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feat: generate taxa tree from assemblies and display accurate assembly count in sunburst (#522) #550

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Merged
merged 9 commits into from
May 29, 2025
Merged

feat: generate taxa tree from assemblies and display accurate assembly count in sunburst (#522) #550

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fba9bac
feat: update taxa tree to build from assemblies and include assembly …
hunterckx May 23, 2025
6e907f0
chore: apply ruff (#522)
hunterckx May 23, 2025
36300c8
feat: use assembly count from tree data in sunburst (#522)
hunterckx May 23, 2025
7ed661b
docs: add a couple comments to `get_species_subtree` (#522)
hunterckx May 23, 2025
f7f4171
docs: add `build_files` docstring to emphasize requirements for `taxo…
hunterckx May 24, 2025
2f92b0a
docs: add additional comment and detail regarding order of taxonomic …
hunterckx May 28, 2025
10bea59
feat: add a couple taxonomy tree checks to qc report (#522)
hunterckx May 28, 2025
602f7b2
feat: fix assembly count check and add species node check (#522)
hunterckx May 29, 2025
1994a53
feat: add qc check for list of taxonomic levels (#522)
hunterckx May 29, 2025
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4 changes: 3 additions & 1 deletion app/components/Home/components/Section/components/SectionViz/NodeDetails.tsx
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Expand Up @@ -121,7 +121,9 @@ export const NodeDetails: React.FC<NodeDetailsProps> = ({
// Create the appropriate display text based on node type
let filterLinkText = "Browse All Assemblies";
if (!isRoot) {
filterLinkText = `View assemblies for ${nodeName}`;
const assemblyCount = node.data.assembly_count;
const assemblySuffix = assemblyCount > 1 ? "ies" : "y";
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Copilot AI May 24, 2025

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The pluralization logic treats 0 as singular ("Assembly"). Change the condition to assemblyCount !== 1 so that 0, 2+ use the plural form.

Suggested change
const assemblySuffix = assemblyCount > 1 ? "ies" : "y";
const assemblySuffix = assemblyCount !== 1 ? "ies" : "y";

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filterLinkText = `View ${assemblyCount} Assembl${assemblySuffix} for ${nodeName}`;
}

return (
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5 changes: 5 additions & 0 deletions app/components/Home/components/Section/components/SectionViz/data.ts
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Expand Up @@ -4,6 +4,11 @@ import data from "catalog/output/ncbi-taxa-tree.json";
* Interface representing a node in the NCBI taxonomy tree
*/
export interface TaxonomyNode {
/**
* The number of assemblies for the taxon that are present in the catalog
*/
assembly_count: number;

/**
* Child nodes in the taxonomy tree
*/
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2,284 changes: 1,142 additions & 1,142 deletions catalog/build/intermediate/genomes-from-ncbi.tsv
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34 changes: 17 additions & 17 deletions catalog/build/intermediate/outbreak-taxonomy-mapping.tsv
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Original file line number Diff line number Diff line change
@@ -1,25 +1,25 @@
taxonomy_id name rank
5207 Cryptococcus neoformans SPECIES
11050 Flaviviridae FAMILY
11320 Influenza A virus
4827 Mucorales ORDER
5052 Aspergillus GENUS
11018 Togaviridae FAMILY
199306 Coccidioides posadasii SPECIES
12058 Picornaviridae FAMILY
5037 Histoplasma capsulatum SPECIES
1980415 Nairoviridae FAMILY
3418604 Betacoronavirus pandemicum SPECIES
11158 Paramyxoviridae FAMILY
38574 Leishmania donovani species complex SPECIES_GROUP
1773 Mycobacterium tuberculosis SPECIES
5807 Cryptosporidium parvum SPECIES
1980418 Phenuiviridae FAMILY
1980413 Hantaviridae FAMILY
11266 Filoviridae FAMILY
11018 Togaviridae FAMILY
10244 Monkeypox virus SPECIES
5763 Naegleria fowleri SPECIES
1980416 Peribunyaviridae FAMILY
5833 Plasmodium falciparum SPECIES
1980418 Phenuiviridae FAMILY
3418604 Betacoronavirus pandemicum SPECIES
498019 Candidozyma auris SPECIES
11158 Paramyxoviridae FAMILY
38574 Leishmania donovani species complex SPECIES_GROUP
5763 Naegleria fowleri SPECIES
10244 Monkeypox virus SPECIES
1980413 Hantaviridae FAMILY
5207 Cryptococcus neoformans SPECIES
5807 Cryptosporidium parvum SPECIES
11320 Influenza A virus
5052 Aspergillus GENUS
1980416 Peribunyaviridae FAMILY
11050 Flaviviridae FAMILY
1980415 Nairoviridae FAMILY
4827 Mucorales ORDER
11617 Arenaviridae FAMILY
5037 Histoplasma capsulatum SPECIES
3 changes: 3 additions & 0 deletions catalog/build/py/build-files-from-ncbi.py
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Expand Up @@ -31,6 +31,9 @@
1913637: "Mucoromycota",
}

# TAXONOMIC_LEVELS_FOR_TREE should be listed in order, as the order is used in building the taxonomy tree;
# higher-level categories should be listed earlier than lower-level categories (while categories that are
# at the same level, such as domain and realm, can be listed in any order relative to each other)
TAXANOMIC_LEVELS_FOR_TREE = [
"domain",
"realm",
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