Skip to content

Conversation

@CarolineDenis
Copy link
Contributor

@CarolineDenis CarolineDenis commented Jul 24, 2024

Fixes #752

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

Testing instructions

  • open query builder and select a tree table
  • make a search on any rank
  • add name field in the mapper line
  • enter the name of a node that has a synonym for the value
  • check the box search synonyms
  • run the query
  • verify that the node is being return as well as its synonym

@gitguardian
Copy link

gitguardian bot commented Oct 24, 2025

️✅ There are no secrets present in this pull request anymore.

If these secrets were true positive and are still valid, we highly recommend you to revoke them.
While these secrets were previously flagged, we no longer have a reference to the
specific commits where they were detected. Once a secret has been leaked into a git
repository, you should consider it compromised, even if it was deleted immediately.
Find here more information about risks.


🦉 GitGuardian detects secrets in your source code to help developers and security teams secure the modern development process. You are seeing this because you or someone else with access to this repository has authorized GitGuardian to scan your pull request.

@acwhite211 acwhite211 added this to the 7.12.0 milestone Oct 31, 2025
@acwhite211 acwhite211 marked this pull request as ready for review October 31, 2025 21:07
@acwhite211 acwhite211 requested review from a team and grantfitzsimmons October 31, 2025 21:08
Copy link
Collaborator

@emenslin emenslin left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This does not appear to be working unless I am misunderstanding the instructions. I query on any rank -> name and set equal to a taxon that has synonyms but when I check 'search synonyms' only the one node appears.

image image

If I check 'search synonyms' in any tree aside from taxon I get an error.

11-07_15.21.mp4

Specify 7 Crash Report - 2025-11-07T21_21_43.622Z.txt

@github-project-automation github-project-automation bot moved this from 📋Back Log to Dev Attention Needed in General Tester Board Nov 7, 2025
@acwhite211
Copy link
Member

Fixed it so that it will work on all tree tables, not just Taxon. Try it out again @emenslin, thanks.

image image image

@acwhite211 acwhite211 requested a review from emenslin November 13, 2025 18:58
@CarolineDenis CarolineDenis requested review from a team and melton-jason November 18, 2025 13:44
Copy link
Collaborator

@emenslin emenslin left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

  • verify that the node is being return as well as its synonym

Looks good, I'm no longer getting an error when search synonyms is checked.
image

@emenslin emenslin requested a review from a team November 18, 2025 15:44
@grantfitzsimmons
Copy link
Member

@specify/ux-testing Can you please check this behavior against Specify 6 and make sure it matches?

Copy link
Contributor

@Iwantexpresso Iwantexpresso left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

  • verify that the node is being return as well as its synonym
image

this looks great so far!

@Iwantexpresso Iwantexpresso requested a review from a team December 10, 2025 21:35
Copy link
Member

@grantfitzsimmons grantfitzsimmons left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The fundamental issue here is that 'Search Synonyms' is used most often for searching Collection Objects rather than tree names via a tree base table. The inadequate request this PR is based on unfortunately did not clarify this well enough.

See #752 (comment):

Hey guys, this one is quite important. If I create a collection object query and search for a preferred taxon name, it does not return collection objects with the original taxon name that are different (i.e. junior synonyms) to the preferred taxon name. The functionality is as expected in Specify 6.

Also related to this is that when querying collection objects from a taxon name in the taxon tree, the behaviour differs from Specify 6. In 6 you get records where either the taxon name or the preferred taxon name match the searched name, but in 7 it only searches on taxon name, so searches for a senior synonym don't return collection objects identified as the junior synonyms.

See that if I search for a synonym in a database (e.g. Opsanus tau) with Collection Object as the base table, I can still check "Search Synonyms":
Image

In the results:
Image

This same behavior is expected in 7.


Using a copy of herb_rbge, I see the following:

Left: v7.11.2.1, Right: issue-752
Image

Same query, exported and imported in both: Taxon Synonyms.json

On the v7.11.2.1, only results where synonyms do have an ID that isn't empty are returned (67532). On issue-752, all taxon records are returned (370611).

Image

In neither scenario is "Search Synonyms" checked.


Searching directly for a Full Name for a synonymized node (e.g. Ericaceae) does yield correct results when querying Taxon directly:

Image Image

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

Status: Dev Attention Needed

Development

Successfully merging this pull request may close these issues.

Add ability for query to find synonymized taxa

6 participants