestone Jul 29, 2026

github-project-automation Bot added this to General Tester Board Jul 29, 2026

github-project-automation Bot moved this to 📋Back Log in General Tester Board Jul 29, 2026

coderabbitai Bot requested changes Jul 29, 2026

View reviewed changes

Comment thread specifyweb/frontend/js_src/lib/components/WbToolkit/GeoLocate.tsx

github-project-automation Bot moved this from 📋Back Log to Dev Attention Needed in General Tester Board Jul 29, 2026

Revert unwanted changes

09cbf24

coderabbitai Bot approved these changes Jul 29, 2026

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coderabbitai Bot requested changes Jul 29, 2026

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Comment thread specifyweb/specify/models.py Outdated

Fix: Reparent when deleting a rank

8a06f94

github-advanced-security Bot found potential problems Jul 29, 2026

View reviewed changes

Comment thread specifyweb/specify/models.py Fixed

coderabbitai Bot approved these changes Jul 29, 2026

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CarolineDenis requested a review from a team July 29, 2026 17:59

Potential fix for pull request finding 'CodeQL / Explicit returns mix…

fb39fa6

…ed with implicit (fall through) returns' Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>

CarolineDenis force-pushed the issue-8310 branch from eef3956 to fb39fa6 Compare July 30, 2026 12:15

Fix: Typing

c621cb1

emenslin approved these changes Aug 19, 2026

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emenslin requested a review from a team August 19, 2026 20:53

kwhuber approved these changes Aug 25, 2026

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CarolineDenis and others added 2 commits August 26, 2026 09:04

Merge remote-tracking branch 'origin/main' into issue-8310

70ad332

Merge branch 'main' into issue-8310

f07bdcb

CarolineDenis merged commit c3fba05 into main Aug 26, 2026
20 checks passed

CarolineDenis deleted the issue-8310 branch August 26, 2026 07:18

github-project-automation Bot moved this from Dev Attention Needed to ✅Done in General Tester Board Aug 26, 2026

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Walkthrough

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Sequence Diagram(s)

❌ Failed checks (2 warnings, 1 inconclusive)

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