feat: use all common names provided by ncbi for each assembly taxon (#1431) by hunterckx · Pull Request #1520 · galaxyproject/brc-analytics

hunterckx · 2026-07-25T00:31:16Z

Description

Updates singular common name fields to instead hold multiple common names, derived from the name lists provided by NCBI

Notes:

The common name table columns in the app (which are hidden by default and mainly there for filtering) are updated to display the lists of names in N-tag cells
Common names for an organism are aggregated from its assemblies
Unlike existing list fields that are saved in the intermediate TSV (which are just comma-separated), common names are saved as JSON, since as far as we're concerned they may contain arbitrary characters
Both catalogs have been rebuilt, which for GA2 is just to get the TSV up-to-date; it doesn't include common names in the ultimate JSON output
- NCBI has moved what is now Megascapheus bottae to its new genus, so I've updated the taxonomy ID in the GA2 source to avoid dropping assemblies from the output
"null" is replaced with "None" as the common name value added to a workflow when an assembly lacks a common name; this was a Claude edit that seemed reasonable enough to me

Related Issue

Closes #1431

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Pull request overview

Expands catalog support for multiple NCBI-provided common names per assembly taxon (and aggregated to organisms), updating build pipelines, API contracts, and UI/table rendering to treat common names as a list rather than a single value.

Changes:

Replace singular commonName with list-valued commonNames across shared types, catalog build steps, and backend search/query surfaces.
Update UI configs and view model builders to render common names as N-tag lists and update workflow facet keys to use assembly.commonNames.
Rebuild and update catalog artifacts (including GA2 taxonomy ID adjustments reflecting NCBI reclassification).

Reviewed changes

Copilot reviewed 31 out of 35 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/views/analyzeWorkflowsView/buildAssemblyWorkflows.scope.test.ts	Update workflow-scope test fixtures to use `commonNames: []`.
tests/analysisMethodCatalogs.utils.test.ts	Update catalog util test fixtures to use `commonNames: []`.
site-config/brc-analytics/local/index/workflow/categoryGroupConfig.ts	Point workflow category config at `assembly.commonNames` for filtering.
site-config/brc-analytics/local/index/organismEntityConfig.ts	Switch common names column to `NTagCell` and `buildCommonNames`.
site-config/brc-analytics/local/index/genomeEntityConfig.ts	Switch common names column to `NTagCell` and `buildCommonNames`.
site-config/brc-analytics/category.ts	Rename category key from `commonName` to `commonNames`.
packages/shared/apis/types.ts	Update `AssemblyContract` to optional list `commonNames?: string[]`.
catalog/py_package/catalog_build/build.py	Emit `commonNames` as JSON-serialized list in species TSV dataframe.
catalog/output/qc-report.data.md	Updated QC report output after rebuild.
catalog/output/data-build-meta.json	Updated build metadata timestamps and taxdump checksum.
catalog/ga2/source/organisms.yml	Update GA2 taxonomy ID to avoid dropping assemblies after NCBI reclassification.
catalog/ga2/output/qc-report.data.md	Updated GA2 QC report output after rebuild.
catalog/ga2/output/organisms.json	Updated GA2 organisms output after rebuild.
catalog/ga2/output/ncbi-taxa-tree.json	Updated GA2 taxa tree reflecting taxonomy/genus changes.
catalog/ga2/output/data-build-meta.json	Updated GA2 build metadata timestamps and taxdump checksum.
catalog/ga2/output/assemblies.json	Updated GA2 assemblies output after rebuild.
catalog/build/ts/utils.ts	Add `parseJsonList` helper for JSON list parsing.
catalog/build/ts/constants.ts	Rename core TSV column key to `commonNames`.
catalog/build/ts/build-organisms.ts	Aggregate organism-level `commonNames` from assembly-level lists.
catalog/build/ts/build-assemblies.ts	Parse `row.commonNames` as JSON list into assembly entities.
catalog/build/intermediate/outbreak-taxonomy-mapping.tsv	Updated intermediate mapping output ordering/content after rebuild.
backend/tests/test_catalog_data.py	Update backend tests to validate searching across `commonNames`.
backend/api/tests/test_catalog_query.py	Update organism schema/fixtures to use `commonNames` arrays and projection expectations.
backend/api/tests/test_catalog_data.py	Update API fixtures and add test ensuring secondary common name is searchable.
backend/api/app/services/tools/catalog_query.py	Treat `commonNames` as list field in query allowlists/projections.
backend/api/app/services/tools/catalog_data.py	Update search/exact-match/summarization to use `commonNames` list semantics.
backend/api/app/services/catalog_data.py	Update condensed organism records/search field list to `commonNames`.
app/views/WorkflowsView/utils.ts	Map workflow assembly `commonNames` into facet buckets with defaults.
app/views/WorkflowsView/types.ts	Update workflow assembly type to `commonNames: string[]`.
app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.tsx	Replace `buildCommonName` with `buildCommonNames` returning `NTagCell` props.
app/apis/catalog/brc-analytics-catalog/common/entities.ts	Update BRC catalog entity types to require `commonNames: string[]`.

Comments suppressed due to low confidence (1)

backend/api/app/services/catalog_data.py:123

search_organisms now includes commonNames in a generic str(...).lower() search. Since commonNames is a list, this relies on Python's list stringification (e.g. "['yeast', 'brewer's yeast']"), which is brittle and can introduce surprising matches; it also differs from the dedicated implementation in backend/api/app/services/tools/catalog_data.py that checks each name individually.

        for org in self.organisms:
            if any(
                q in str(org.get(field, "")).lower()
                for field in (
                    "taxonomicLevelSpecies",
                    "taxonomicLevelGenus",
                    "commonNames",
                    "ncbiTaxonomyId",
                    "taxonomicGroup",
                    "taxonomicLevelStrain",
                    "taxonomicLevelIsolate",
                )
            ):

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Pull request overview

Copilot reviewed 31 out of 35 changed files in this pull request and generated 2 comments.

Copilot

Pull request overview

Copilot reviewed 31 out of 35 changed files in this pull request and generated no new comments.

hunterckx added 7 commits July 24, 2026 15:36

feat: use all common names provided for a taxon (#1431)

11d6f91

chore: build brc analytics catalog (#1431)

4fc6dd4

chore: build ga2 catalog (#1431)

9c04c5e

feat: save common names in tsv as json for safety (#1431)

b161a3e

chore: build brc analytics catalog (#1431)

172e662

chore: build ga2 catalog (#1431)

0b27898

feat: update megascapheus bottae taxonomy id for ga2 (#1431)

a7be289

Copilot AI review requested due to automatic review settings July 25, 2026 00:31

github-project-automation Bot added this to BRC development tasks Jul 25, 2026

github-actions Bot added the feat label Jul 25, 2026

Copilot started reviewing on behalf of hunterckx July 25, 2026 00:31 View session

Copilot AI reviewed Jul 25, 2026

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Comment thread catalog/py_package/catalog_build/build.py

docs: update comment on common names serialization (#1431)

8f92614

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

Copilot AI review requested due to automatic review settings July 25, 2026 00:41

Copilot started reviewing on behalf of hunterckx July 25, 2026 00:42 View session

Copilot AI reviewed Jul 25, 2026

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Comment thread catalog/build/ts/utils.ts

Comment thread backend/api/app/services/tools/catalog_data.py

hunterckx added 2 commits July 24, 2026 18:00

feat: report value when json list parsing fails (#1431)

2a34d28

chore: rename common name loop variable for clarity (#1431)

33770e1

Copilot AI review requested due to automatic review settings July 25, 2026 01:00

Copilot started reviewing on behalf of hunterckx July 25, 2026 01:01 View session

Copilot AI reviewed Jul 25, 2026

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feat: use all common names provided by ncbi for each assembly taxon (#1431)#1520

feat: use all common names provided by ncbi for each assembly taxon (#1431)#1520
hunterckx wants to merge 10 commits into
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hunterckx commented Jul 25, 2026 •

edited

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hunterckx commented Jul 25, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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hunterckx commented Jul 25, 2026 •

edited

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