Fix duplicate nodes being removed in tree imports

[alesan99]

Fixes #7853

Tree imports de-duplicate nodes with the same name (ParentNode -> ChildNode1 and ParentNode -> ChildNode2 need to have the same).
However, it looks like some tree files intentionally have non-parent nodes with the same names. To allows those to be imported, I disabled de-duplication for leaf nodes.

Dev note: Also added some minor fixes to some mistakes I saw in the code

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

• Look at https://files.specifysoftware.org/taxonfiles/taxonfiles.json. Download one or more tree csv files (The download links are proceeded by "file": )
• Go to the taxon tree view
• Create a new tree and choose to import the same trees that you downloaded.
• Run a Query on all taxon records in that tree. Look at the total count (Excluding the root node).
• Open the taxon tree csv file for that same tree. Look at the total number of rows (Excluding the header).
• The taxon tree in Specify and the csv file should have the same number of trees.
• Repeat for all the trees you downloaded

[alesan99]

I have personally checked the following trees so far:

• Geography
• Chronostratigraphy
• Aves
• Botany (Bryophyta)
• Botany (Polypodiopsida)
• Botany (Tracheophyta)
• Fungi -- This one has extra records, not sure which ones yet

---

This tree looks like it gains extra records

• Entomology

Though this is likely only because the tree file is formatted differently. It should still be the same number of records if reformatted, but I haven't verified it.

[lexiclevenger]

• The taxon tree in Specify and the csv file should have the same number of trees.

---

Based on the query below, the counts for Ichthyology and Mammology match those in the CSV.

The following do not match::

Fungi: CSV 159,229, Query, 159,232
Herpetology: CSV 24,730, Query 24,732
Invertebrate: CSV 79,276 Query 79,282

Database: lsumz_herps_2025_09_09

[bhumikaguptaa]

• The taxon tree in Specify and the csv file should have the same number of trees.

--
There is discrepancy in some trees the number of records uploaded versus the number of records in the query.

Botany (bryophyta):
Uploaded: 14425
Queried: 14428

Mammals:
Uploaded: 13557
Queried: 13557

Minerals:
Uploaded: 6202
Queried: 6202

I am changing requests because I had mixed results and also the number of records uploaded were different from the .json file. (eg. minerals was 6189 rows but 6202 got uploaded).

[alesan99]

It looks like nodes were being added to the incorrect parents all along (even on main) if there were multiple parents with the same name in the same rank.
Currently working on a fix

[bhumikaguptaa]

• The taxon tree in Specify and the csv file should have the same number of trees.

--
It works as expected. For botany trees the number of records match the ones in the query. However, I think it is worth noting that the file for geology shows the wrong number of rows, and I verified that the correct number is 6202 (which is the number being uploaded).

[grantfitzsimmons]

@bhumikaguptaa I've updated this! It should be 6202 rows now.

[grantfitzsimmons]

Stated is what is shown in the progress dialog as the total. Actual is the result of the query

Mammals ⚠️

Stated: 13,556
Actual: 13,640

Minerals ✅

'Root' is not counted
Stated: 6,201
Actual: 6,202

Ichthyology ⚠️

Stated: 37,958
Actual: 38,175

Bryophyta ⚠️

Stated: 14,425
Actual: 14,512

Hmm.. query I'm using below:

[kwhuber]

Riffing off @grantfitzsimmons stylistically pleasing review:
Stated is what is shown in the progress dialog as the total (and the CSV). Actual is the result of the query

Aves ⚠️

Stated: 34,038
Actual: 34,263

Fungi ⚠️

Stated: 159,228
Actual: 160,294

Herpetology ⚠️

Stated: 24,730
Actual: 24,880

Mammalogy ⚠️

Stated: 13,556
Actual: 13,640

Tested with the query:

[lexiclevenger]

• The taxon tree in Specify and the csv file should have the same number of trees.

---

Looks like there are still some inconsistencies

• Birds
• Botany (Bryophyta): 14,427 (query) vs 14,425 (csv)
• Botany (Polypodiopsima)
• Botany (Tracheophyta) 395,041 vs 395,040
• Entomology 29,981 vs 25,064
• Fungi 159,321 vs 159,229
• Herpetology 34,732 vs 24,730
• Ichthyology
• Invertebrate Zoology 79,356 vs 79,376
• Mammalogy