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feat: link species name to ncbi taxon page (#82) #110

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merged 2 commits into from
Oct 1, 2024
Merged

feat: link species name to ncbi taxon page (#82) #110

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047bd18
feat: link species name to ncbi taxon page (#82)
hunterckx Sep 28, 2024
0382077
fix: uri-encode taxonomy id in ncbi url (#82)
hunterckx Sep 28, 2024
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1 change: 1 addition & 0 deletions app/apis/catalog/brc-analytics-catalog/common/entities.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ export interface BRCDataCatalogGenome {
chromosomes: number;
contigs: number;
genomeVersionAssemblyId: string;
ncbiTaxonomyId: string;
organism: string;
species: string;
strain: string;
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17 changes: 14 additions & 3 deletions app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
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Expand Up @@ -124,7 +124,15 @@ export const buildGenomeDetails = (
genome: BRCDataCatalogGenome
): ComponentProps<typeof C.KeyValuePairs> => {
const keyValuePairs = new Map<Key, Value>();
keyValuePairs.set("Species", genome.species);
keyValuePairs.set(
"Species",
C.Link({
label: genome.species,
url: `https://www.ncbi.nlm.nih.gov/datasets/taxonomy/${encodeURIComponent(
genome.ncbiTaxonomyId
)}/`,
})
);
keyValuePairs.set("Strain", genome.strain);
keyValuePairs.set("Assembly Version ID", genome.genomeVersionAssemblyId);
keyValuePairs.set("VeUPathDB Project", genome.vEuPathDbProject);
Expand Down Expand Up @@ -173,9 +181,12 @@ export const buildOrganismListHero = (): ComponentProps<
*/
export const buildSpecies = (
genome: BRCDataCatalogGenome
): ComponentProps<typeof C.BasicCell> => {
): ComponentProps<typeof C.Link> => {
return {
value: genome.species,
label: genome.species,
url: `https://www.ncbi.nlm.nih.gov/datasets/taxonomy/${encodeURIComponent(
genome.ncbiTaxonomyId
)}/`,
};
};

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1 change: 1 addition & 0 deletions files/build-catalog.ts
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Expand Up @@ -23,6 +23,7 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
chromosomes: parseNumber(row.Chromosomes),
contigs: parseNumber(row.Contigs),
genomeVersionAssemblyId: row["Genome Version/Assembly ID"],
ncbiTaxonomyId: row.taxId,
organism: row.Organism,
species: row.Species,
strain: row.Strain,
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2 changes: 2 additions & 0 deletions files/build-genomes-files.py
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Expand Up @@ -34,6 +34,8 @@ def build_genomes_files():
if (len(unmatched_assemblies) != 0):
print(f"Omitted {len(unmatched_assemblies)} assemblies that had no matches: {", ".join(unmatched_assemblies)}")

result_df["taxId"] = result_df["taxId"].astype(int)

result_df.to_csv(OUTPUT_PATH, index=False, sep="\t")

print(f"Wrote to {OUTPUT_PATH}")
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