Create indexes in django models and migration files

[acwhite211]

Fixes #7482

Create indexes mentioned in the issue into the models and migration files. Some of the indexes mentioned were already present in the existing model, the rest have been added.

The main downside I could see is with adding the tree field indexes is that writes might be too slow. With an index like taxon.name, write operations like INSERT, UPDATE, and DELETE will take longer, but with the upside of read operations being faster. I know that some of our tree operations make bulk edits to the tree record fields, like the 'Move' action in the tree viewer, so we'll want to be careful in our performance evaluation testing. We'll want to test this on large databases with a big taxon tree to make sure the read and write performance is acceptable.

I ran into a problem with the tree viewer timing out after running the index migrations. Solved the issue by rewriting the get_tree_rows() function to avoid the expensive grouped self-join on tree tables. Instead of joining child and synonym rows and collapsing them with GROUP BY, it now computes child counts and synonym lists with correlated subqueries, which preserves the same response shape while producing a faster query for taxon tree requests.

Indexed fields

Table	Indexed field(s)
agentidentifier	identifier, identifiertype
agentspecialty	ordernumber, specialtyname
agentvariant	name
attachmentmetadata	name
author	ordernumber
collectionobject	name, projectnumber
collectionobjectgroup	guid, name
collectionobjectgrouptype	name
collectionobjectproperty	guid
collectionobjecttype	name
collectionreltype	name
exchangein	exchangeinnumber
exsiccataitem	number
geography	commonname, guid, highestchildnodenumber, nodenumber
geographytreedef	name
geographytreedefitem	name
geologictimeperiod	highestchildnodenumber, nodenumber
geologictimeperiodtreedef	name
geologictimeperiodtreedefitem	name
institutionnetwork	altname
latlonpolygon	name
lithostrat	highestchildnodenumber, nodenumber
lithostrattreedef	name
lithostrattreedefitem	name
locality	guid
materialsample	guid
morphbankview	viewname
otheridentifier	identifier
picklist	fieldname, filterfieldname, tablename
preparationproperty	guid
preptype	name
referencework	librarynumber
spauditlogfield	fieldname
specifyuser	name
spexportschema	schemaname
spexportschemaitem	fieldname
spexportschemaitemmapping	exportedfieldname
spexportschemamapping	mappingname
spfieldvaluedefault	fieldname, tablename
splocalecontainer	picklistname
splocalecontaineritem	picklistname, weblinkname
sppermission	name
spprincipal	name
spquery	contextname
spqueryfield	fieldname, formatname
spviewsetobj	filename
storage	highestchildnodenumber, nodenumber
storagetreedef	name
storagetreedefitem	name
taxon	cultivarname, groupnumber, highestchildnodenumber, nodenumber
taxontreedef	name
taxontreedefitem	name
tectonicunit	fullname, guid, highestchildnodenumber, name, nodenumber
tectonicunittreedef	name
tectonicunittreedefitem	name
voucherrelationship	vouchernumber

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

• See that the new migration step for adding the indexes completes successfully.
• Use the QB on fields that have been indexed to see that they run correctly and in a timely manner.
• Use the taxon tree viewer on a database with a large taxon tree. Try all of the tree operations to see that they run in a timely manner.

[acwhite211]

Let me know if anyone thinks of any additional fields that they think would benefit from indexing?

[alesan99]

• See that the new migration step for adding the indexes completes successfully.
• Use the QB on fields that have been indexed to see that they run correctly and in a timely manner.
• Use the taxon tree viewer on a database with a large taxon tree. Try all of the tree operations to see that they run in a timely manner.

---

Migration runs correctly on KUBirds and read operations are snappy 👍
Tried deleting, moves, merges, searching, and importing big trees.
I didn't notice any speed drops either when running this locally.

[bhumikaguptaa]

• See that the new migration step for adding the indexes completes successfully.
• Use the QB on fields that have been indexed to see that they run correctly and in a timely manner.
• Use the taxon tree viewer on a database with a large taxon tree. Try all of the tree operations to see that they run in a timely manner.

---

When I tried to run the MaterialSample table I got the following error:

Specify 7 Crash Report - 2026-03-18T18_28_32.334Z.txt

Link to DB: https://ojsmnh20251211-issue-7482.test.specifysystems.org/specify/query

[acwhite211]

• See that the new migration step for adding the indexes completes successfully.

  • Use the QB on fields that have been indexed to see that they run correctly and in a timely manner.

  • Use the taxon tree viewer on a database with a large taxon tree. Try all of the tree operations to see that they run in a timely manner.

When I tried to run the MaterialSample table I got the following error:

Specify 7 Crash Report - 2026-03-18T18_28_32.334Z.txt

Link to DB: https://ojsmnh20251211-issue-7482.test.specifysystems.org/specify/query

This looks to be caused by duplicate splocalecontainer records in that database. I added a commit to handle that case 👍

[bhumikaguptaa]

• See that the new migration step for adding the indexes completes successfully.
• Use the QB on fields that have been indexed to see that they run correctly and in a timely manner.
• Use the taxon tree viewer on a database with a large taxon tree. Try all of the tree operations to see that they run in a timely manner.

--

It works as expected. I was able to query on indexed fields without any errors, including materialsample.

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[acwhite211]

Working on doing some more thorough testing to make sure that no action or process in Specify is significantly slowed down from re-indexing.

[grantfitzsimmons]

• See that the new migration step for adding the indexes completes successfully.
• Use the QB on fields that have been indexed to see that they run correctly and in a timely manner.
• Use the taxon tree viewer on a database with a large taxon tree. Try all of the tree operations to see that they run in a timely manner.

---

I did the same as @alesan99– made some really big tree moves and imports. I don't feel the speed difference, but waiting for your testing to be done @acwhite211