From 9f6514b702297c84fbfb105aca15632fcc7333af Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Sat, 16 Nov 2024 15:54:18 -0800
Subject: [PATCH 01/19] feat: update genome list to use data from ncbi (#177)

---
 .../brc-analytics-catalog/common/entities.ts  |   21 +-
 .../brc-analytics-catalog/common/utils.ts     |    4 +-
 .../common/viewModelBuilders.ts               |  258 +-
 files/build-catalog.ts                        |   44 +-
 files/entities.ts                             |   31 +-
 files/out/genomes.json                        | 9916 +----------------
 site-config/brc-analytics/category.ts         |   36 +-
 .../local/index/genomeEntityConfig.ts         |  138 +-
 8 files changed, 634 insertions(+), 9814 deletions(-)

diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
index 6ec031a..8e69429 100644
--- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts
+++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
@@ -10,17 +10,20 @@ export enum ANALYSIS_METHOD {
 export type BRCCatalog = BRCDataCatalogGenome;
 
 export interface BRCDataCatalogGenome {
-  chromosomes: number;
-  contigs: number;
-  geneModelUrl: string;
-  genomeVersionAssemblyId: string;
+  accession: string;
+  annotationStatus: string | null;
+  chromosomes: number | null;
+  coverage: string | null;
+  gcPercent: number;
+  isRef: boolean;
+  length: number;
+  level: string;
   ncbiTaxonomyId: string;
   organism: string;
-  species: string;
-  strain: string;
-  supercontigs: number;
-  ucscBrowserUrl: string;
-  vEuPathDbProject: string;
+  scaffoldCount: number;
+  scaffoldL50: number;
+  scaffoldN50: number;
+  ucscBrowserUrl: string | null;
 }
 
 export interface EntitiesResponse<R> {
diff --git a/app/apis/catalog/brc-analytics-catalog/common/utils.ts b/app/apis/catalog/brc-analytics-catalog/common/utils.ts
index 8146c3b..935fde0 100644
--- a/app/apis/catalog/brc-analytics-catalog/common/utils.ts
+++ b/app/apis/catalog/brc-analytics-catalog/common/utils.ts
@@ -1,12 +1,12 @@
 import { BRCDataCatalogGenome } from "./entities";
 
 export function getGenomeId(genome: BRCDataCatalogGenome): string {
-  return sanitizeEntityId(genome.genomeVersionAssemblyId);
+  return sanitizeEntityId(genome.accession);
 }
 
 export function getGenomeTitle(genome?: BRCDataCatalogGenome): string {
   if (!genome) return "";
-  return `${genome.species} - ${genome.strain}`;
+  return `${genome.organism}`;
 }
 
 export function sanitizeEntityId(entityId?: string): string {
diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
index 49a7e47..022a1a2 100644
--- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
+++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -10,6 +10,19 @@ import { BRCDataCatalogGenome } from "../../../../apis/catalog/brc-analytics-cat
 import * as C from "../../../../components";
 import { GENOME_BROWSER, NCBI_DATASETS_URL } from "./constants";
 
+/**
+ * Build props for the accession cell.
+ * @param genome - Genome entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildAccession = (
+  genome: BRCDataCatalogGenome
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: genome.accession,
+  };
+};
+
 /**
  * Build props for the genome analysis cell.
  * @param genome - Genome entity.
@@ -20,7 +33,7 @@ export const buildAnalyzeGenome = (
   genome: BRCDataCatalogGenome,
   viewContext: ViewContext<BRCDataCatalogGenome>
 ): ComponentProps<typeof C.AnalyzeGenome> => {
-  const { genomeVersionAssemblyId, ncbiTaxonomyId, ucscBrowserUrl } = genome;
+  const { accession, ncbiTaxonomyId, ucscBrowserUrl } = genome;
   const rowId = viewContext.cellContext?.row?.id;
   return {
     analyze: {
@@ -28,10 +41,12 @@ export const buildAnalyzeGenome = (
       url: rowId ? `${ROUTES.ORGANISMS}/${rowId}` : "",
     },
     views: [
-      { label: "UCSC Genome Browser", url: ucscBrowserUrl },
+      ...(ucscBrowserUrl
+        ? [{ label: "UCSC Genome Browser", url: ucscBrowserUrl }]
+        : []),
       {
         label: "NCBI Genome Assembly",
-        url: `${NCBI_DATASETS_URL}/genome/${genomeVersionAssemblyId}`,
+        url: `${NCBI_DATASETS_URL}/genome/${accession}`,
       },
       {
         label: "NCBI Taxonomy",
@@ -43,6 +58,19 @@ export const buildAnalyzeGenome = (
   };
 };
 
+/**
+ * Build props for the annotation status cell.
+ * @param genome - Genome entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildAnnotationStatus = (
+  genome: BRCDataCatalogGenome
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: genome.annotationStatus,
+  };
+};
+
 /**
  * Build props for the chromosomes cell.
  * @param genome - Genome entity.
@@ -57,179 +85,229 @@ export const buildChromosomes = (
 };
 
 /**
- * Build props for the contigs cell.
+ * Build props for the coverage cell.
  * @param genome - Genome entity.
  * @returns Props to be used for the cell.
  */
-export const buildContigs = (
+export const buildCoverage = (
   genome: BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: genome.contigs,
+    value: genome.coverage,
   };
 };
 
 /**
- * Build props for the genome AnalysisMethod component.
+ * Build props for the GC% cell.
  * @param genome - Genome entity.
- * @param analysisMethodProps - Analysis Method properties.
- * @param analysisMethodProps.analysisMethod - Analysis method.
- * @param analysisMethodProps.content - Content to be displayed.
- * @returns Props to be used for the AnalysisMethod component.
+ * @returns Props to be used for the cell.
  */
-export const buildGenomeAnalysisMethod = (
-  genome: BRCDataCatalogGenome,
-  analysisMethodProps: Pick<
-    ComponentProps<typeof C.AnalysisMethod>,
-    "analysisMethod" | "content"
-  >
-): ComponentProps<typeof C.AnalysisMethod> => {
+export const buildGcPercent = (
+  genome: BRCDataCatalogGenome
+): ComponentProps<typeof C.BasicCell> => {
   return {
-    ...analysisMethodProps,
-    geneModelUrl: genome.geneModelUrl,
-    genomeVersionAssemblyId: genome.genomeVersionAssemblyId,
+    value: genome.gcPercent,
   };
 };
 
 /**
- * Build props for the genome AnalysisPortals component.
+ * Build props for the "is ref" cell.
  * @param genome - Genome entity.
- * @returns Props to be used for the AnalysisPortals component.
+ * @returns Props to be used for the cell.
  */
-export const buildGenomeAnalysisPortals = (
+export const buildIsRef = (
   genome: BRCDataCatalogGenome
-): ComponentProps<typeof C.AnalysisPortals> => {
+): ComponentProps<typeof C.BasicCell> => {
   return {
-    portals: [
-      {
-        imageProps: {
-          alt: GENOME_BROWSER,
-          src: "/analysis-portals/ucsc-genome.png",
-          width: 20,
-        },
-        label: GENOME_BROWSER,
-        url: genome.ucscBrowserUrl,
-      },
-    ],
+    value: genome.isRef ? "Yes" : "No",
   };
 };
 
 /**
- * Build props for the genome DetailViewHero component.
+ * Build props for the length cell.
  * @param genome - Genome entity.
- * @returns Props to be used for the DetailViewHero component.
+ * @returns Props to be used for the cell.
  */
-export const buildGenomeChooseAnalysisMethodDetailViewHero = (
+export const buildLength = (
   genome: BRCDataCatalogGenome
-): ComponentProps<typeof C.DetailViewHero> => {
+): ComponentProps<typeof C.BasicCell> => {
   return {
-    breadcrumbs: C.Breadcrumbs({
-      breadcrumbs: getGenomeEntityChooseAnalysisMethodBreadcrumbs(genome),
-    }),
-    title: "Choose Analysis Methods",
+    value: genome.length,
   };
 };
 
 /**
- * Build props for the genome detail KeyValuePairs component.
+ * Build props for the level cell.
  * @param genome - Genome entity.
- * @returns Props to be used for the KeyValuePairs component.
+ * @returns Props to be used for the cell.
  */
-export const buildGenomeDetails = (
+export const buildLevel = (
   genome: BRCDataCatalogGenome
-): ComponentProps<typeof C.KeyValuePairs> => {
-  const keyValuePairs = new Map<Key, Value>();
-  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",
-    C.CopyText({
-      children: genome.genomeVersionAssemblyId,
-      value: genome.genomeVersionAssemblyId,
-    })
-  );
-  keyValuePairs.set("VeUPathDB Project", genome.vEuPathDbProject);
-  keyValuePairs.set("Contigs", genome.contigs);
-  keyValuePairs.set("Super Contigs", genome.supercontigs);
-  keyValuePairs.set("Chromosomes", genome.chromosomes);
+): ComponentProps<typeof C.BasicCell> => {
   return {
-    KeyElType: C.KeyElType,
-    KeyValuesElType: (props) => C.Stack({ gap: 4, ...props }),
-    ValueElType: C.ValueElType,
-    keyValuePairs,
+    value: genome.level,
   };
 };
 
 /**
- * Build props for the genome version/assembly ID cell.
+ * Build props for the organism cell.
  * @param genome - Genome entity.
  * @returns Props to be used for the cell.
  */
-export const buildGenomeVersionAssemblyId = (
+export const buildOrganism = (
   genome: BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: genome.genomeVersionAssemblyId,
+    value: genome.organism,
   };
 };
 
 /**
- * Build props for the species cell.
+ * Build props for the scaffold count cell.
  * @param genome - Genome entity.
  * @returns Props to be used for the cell.
  */
-export const buildSpecies = (
+export const buildScaffoldCount = (
   genome: BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: genome.species,
+    value: genome.scaffoldCount,
   };
 };
 
 /**
- * Build props for the strain cell.
+ * Build props for the scaffold L50 cell.
  * @param genome - Genome entity.
  * @returns Props to be used for the cell.
  */
-export const buildStrain = (
+export const buildScaffoldL50 = (
   genome: BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: genome.strain,
+    value: genome.scaffoldL50,
   };
 };
 
 /**
- * Build props for the supercontigs cell.
+ * Build props for the scaffold N50 cell.
  * @param genome - Genome entity.
  * @returns Props to be used for the cell.
  */
-export const buildSupercontigs = (
+export const buildScaffoldN50 = (
   genome: BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: genome.supercontigs,
+    value: genome.scaffoldN50,
   };
 };
 
 /**
- * Build props for the VEuPathDB project cell.
+ * Build props for the taxonomy ID cell.
  * @param genome - Genome entity.
  * @returns Props to be used for the cell.
  */
-export const buildVEuPathDbProject = (
+export const buildTaxonomyId = (
   genome: BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: genome.vEuPathDbProject,
+    value: genome.ncbiTaxonomyId,
+  };
+};
+
+/**
+ * Build props for the genome AnalysisMethod component.
+ * @param genome - Genome entity.
+ * @param analysisMethodProps - Analysis Method properties.
+ * @param analysisMethodProps.analysisMethod - Analysis method.
+ * @param analysisMethodProps.content - Content to be displayed.
+ * @returns Props to be used for the AnalysisMethod component.
+ */
+export const buildGenomeAnalysisMethod = (
+  genome: BRCDataCatalogGenome,
+  analysisMethodProps: Pick<
+    ComponentProps<typeof C.AnalysisMethod>,
+    "analysisMethod" | "content"
+  >
+): ComponentProps<typeof C.AnalysisMethod> => {
+  return {
+    ...analysisMethodProps,
+    geneModelUrl: "",
+    genomeVersionAssemblyId: genome.accession,
+  };
+};
+
+/**
+ * Build props for the genome AnalysisPortals component.
+ * @param genome - Genome entity.
+ * @returns Props to be used for the AnalysisPortals component.
+ */
+export const buildGenomeAnalysisPortals = (
+  genome: BRCDataCatalogGenome
+): ComponentProps<typeof C.AnalysisPortals> => {
+  return {
+    portals: genome.ucscBrowserUrl
+      ? [
+          {
+            imageProps: {
+              alt: GENOME_BROWSER,
+              src: "/analysis-portals/ucsc-genome.png",
+              width: 20,
+            },
+            label: GENOME_BROWSER,
+            url: genome.ucscBrowserUrl,
+          },
+        ]
+      : [],
+  };
+};
+
+/**
+ * Build props for the genome DetailViewHero component.
+ * @param genome - Genome entity.
+ * @returns Props to be used for the DetailViewHero component.
+ */
+export const buildGenomeChooseAnalysisMethodDetailViewHero = (
+  genome: BRCDataCatalogGenome
+): ComponentProps<typeof C.DetailViewHero> => {
+  return {
+    breadcrumbs: C.Breadcrumbs({
+      breadcrumbs: getGenomeEntityChooseAnalysisMethodBreadcrumbs(genome),
+    }),
+    title: "Choose Analysis Methods",
+  };
+};
+
+/**
+ * Build props for the genome detail KeyValuePairs component.
+ * @param genome - Genome entity.
+ * @returns Props to be used for the KeyValuePairs component.
+ */
+export const buildGenomeDetails = (
+  genome: BRCDataCatalogGenome
+): ComponentProps<typeof C.KeyValuePairs> => {
+  const keyValuePairs = new Map<Key, Value>();
+  keyValuePairs.set(
+    "Taxon",
+    C.Link({
+      label: genome.organism,
+      url: `https://www.ncbi.nlm.nih.gov/datasets/taxonomy/${encodeURIComponent(
+        genome.ncbiTaxonomyId
+      )}/`,
+    })
+  );
+  keyValuePairs.set(
+    "Accession",
+    C.CopyText({
+      children: genome.accession,
+      value: genome.accession,
+    })
+  );
+  keyValuePairs.set("Chromosomes", genome.chromosomes);
+  return {
+    KeyElType: C.KeyElType,
+    KeyValuesElType: (props) => C.Stack({ gap: 4, ...props }),
+    ValueElType: C.ValueElType,
+    keyValuePairs,
   };
 };
 
@@ -243,7 +321,7 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs(
 ): Breadcrumb[] {
   return [
     { path: ROUTES.ORGANISMS, text: "Organisms" },
-    { path: "", text: `${genome.species} - ${genome.strain}` },
+    { path: "", text: `${genome.organism}` },
     { path: "", text: "Choose Analysis Methods" },
   ];
 }
diff --git a/files/build-catalog.ts b/files/build-catalog.ts
index 8573975..49229d0 100644
--- a/files/build-catalog.ts
+++ b/files/build-catalog.ts
@@ -3,7 +3,7 @@ import fsp from "fs/promises";
 import { BRCDataCatalogGenome } from "../app/apis/catalog/brc-analytics-catalog/common/entities";
 import { SourceGenome } from "./entities";
 
-const SOURCE_PATH_GENOMES = "files/source/genomes.tsv";
+const SOURCE_PATH_GENOMES = "files/source/genomes-from-ncbi.tsv";
 
 buildCatalog();
 
@@ -20,22 +20,23 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
   const sourceRows = await readValuesFile<SourceGenome>(SOURCE_PATH_GENOMES);
   const mappedRows = sourceRows.map(
     (row): BRCDataCatalogGenome => ({
-      chromosomes: parseNumber(row.Chromosomes),
-      contigs: parseNumber(row.Contigs),
-      geneModelUrl: row.geneModelUrl,
-      genomeVersionAssemblyId: row["Genome Version/Assembly ID"],
-      ncbiTaxonomyId: row.taxId,
-      organism: row.Organism,
-      species: row.Species,
-      strain: row.Strain,
-      supercontigs: parseNumber(row.Supercontigs),
-      ucscBrowserUrl: row.ucscBrowser,
-      vEuPathDbProject: row["VEuPathDB Project"],
+      accession: row.accession,
+      annotationStatus: parseStringOrNull(row.annotationStatus),
+      chromosomes: parseNumberOrNull(row.chromosomeCount),
+      coverage: parseStringOrNull(row.coverage),
+      gcPercent: parseNumber(row.gcPercent),
+      isRef: parseBoolean(row.isRef),
+      length: parseNumber(row.length),
+      level: row.level,
+      ncbiTaxonomyId: row.taxonomyId,
+      organism: row.taxon,
+      scaffoldCount: parseNumber(row.scaffoldCount),
+      scaffoldL50: parseNumber(row.scaffoldL50),
+      scaffoldN50: parseNumber(row.scaffoldN50),
+      ucscBrowserUrl: parseStringOrNull(row.ucscBrowser),
     })
   );
-  return mappedRows.sort((a, b) =>
-    a.genomeVersionAssemblyId.localeCompare(b.genomeVersionAssemblyId)
-  );
+  return mappedRows.sort((a, b) => a.accession.localeCompare(b.accession));
 }
 
 async function readValuesFile<T>(
@@ -54,6 +55,15 @@ async function saveJson(filePath: string, data: unknown): Promise<void> {
   await fsp.writeFile(filePath, JSON.stringify(data, undefined, 2) + "\n");
 }
 
+function parseStringOrNull(value: string): string | null {
+  return value || null;
+}
+
+function parseNumberOrNull(value: string): number | null {
+  if (!value) return null;
+  return parseNumber(value);
+}
+
 function parseNumber(value: string): number {
   value = value.trim();
   const n = Number(value);
@@ -61,3 +71,7 @@ function parseNumber(value: string): number {
     throw new Error(`Invalid number value: ${JSON.stringify(value)}`);
   return n;
 }
+
+function parseBoolean(value: string): boolean {
+  return value[0].toLowerCase() === "t";
+}
diff --git a/files/entities.ts b/files/entities.ts
index dad7cc1..6f5b6f6 100644
--- a/files/entities.ts
+++ b/files/entities.ts
@@ -1,21 +1,16 @@
 export interface SourceGenome {
-  asmId: string;
-  Chromosomes: string;
-  comName: string;
-  Contigs: string;
-  genBank: string;
-  geneModelUrl: string;
-  "Genome Source": string;
-  "Genome Version/Assembly ID": string;
-  identical: string;
-  "Is Reference Strain": string;
-  Organism: string;
-  refSeq: string;
-  sciName: string;
-  Species: string;
-  Strain: string;
-  Supercontigs: string;
-  taxId: string;
+  accession: string;
+  annotationStatus: string;
+  chromosomeCount: string;
+  coverage: string;
+  gcPercent: string;
+  isRef: string;
+  length: string;
+  level: string;
+  scaffoldCount: string;
+  scaffoldL50: string;
+  scaffoldN50: string;
+  taxon: string;
+  taxonomyId: string;
   ucscBrowser: string;
-  "VEuPathDB Project": string;
 }
diff --git a/files/out/genomes.json b/files/out/genomes.json
index 14bb70e..abbeba6 100644
--- a/files/out/genomes.json
+++ b/files/out/genomes.json
@@ -1,9674 +1,322 @@
 [
   {
-    "chromosomes": 7,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCA_000001215.4",
-    "ncbiTaxonomyId": "7227",
-    "organism": "Drosophila melanogaster iso-1",
-    "species": "Drosophila melanogaster",
-    "strain": "iso-1",
-    "supercontigs": 1862,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000001215.4",
-    "vEuPathDbProject": "VectorBase",
-    "geneModelUrl": ""
-  },
-  {
-    "chromosomes": 0,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCA_000001985.1",
-    "ncbiTaxonomyId": "441960",
-    "organism": "Talaromyces marneffei ATCC 18224",
-    "species": "Talaromyces marneffei",
-    "strain": "ATCC 18224",
-    "supercontigs": 452,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000001985.1",
-    "vEuPathDbProject": "FungiDB",
-    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCA/000/001/985/GCA_000001985.1/genes/GCA_000001985.1_JCVI-PMFA1-2.0.augustus.gtf.gz"
-  },
-  {
-    "chromosomes": 14,
-    "contigs": 2733,
-    "genomeVersionAssemblyId": "GCA_000002415.2",
+    "accession": "GCF_000002415.2",
+    "annotationStatus": "Full annotation",
+    "chromosomes": 14,
+    "coverage": null,
+    "gcPercent": 42.5,
+    "isRef": true,
+    "length": 27007701,
+    "level": "Chromosome",
     "ncbiTaxonomyId": "5855",
-    "organism": "Plasmodium vivax Sal-1",
-    "species": "Plasmodium vivax",
-    "strain": "Sal-1",
-    "supercontigs": 0,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2",
-    "vEuPathDbProject": "PlasmoDB",
-    "geneModelUrl": ""
-  },
-  {
-    "chromosomes": 5,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCA_000002435.2",
-    "ncbiTaxonomyId": "5741",
-    "organism": "Giardia Assemblage A isolate WB 2019",
-    "species": "Giardia Assemblage A",
-    "strain": "isolate WB 2019",
-    "supercontigs": 30,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002435.2",
-    "vEuPathDbProject": "GiardiaDB",
-    "geneModelUrl": ""
+    "organism": "Plasmodium vivax",
+    "scaffoldCount": 2747,
+    "scaffoldL50": 6,
+    "scaffoldN50": 1678596,
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2"
   },
   {
-    "chromosomes": 16,
-    "contigs": 115,
-    "genomeVersionAssemblyId": "GCA_000002445.1",
+    "accession": "GCF_000002445.2",
+    "annotationStatus": "Full annotation",
+    "chromosomes": 11,
+    "coverage": null,
+    "gcPercent": 46.5,
+    "isRef": true,
+    "length": 26075494,
+    "level": "Chromosome",
     "ncbiTaxonomyId": "185431",
     "organism": "Trypanosoma brucei brucei TREU927",
-    "species": "Trypanosoma brucei",
-    "strain": "brucei TREU927",
-    "supercontigs": 0,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2",
-    "vEuPathDbProject": "TriTrypDB",
-    "geneModelUrl": ""
-  },
-  {
-    "chromosomes": 7,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCA_000002495.2",
-    "ncbiTaxonomyId": "242507",
-    "organism": "Pyricularia oryzae 70-15",
-    "species": "Pyricularia oryzae",
-    "strain": "70-15",
-    "supercontigs": 46,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002495.2",
-    "vEuPathDbProject": "FungiDB",
-    "geneModelUrl": ""
-  },
-  {
-    "chromosomes": 6,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCA_000002515.1",
-    "ncbiTaxonomyId": "28985",
-    "organism": "Kluyveromyces lactis NRRL Y-1140",
-    "species": "Kluyveromyces lactis",
-    "strain": "NRRL Y-1140",
-    "supercontigs": 0,
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-  },
-  {
-    "chromosomes": 3,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCF_943734755.1",
-    "ncbiTaxonomyId": "186751",
-    "organism": "Anopheles moucheti AmouCM1",
-    "species": "Anopheles moucheti",
-    "strain": "AmouCM1",
-    "supercontigs": 342,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734755.1",
-    "vEuPathDbProject": "VectorBase",
-    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/755/GCF_943734755.1/genes/GCF_943734755.1_idAnoMoucSN_F20_07.ncbiRefSeq.gtf.gz"
-  },
-  {
-    "chromosomes": 3,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCF_943734765.1",
-    "ncbiTaxonomyId": "345580",
-    "organism": "Anopheles ziemanni AzieGA1",
-    "species": "Anopheles ziemanni",
-    "strain": "AzieGA1",
-    "supercontigs": 416,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734765.1",
-    "vEuPathDbProject": "VectorBase",
-    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/765/GCF_943734765.1/genes/GCF_943734765.1_idAnoZiCoDA_A2_x.2.ncbiRefSeq.gtf.gz"
-  },
-  {
-    "chromosomes": 3,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCF_943734845.2",
-    "ncbiTaxonomyId": "62324",
-    "organism": "Anopheles funestus AfunGA1",
-    "species": "Anopheles funestus",
-    "strain": "AfunGA1",
-    "supercontigs": 326,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734845.2",
-    "vEuPathDbProject": "VectorBase",
-    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/845/GCF_943734845.2/genes/GCF_943734845.2_idAnoFuneDA-416_04.ncbiRefSeq.gtf.gz"
-  },
-  {
-    "chromosomes": 3,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCF_943735745.2",
-    "ncbiTaxonomyId": "139047",
-    "organism": "Anopheles bellator AbelBR1",
-    "species": "Anopheles bellator",
-    "strain": "AbelBR1",
-    "supercontigs": 2982,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943735745.2",
-    "vEuPathDbProject": "VectorBase",
-    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/735/745/GCF_943735745.2/genes/GCF_943735745.2_idAnoBellAS_SP24_06.2.ncbiRefSeq.gtf.gz"
-  },
-  {
-    "chromosomes": 3,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCF_943737925.1",
-    "ncbiTaxonomyId": "185578",
-    "organism": "Anopheles nili AnilCM1",
-    "species": "Anopheles nili",
-    "strain": "AnilCM1",
-    "supercontigs": 153,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943737925.1",
-    "vEuPathDbProject": "VectorBase",
-    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/737/925/GCF_943737925.1/genes/GCF_943737925.1_idAnoNiliSN_F5_01.ncbiRefSeq.gtf.gz"
-  },
-  {
-    "chromosomes": 0,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCF_947086385.1",
-    "ncbiTaxonomyId": "94469",
-    "organism": "Phlebotomus argentipes India",
-    "species": "Phlebotomus argentipes",
-    "strain": "India",
-    "supercontigs": 64,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_947086385.1",
-    "vEuPathDbProject": "VectorBase",
-    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/947/086/385/GCF_947086385.1/genes/GCF_947086385.1_Phlebotomus_argentipes_genome_assembly.ncbiRefSeq.gtf.gz"
-  },
-  {
-    "chromosomes": 18,
-    "contigs": 0,
-    "genomeVersionAssemblyId": "GCF_947242115.1",
-    "ncbiTaxonomyId": "6526",
-    "organism": "Biomphalaria glabrata XG47",
-    "species": "Biomphalaria glabrata",
-    "strain": "XG47",
-    "supercontigs": 25,
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_947242115.1",
-    "vEuPathDbProject": "VectorBase",
-    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/947/242/115/GCF_947242115.1/genes/GCF_947242115.1_xgBioGlab47.1.ncbiRefSeq.gtf.gz"
+    "organism": "Anopheles gambiae",
+    "scaffoldCount": 190,
+    "scaffoldL50": 2,
+    "scaffoldN50": 99149756,
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2"
+  },
+  {
+    "accession": "GCF_963525475.1",
+    "annotationStatus": null,
+    "chromosomes": 1,
+    "coverage": "100.0x",
+    "gcPercent": 65.5,
+    "isRef": false,
+    "length": 4469156,
+    "level": "Complete Genome",
+    "ncbiTaxonomyId": "1773",
+    "organism": "Mycobacterium tuberculosis",
+    "scaffoldCount": 1,
+    "scaffoldL50": 1,
+    "scaffoldN50": 4469156,
+    "ucscBrowserUrl": null
   }
 ]
diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts
index 825f5d8..7a4519f 100644
--- a/site-config/brc-analytics/category.ts
+++ b/site-config/brc-analytics/category.ts
@@ -1,23 +1,35 @@
 export const BRC_DATA_CATALOG_CATEGORY_KEY = {
+  ACCESSION: "accession",
   ANALYZE_GENOME: "analyzeGenome",
+  ANNOTATION_STATUS: "annotationStatus",
   CHROMOSOMES: "chromosomes",
-  CONTIGS: "contigs",
-  GENOME_VERSION_ASSEMBLY_ID: "genomeVersionAssemblyId",
-  SPECIES: "species",
-  STRAIN: "strain",
-  SUPERCONTIGS: "supercontigs",
+  COVERAGE: "coverage",
+  GC_PERCENT: "gcPercent",
+  IS_REF: "isRef",
+  LENGTH: "length",
+  LEVEL: "level",
+  ORGANISM: "organism",
+  SCAFFOLD_COUNT: "scaffoldCount",
+  SCAFFOLD_L50: "scaffoldL50",
+  SCAFFOLD_N50: "scaffoldN50",
+  TAXONOMY_ID: "ncbiTaxonomyId",
   UCSC_BROWSER_URL: "ucscBrowserUrl",
-  VEUPATHDB_PROJECT: "vEuPathDbProject",
 };
 
 export const BRC_DATA_CATALOG_CATEGORY_LABEL = {
+  ACCESSION: "Accession",
   ANALYZE_GENOME: "Action",
+  ANNOTATION_STATUS: "Annotation Status",
   CHROMOSOMES: "Chromosomes",
-  CONTIGS: "Contigs",
-  GENOME_VERSION_ASSEMBLY_ID: "Assembly Version ID",
-  SPECIES: "Species",
-  STRAIN: "Strain",
-  SUPERCONTIGS: "Supercontigs",
+  COVERAGE: "Coverage",
+  GC_PERCENT: "GC%",
+  IS_REF: "Is Reference",
+  LENGTH: "Length",
+  LEVEL: "Level",
+  ORGANISM: "Organism",
+  SCAFFOLD_COUNT: "Scaffolds",
+  SCAFFOLD_L50: "Scaffold L50",
+  SCAFFOLD_N50: "Scaffold N50",
+  TAXONOMY_ID: "Taxonomy ID",
   UCSC_BROWSER_URL: "UCSC Browser",
-  VEUPATHDB_PROJECT: "VEuPathDB Project",
 };
diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
index 63f37fa..cc61338 100644
--- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts
+++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
@@ -30,20 +30,36 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
       {
         categoryConfigs: [
           {
-            key: BRC_DATA_CATALOG_CATEGORY_KEY.SPECIES,
-            label: BRC_DATA_CATALOG_CATEGORY_LABEL.SPECIES,
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.ORGANISM,
           },
           {
-            key: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN,
-            label: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN,
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID,
           },
           {
-            key: BRC_DATA_CATALOG_CATEGORY_KEY.GENOME_VERSION_ASSEMBLY_ID,
-            label: BRC_DATA_CATALOG_CATEGORY_LABEL.GENOME_VERSION_ASSEMBLY_ID,
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.ACCESSION,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION,
           },
           {
-            key: BRC_DATA_CATALOG_CATEGORY_KEY.VEUPATHDB_PROJECT,
-            label: BRC_DATA_CATALOG_CATEGORY_LABEL.VEUPATHDB_PROJECT,
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.IS_REF,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.IS_REF,
+            mapSelectCategoryValue: (value) => ({
+              ...value,
+              label: value.label ? "Yes" : "No",
+            }),
+          },
+          {
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.LEVEL,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.LEVEL,
+          },
+          {
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.COVERAGE,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.COVERAGE,
+          },
+          {
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.ANNOTATION_STATUS,
           },
         ],
       },
@@ -83,71 +99,125 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
       {
         componentConfig: {
           component: C.BasicCell,
-          viewBuilder: V.buildSpecies,
+          viewBuilder: V.buildOrganism,
         } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
-        header: BRC_DATA_CATALOG_CATEGORY_LABEL.SPECIES,
-        id: BRC_DATA_CATALOG_CATEGORY_KEY.SPECIES,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.ORGANISM,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM,
         width: { max: "1fr", min: "284px" },
       },
       {
         componentConfig: {
           component: C.BasicCell,
-          viewBuilder: V.buildStrain,
+          viewBuilder: V.buildTaxonomyId,
         } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
-        header: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN,
-        id: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN,
-        width: { max: "1fr", min: "124px" },
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID,
+        width: { max: "0.5fr", min: "100px" },
       },
       {
         columnPinned: true,
         componentConfig: {
           component: C.BasicCell,
-          viewBuilder: V.buildGenomeVersionAssemblyId,
+          viewBuilder: V.buildAccession,
         } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
-        header: BRC_DATA_CATALOG_CATEGORY_LABEL.GENOME_VERSION_ASSEMBLY_ID,
-        id: BRC_DATA_CATALOG_CATEGORY_KEY.GENOME_VERSION_ASSEMBLY_ID,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.ACCESSION,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.ACCESSION,
         width: { max: "1fr", min: "164px" },
       },
       {
         componentConfig: {
           component: C.BasicCell,
-          viewBuilder: V.buildVEuPathDbProject,
+          viewBuilder: V.buildIsRef,
         } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
-        header: BRC_DATA_CATALOG_CATEGORY_LABEL.VEUPATHDB_PROJECT,
-        id: BRC_DATA_CATALOG_CATEGORY_KEY.VEUPATHDB_PROJECT,
-        width: { max: "1fr", min: "140px" },
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.IS_REF,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.IS_REF,
+        width: { max: "0.5fr", min: "100px" },
       },
       {
         componentConfig: {
           component: C.BasicCell,
-          viewBuilder: V.buildContigs,
+          viewBuilder: V.buildLevel,
         } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
-        header: BRC_DATA_CATALOG_CATEGORY_LABEL.CONTIGS,
-        id: BRC_DATA_CATALOG_CATEGORY_KEY.CONTIGS,
-        width: { max: "0.5fr", min: "100px" },
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.LEVEL,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.LEVEL,
+        width: { max: "0.5fr", min: "142px" },
+      },
+      {
+        componentConfig: {
+          component: C.BasicCell,
+          viewBuilder: V.buildChromosomes,
+        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.CHROMOSOMES,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.CHROMOSOMES,
+        width: { max: "0.5fr", min: "142px" },
       },
       {
         componentConfig: {
           component: C.BasicCell,
-          viewBuilder: V.buildSupercontigs,
+          viewBuilder: V.buildLength,
         } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
-        header: BRC_DATA_CATALOG_CATEGORY_LABEL.SUPERCONTIGS,
-        id: BRC_DATA_CATALOG_CATEGORY_KEY.SUPERCONTIGS,
-        width: { max: "0.5fr", min: "140px" },
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.LENGTH,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.LENGTH,
+        width: { max: "0.5fr", min: "120px" },
       },
       {
         componentConfig: {
           component: C.BasicCell,
-          viewBuilder: V.buildChromosomes,
+          viewBuilder: V.buildScaffoldCount,
         } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
-        header: BRC_DATA_CATALOG_CATEGORY_LABEL.CHROMOSOMES,
-        id: BRC_DATA_CATALOG_CATEGORY_KEY.CHROMOSOMES,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_COUNT,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_COUNT,
+        width: { max: "0.5fr", min: "80px" },
+      },
+      {
+        componentConfig: {
+          component: C.BasicCell,
+          viewBuilder: V.buildScaffoldN50,
+        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_N50,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_N50,
+        width: { max: "0.5fr", min: "142px" },
+      },
+      {
+        componentConfig: {
+          component: C.BasicCell,
+          viewBuilder: V.buildScaffoldL50,
+        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.SCAFFOLD_L50,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.SCAFFOLD_L50,
+        width: { max: "0.5fr", min: "80px" },
+      },
+      {
+        componentConfig: {
+          component: C.BasicCell,
+          viewBuilder: V.buildCoverage,
+        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.COVERAGE,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.COVERAGE,
+        width: { max: "0.5fr", min: "80px" },
+      },
+      {
+        componentConfig: {
+          component: C.BasicCell,
+          viewBuilder: V.buildGcPercent,
+        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.GC_PERCENT,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.GC_PERCENT,
+        width: { max: "0.5fr", min: "80px" },
+      },
+      {
+        componentConfig: {
+          component: C.BasicCell,
+          viewBuilder: V.buildAnnotationStatus,
+        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.ANNOTATION_STATUS,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS,
         width: { max: "0.5fr", min: "142px" },
       },
     ],
     defaultSort: {
       desc: SORT_DIRECTION.ASCENDING,
-      id: BRC_DATA_CATALOG_CATEGORY_KEY.SPECIES,
+      id: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM,
     },
   } as ListConfig<BRCDataCatalogGenome>,
   listView: {

From fab3f77539727b4e9a3765e1d593f2cfe10ed50f Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Sat, 16 Nov 2024 16:39:54 -0800
Subject: [PATCH 02/19] feat: restore gene model url (#177)

---
 .../brc-analytics-catalog/common/entities.ts  |  1 +
 .../Entity/components/AnalysisMethod/types.ts |  2 +-
 app/utils/galaxy-api.ts                       |  4 +-
 .../common/viewModelBuilders.ts               |  2 +-
 files/build-catalog.ts                        |  1 +
 files/build-files-from-ncbi.py                | 39 +++++++++++++++--
 files/entities.ts                             |  1 +
 files/out/genomes.json                        | 20 +++++++++
 files/source/genomes-from-ncbi.tsv            | 42 +++++++++----------
 files/source/organisms-from-ncbi.tsv          |  4 +-
 10 files changed, 86 insertions(+), 30 deletions(-)

diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
index 8e69429..3087c32 100644
--- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts
+++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
@@ -15,6 +15,7 @@ export interface BRCDataCatalogGenome {
   chromosomes: number | null;
   coverage: string | null;
   gcPercent: number;
+  geneModelUrl: string | null;
   isRef: boolean;
   length: number;
   level: string;
diff --git a/app/components/Entity/components/AnalysisMethod/types.ts b/app/components/Entity/components/AnalysisMethod/types.ts
index 3c8fb1a..852c04a 100644
--- a/app/components/Entity/components/AnalysisMethod/types.ts
+++ b/app/components/Entity/components/AnalysisMethod/types.ts
@@ -4,6 +4,6 @@ import { ANALYSIS_METHOD } from "../../../../apis/catalog/brc-analytics-catalog/
 export interface Props {
   analysisMethod: ANALYSIS_METHOD;
   content: ReactNode;
-  geneModelUrl: string;
+  geneModelUrl: string | null;
   genomeVersionAssemblyId: string;
 }
diff --git a/app/utils/galaxy-api.ts b/app/utils/galaxy-api.ts
index 4063b9d..be3705f 100644
--- a/app/utils/galaxy-api.ts
+++ b/app/utils/galaxy-api.ts
@@ -32,7 +32,7 @@ const WORKFLOW_LANDING_URL_PREFIX =
 export async function getWorkflowLandingUrl(
   workflowId: WORKFLOW_ID,
   referenceGenome: string,
-  geneModelUrl: string
+  geneModelUrl: string | null
 ): Promise<string> {
   const body: WorkflowLandingsBody = {
     public: true,
@@ -74,7 +74,7 @@ function buildFastaUrl(identifier: string): string {
 function getWorkflowLandingsRequestState(
   workflowId: WORKFLOW_ID,
   referenceGenome: string,
-  geneModelUrl: string
+  geneModelUrl: string | null
 ): WorkflowLandingsBodyRequestState {
   if (workflowId === WORKFLOW_ID.VARIANT_CALLING && geneModelUrl) {
     return {
diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
index 022a1a2..d45adc9 100644
--- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
+++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -231,7 +231,7 @@ export const buildGenomeAnalysisMethod = (
 ): ComponentProps<typeof C.AnalysisMethod> => {
   return {
     ...analysisMethodProps,
-    geneModelUrl: "",
+    geneModelUrl: genome.geneModelUrl,
     genomeVersionAssemblyId: genome.accession,
   };
 };
diff --git a/files/build-catalog.ts b/files/build-catalog.ts
index 49229d0..3576b9b 100644
--- a/files/build-catalog.ts
+++ b/files/build-catalog.ts
@@ -25,6 +25,7 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
       chromosomes: parseNumberOrNull(row.chromosomeCount),
       coverage: parseStringOrNull(row.coverage),
       gcPercent: parseNumber(row.gcPercent),
+      geneModelUrl: parseStringOrNull(row.geneModelUrl),
       isRef: parseBoolean(row.isRef),
       length: parseNumber(row.length),
       level: row.level,
diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py
index 8a0717b..0690d18 100644
--- a/files/build-files-from-ncbi.py
+++ b/files/build-files-from-ncbi.py
@@ -1,6 +1,7 @@
-from urllib.parse import quote as url_quote
 import pandas as pd
 import requests
+import urllib.parse
+import re
 
 TAXA_URL = "https://docs.google.com/spreadsheets/d/1Gg9sw2Qw765tOx2To53XkTAn-RAMiBtqYrfItlLXXrc/gviz/tq?tqx=out:csv&sheet=Sheet1.csv"
 
@@ -28,7 +29,7 @@ def get_tax_ids(organisms_df):
   return list(organisms_df["taxonomyId"])
 
 def build_genomes_url(tax_ids):
-  return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{url_quote(",".join([str(id) for id in tax_ids]))}/dataset_report?filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome"
+  return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{urllib.parse.quote(",".join([str(id) for id in tax_ids]))}/dataset_report?filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome"
 
 def get_genome_row(genome_info):
   refseq_category = genome_info["assembly_info"].get("refseq_category")
@@ -52,6 +53,38 @@ def get_genome_row(genome_info):
 def get_genomes_df(tax_ids):
   return pd.DataFrame(data=[get_genome_row(genome_info) for genome_info in requests.get(build_genomes_url(tax_ids)).json()["reports"]])
 
+def _id_to_gene_model_url(asm_id):
+  hubs_url = "https://hgdownload.soe.ucsc.edu/hubs/"
+  components = [asm_id[0:3], asm_id[4:7], asm_id[7:10], asm_id[10:13], asm_id, "genes"]
+  url = urllib.parse.urljoin(hubs_url, "/".join(components))
+  # url looks something like https://hgdownload.soe.ucsc.edu/hubs/GCF/030/504/385/GCF_030504385.1/genes/
+  # and contains html content with links to gene models.
+  # we need to scrape this to get the gtf
+  print(f"fetching url {url}")
+  response = requests.get(url)
+  try:
+    response.raise_for_status()
+  except Exception:
+    # FIXME?: Some accessions don't have a gene folder
+    return None
+  # find link to gtf, should ideally be ncbiRefSeq, but augustus will do
+  html_content = response.text
+  pattern = rf"{asm_id.replace('.', r'\.')}.*?\.gtf\.gz"
+  augustus_file = None
+  for match in re.findall(pattern, html_content):
+    if "ncbiRefSeq" in match:
+      return urllib.parse.urljoin(f"{url}/", match)
+    elif "augustus" in match:
+      augustus_file = match
+  if augustus_file:
+    return urllib.parse.urljoin(f"{url}/", augustus_file)
+  # No match, I guess that's OK ?
+  return None
+
+
+def add_gene_model_url(genomes_df: pd.DataFrame):
+  return pd.concat([genomes_df, genomes_df["accession"].apply(_id_to_gene_model_url).rename("geneModelUrl")], axis="columns")
+
 def build_files():
   print("Building files")
 
@@ -71,7 +104,7 @@ def build_files():
   gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="pairedAccession", right_on="genBank")
   ref_seq_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="refSeq")
 
-  genomes_df = gen_bank_merge_df.combine_first(ref_seq_merge_df)
+  genomes_df = add_gene_model_url(gen_bank_merge_df.combine_first(ref_seq_merge_df))
 
   genomes_df.to_csv(GENOMES_OUTPUT_PATH, index=False, sep="\t")
 
diff --git a/files/entities.ts b/files/entities.ts
index 6f5b6f6..3aa6edd 100644
--- a/files/entities.ts
+++ b/files/entities.ts
@@ -4,6 +4,7 @@ export interface SourceGenome {
   chromosomeCount: string;
   coverage: string;
   gcPercent: string;
+  geneModelUrl: string;
   isRef: string;
   length: string;
   level: string;
diff --git a/files/out/genomes.json b/files/out/genomes.json
index abbeba6..203502b 100644
--- a/files/out/genomes.json
+++ b/files/out/genomes.json
@@ -5,6 +5,7 @@
     "chromosomes": 14,
     "coverage": null,
     "gcPercent": 42.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 27007701,
     "level": "Chromosome",
@@ -21,6 +22,7 @@
     "chromosomes": 11,
     "coverage": null,
     "gcPercent": 46.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 26075494,
     "level": "Chromosome",
@@ -37,6 +39,7 @@
     "chromosomes": 36,
     "coverage": null,
     "gcPercent": 59.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 32855089,
     "level": "Complete Genome",
@@ -53,6 +56,7 @@
     "chromosomes": 14,
     "coverage": "100.0x",
     "gcPercent": 19.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 23292622,
     "level": "Complete Genome",
@@ -69,6 +73,7 @@
     "chromosomes": 35,
     "coverage": null,
     "gcPercent": 58,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 32068771,
     "level": "Chromosome",
@@ -85,6 +90,7 @@
     "chromosomes": 14,
     "coverage": "26.5x",
     "gcPercent": 52.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 65633124,
     "level": "Chromosome",
@@ -101,6 +107,7 @@
     "chromosomes": null,
     "coverage": null,
     "gcPercent": 46,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 28947925,
     "level": "Scaffold",
@@ -117,6 +124,7 @@
     "chromosomes": 1,
     "coverage": null,
     "gcPercent": 65.5,
+    "geneModelUrl": null,
     "isRef": true,
     "length": 4411532,
     "level": "Complete Genome",
@@ -133,6 +141,7 @@
     "chromosomes": null,
     "coverage": null,
     "gcPercent": 51.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 89937456,
     "level": "Scaffold",
@@ -149,6 +158,7 @@
     "chromosomes": 36,
     "coverage": null,
     "gcPercent": 59.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 32444968,
     "level": "Chromosome",
@@ -165,6 +175,7 @@
     "chromosomes": 1,
     "coverage": null,
     "gcPercent": 65.5,
+    "geneModelUrl": null,
     "isRef": false,
     "length": 4411709,
     "level": "Complete Genome",
@@ -181,6 +192,7 @@
     "chromosomes": 1,
     "coverage": null,
     "gcPercent": 33,
+    "geneModelUrl": null,
     "isRef": false,
     "length": 196858,
     "level": "Complete Genome",
@@ -197,6 +209,7 @@
     "chromosomes": 1,
     "coverage": null,
     "gcPercent": 38,
+    "geneModelUrl": null,
     "isRef": false,
     "length": 29903,
     "level": "Complete Genome",
@@ -213,6 +226,7 @@
     "chromosomes": 3,
     "coverage": "250.0x",
     "gcPercent": 37,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 566339288,
     "level": "Chromosome",
@@ -229,6 +243,7 @@
     "chromosomes": 9,
     "coverage": "475.0x",
     "gcPercent": 46.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 28193268,
     "level": "Complete Genome",
@@ -245,6 +260,7 @@
     "chromosomes": 1,
     "coverage": "20.0x",
     "gcPercent": 65.5,
+    "geneModelUrl": null,
     "isRef": false,
     "length": 4516435,
     "level": "Complete Genome",
@@ -261,6 +277,7 @@
     "chromosomes": 14,
     "coverage": "100.0x",
     "gcPercent": 21.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 23043114,
     "level": "Complete Genome",
@@ -277,6 +294,7 @@
     "chromosomes": 14,
     "coverage": "155.0x",
     "gcPercent": 23,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 18338688,
     "level": "Complete Genome",
@@ -293,6 +311,7 @@
     "chromosomes": 3,
     "coverage": "54.0x",
     "gcPercent": 44.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz",
     "isRef": true,
     "length": 264451381,
     "level": "Chromosome",
@@ -309,6 +328,7 @@
     "chromosomes": 1,
     "coverage": "100.0x",
     "gcPercent": 65.5,
+    "geneModelUrl": null,
     "isRef": false,
     "length": 4469156,
     "level": "Complete Genome",
diff --git a/files/source/genomes-from-ncbi.tsv b/files/source/genomes-from-ncbi.tsv
index 8876bf3..79d5b1b 100644
--- a/files/source/genomes-from-ncbi.tsv
+++ b/files/source/genomes-from-ncbi.tsv
@@ -1,21 +1,21 @@
-taxon	taxonomyId	accession	isRef	level	chromosomeCount	length	scaffoldCount	scaffoldN50	scaffoldL50	coverage	gcPercent	annotationStatus	pairedAccession	ucscBrowser	genBank	refSeq
-Mycobacterium tuberculosis H37Rv	83332	GCF_000195955.2	True	Complete Genome	1.0	4411532	1	4411532	1		65.5		GCA_000195955.2			
-Plasmodium falciparum 3D7	36329	GCF_000002765.6	True	Complete Genome	14.0	23292622	14	1687656	5	100.0x	19.5	Full annotation	GCA_000002765.3	https://genome.ucsc.edu/h/GCF_000002765.5	GCA_000002765.3	GCF_000002765.5
-Leishmania major strain Friedlin	347515	GCF_000002725.2	True	Complete Genome	36.0	32855089	36	1091540	11		59.5	Full annotation	GCA_000002725.2	https://genome.ucsc.edu/h/GCF_000002725.2	GCA_000002725.2	GCF_000002725.2
-Plasmodium yoelii	5861	GCF_900002385.2	True	Complete Genome	14.0	23043114	14	2046250	5	100.0x	21.5	Full annotation	GCA_900002385.2	https://genome.ucsc.edu/h/GCF_900002385.2	GCA_900002385.2	GCF_900002385.2
-Coccidioides posadasii str. Silveira	443226	GCF_018416015.2	True	Complete Genome	9.0	28193268	9	8079863	2	475.0x	46.5	Full annotation	GCA_018416015.2	https://genome.ucsc.edu/h/GCA_018416015.2	GCA_018416015.2	GCF_018416015.1
-Plasmodium vinckei vinckei	54757	GCF_900681995.1	True	Complete Genome	14.0	18338688	14	1692345	5	155.0x	23.0	Full annotation	GCA_900681995.1	https://genome.ucsc.edu/h/GCF_900681995.1	GCA_900681995.1	GCF_900681995.1
-Leishmania donovani	5661	GCF_000227135.1	True	Chromosome	36.0	32444968	36	1024085	11		59.5	Full annotation	GCA_000227135.2	https://genome.ucsc.edu/h/GCF_000227135.1	GCA_000227135.2	GCF_000227135.1
-Toxoplasma gondii ME49	508771	GCF_000006565.2	True	Chromosome	14.0	65633124	2276	4973582	6	26.5x	52.5		GCA_000006565.2	https://genome.ucsc.edu/h/GCF_000006565.2	GCA_000006565.2	GCF_000006565.2
-Trypanosoma brucei brucei TREU927	185431	GCF_000002445.2	True	Chromosome	11.0	26075494	12	2481190	4		46.5	Full annotation	GCA_000002445.1	https://genome.ucsc.edu/h/GCF_000002445.2	GCA_000002445.1	GCF_000002445.2
-Anopheles gambiae	7165	GCF_943734735.2	True	Chromosome	3.0	264451381	190	99149756	2	54.0x	44.5	Full annotation	GCA_943734735.2	https://genome.ucsc.edu/h/GCF_943734735.2	GCA_943734735.2	GCF_943734735.2
-Plasmodium vivax	5855	GCF_000002415.2	True	Chromosome	14.0	27007701	2747	1678596	6		42.5	Full annotation	GCA_000002415.2	https://genome.ucsc.edu/h/GCF_000002415.2	GCA_000002415.2	GCF_000002415.2
-Culex pipiens pallens	42434	GCF_016801865.2	True	Chromosome	3.0	566339288	289	186194774	2	250.0x	37.0	Full annotation	GCA_016801865.2			
-Leishmania braziliensis MHOM/BR/75/M2904	420245	GCF_000002845.2	True	Chromosome	35.0	32068771	138	992961	11		58.0		GCA_000002845.2	https://genome.ucsc.edu/h/GCF_000002845.2	GCA_000002845.2	GCF_000002845.2
-Trypanosoma cruzi	5693	GCF_000209065.1	True	Scaffold		89937456	29495	88624	212		51.5	Full annotation	GCA_000209065.1	https://genome.ucsc.edu/h/GCF_000209065.1	GCA_000209065.1	GCF_000209065.1
-Coccidioides immitis RS	246410	GCF_000149335.2	True	Scaffold		28947925	6	4323945	3		46.0	Full annotation	GCA_000149335.2	https://genome.ucsc.edu/h/GCF_000149335.2	GCA_000149335.2	GCF_000149335.2
-Mycobacterium tuberculosis H37Rv	83332	GCF_000277735.2	False	Complete Genome	1.0	4411709	1	4411709	1		65.5		GCA_000277735.2			
-Severe acute respiratory syndrome coronavirus 2	2697049	GCF_009858895.2	False	Complete Genome	1.0	29903	1	29903	1		38.0		GCA_009858895.3			
-Monkeypox virus	10244	GCF_000857045.1	False	Complete Genome	1.0	196858	1	196858	1		33.0		GCA_000857045.1			
-Mycobacterium tuberculosis	1773	GCF_030566675.1	False	Complete Genome	1.0	4516435	1	4516435	1	20.0x	65.5		GCA_030566675.1			
-Mycobacterium tuberculosis	1773	GCF_963525475.1	False	Complete Genome	1.0	4469156	1	4469156	1	100.0x	65.5		GCA_963525475.1			
+taxon	taxonomyId	accession	isRef	level	chromosomeCount	length	scaffoldCount	scaffoldN50	scaffoldL50	coverage	gcPercent	annotationStatus	pairedAccession	ucscBrowser	genBank	refSeq	geneModelUrl
+Mycobacterium tuberculosis H37Rv	83332	GCF_000195955.2	True	Complete Genome	1.0	4411532	1	4411532	1		65.5		GCA_000195955.2				
+Plasmodium falciparum 3D7	36329	GCF_000002765.6	True	Complete Genome	14.0	23292622	14	1687656	5	100.0x	19.5	Full annotation	GCA_000002765.3	https://genome.ucsc.edu/h/GCF_000002765.5	GCA_000002765.3	GCF_000002765.5	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz
+Leishmania major strain Friedlin	347515	GCF_000002725.2	True	Complete Genome	36.0	32855089	36	1091540	11		59.5	Full annotation	GCA_000002725.2	https://genome.ucsc.edu/h/GCF_000002725.2	GCA_000002725.2	GCF_000002725.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz
+Plasmodium yoelii	5861	GCF_900002385.2	True	Complete Genome	14.0	23043114	14	2046250	5	100.0x	21.5	Full annotation	GCA_900002385.2	https://genome.ucsc.edu/h/GCF_900002385.2	GCA_900002385.2	GCF_900002385.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz
+Coccidioides posadasii str. Silveira	443226	GCF_018416015.2	True	Complete Genome	9.0	28193268	9	8079863	2	475.0x	46.5	Full annotation	GCA_018416015.2	https://genome.ucsc.edu/h/GCA_018416015.2	GCA_018416015.2	GCF_018416015.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz
+Plasmodium vinckei vinckei	54757	GCF_900681995.1	True	Complete Genome	14.0	18338688	14	1692345	5	155.0x	23.0	Full annotation	GCA_900681995.1	https://genome.ucsc.edu/h/GCF_900681995.1	GCA_900681995.1	GCF_900681995.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz
+Leishmania donovani	5661	GCF_000227135.1	True	Chromosome	36.0	32444968	36	1024085	11		59.5	Full annotation	GCA_000227135.2	https://genome.ucsc.edu/h/GCF_000227135.1	GCA_000227135.2	GCF_000227135.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz
+Toxoplasma gondii ME49	508771	GCF_000006565.2	True	Chromosome	14.0	65633124	2276	4973582	6	26.5x	52.5		GCA_000006565.2	https://genome.ucsc.edu/h/GCF_000006565.2	GCA_000006565.2	GCF_000006565.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz
+Trypanosoma brucei brucei TREU927	185431	GCF_000002445.2	True	Chromosome	11.0	26075494	12	2481190	4		46.5	Full annotation	GCA_000002445.1	https://genome.ucsc.edu/h/GCF_000002445.2	GCA_000002445.1	GCF_000002445.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz
+Anopheles gambiae	7165	GCF_943734735.2	True	Chromosome	3.0	264451381	190	99149756	2	54.0x	44.5	Full annotation	GCA_943734735.2	https://genome.ucsc.edu/h/GCF_943734735.2	GCA_943734735.2	GCF_943734735.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz
+Plasmodium vivax	5855	GCF_000002415.2	True	Chromosome	14.0	27007701	2747	1678596	6		42.5	Full annotation	GCA_000002415.2	https://genome.ucsc.edu/h/GCF_000002415.2	GCA_000002415.2	GCF_000002415.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz
+Culex pipiens pallens	42434	GCF_016801865.2	True	Chromosome	3.0	566339288	289	186194774	2	250.0x	37.0	Full annotation	GCA_016801865.2				https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz
+Leishmania braziliensis MHOM/BR/75/M2904	420245	GCF_000002845.2	True	Chromosome	35.0	32068771	138	992961	11		58.0		GCA_000002845.2	https://genome.ucsc.edu/h/GCF_000002845.2	GCA_000002845.2	GCF_000002845.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz
+Trypanosoma cruzi	5693	GCF_000209065.1	True	Scaffold		89937456	29495	88624	212		51.5	Full annotation	GCA_000209065.1	https://genome.ucsc.edu/h/GCF_000209065.1	GCA_000209065.1	GCF_000209065.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz
+Coccidioides immitis RS	246410	GCF_000149335.2	True	Scaffold		28947925	6	4323945	3		46.0	Full annotation	GCA_000149335.2	https://genome.ucsc.edu/h/GCF_000149335.2	GCA_000149335.2	GCF_000149335.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz
+Mycobacterium tuberculosis H37Rv	83332	GCF_000277735.2	False	Complete Genome	1.0	4411709	1	4411709	1		65.5		GCA_000277735.2				
+Severe acute respiratory syndrome coronavirus 2	2697049	GCF_009858895.2	False	Complete Genome	1.0	29903	1	29903	1		38.0		GCA_009858895.3				
+Monkeypox virus	10244	GCF_000857045.1	False	Complete Genome	1.0	196858	1	196858	1		33.0		GCA_000857045.1				
+Mycobacterium tuberculosis	1773	GCF_030566675.1	False	Complete Genome	1.0	4516435	1	4516435	1	20.0x	65.5		GCA_030566675.1				
+Mycobacterium tuberculosis	1773	GCF_963525475.1	False	Complete Genome	1.0	4469156	1	4469156	1	100.0x	65.5		GCA_963525475.1				
diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv
index 83237cd..6686f92 100644
--- a/files/source/organisms-from-ncbi.tsv
+++ b/files/source/organisms-from-ncbi.tsv
@@ -1,7 +1,7 @@
 taxon	taxonomyId	assemblyCount	CustomTags
 Anopheles gambiae	7165	7	VEuPathDb
 Coccidioides immitis	5501	5	
-Coccidioides posadasii	199306	13	
+Coccidioides posadasii	199306	13	VEuPathDb
 Culex pipiens	7175	5	VEuPathDb
 Leishmania braziliensis	5660	11	VEuPathDb
 Leishmania donovani	5661	12	VEuPathDb
@@ -15,4 +15,4 @@ Plasmodium yoelii	5861	15	VEuPathDb
 Severe acute respiratory syndrome coronavirus 2	2697049	92	Virus
 Toxoplasma gondii	5811	29	VEuPathDb
 Trypanosoma brucei	5691	5	VEuPathDb
-Trypanosoma cruzi	5693	45	VEuPathDb
+Trypanosoma cruzi	5693	44	VEuPathDb

From cfe45ce3c2519069bb7dd85ce6e9033db9fa8f8b Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Sat, 16 Nov 2024 17:24:58 -0800
Subject: [PATCH 03/19] feat: relabel "organisms" to "genomes" (#177)

---
 .../Section/components/SectionHero/sectionHero.tsx          | 2 +-
 app/components/Home/content/sectionSubHero.mdx              | 2 +-
 .../brc-analytics-catalog/common/viewModelBuilders.ts       | 4 ++--
 pages/_app.tsx                                              | 2 +-
 routes/constants.ts                                         | 2 +-
 site-config/brc-analytics/local/config.ts                   | 2 +-
 site-config/brc-analytics/local/index/genomeEntityConfig.ts | 6 +++---
 7 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx b/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx
index 0069043..21faa17 100644
--- a/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx
+++ b/app/components/Home/components/Section/components/SectionHero/sectionHero.tsx
@@ -32,7 +32,7 @@ export const SectionHero = (): JSX.Element => {
                   annotations and functional insights into disease-causing
                   organisms and their carriers
                 </Subhead>
-                <Button {...BUTTON_PROPS} href={ROUTES.ORGANISMS}>
+                <Button {...BUTTON_PROPS} href={ROUTES.GENOMES}>
                   Get started
                 </Button>
               </SubHeadline>
diff --git a/app/components/Home/content/sectionSubHero.mdx b/app/components/Home/content/sectionSubHero.mdx
index da94f3a..0512771 100644
--- a/app/components/Home/content/sectionSubHero.mdx
+++ b/app/components/Home/content/sectionSubHero.mdx
@@ -1,5 +1,5 @@
 BRC Analytics is your new destination for analysis of biological
 data related to pathogens. Building on the foundation of VEuPathDb
 the platform will provide access and analysis capabilities for
-[785 eukaryotic pathogens](/data/organisms), hosts, and vectors. The functionality will
+[785 eukaryotic pathogens](/data/genomes), hosts, and vectors. The functionality will
 be developed and made available incrementally over the [following months](/roadmap).
diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
index d45adc9..c364d2c 100644
--- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
+++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -38,7 +38,7 @@ export const buildAnalyzeGenome = (
   return {
     analyze: {
       label: "Analyze",
-      url: rowId ? `${ROUTES.ORGANISMS}/${rowId}` : "",
+      url: rowId ? `${ROUTES.GENOMES}/${rowId}` : "",
     },
     views: [
       ...(ucscBrowserUrl
@@ -320,7 +320,7 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs(
   genome: BRCDataCatalogGenome
 ): Breadcrumb[] {
   return [
-    { path: ROUTES.ORGANISMS, text: "Organisms" },
+    { path: ROUTES.GENOMES, text: "Genomes" },
     { path: "", text: `${genome.organism}` },
     { path: "", text: "Choose Analysis Methods" },
   ];
diff --git a/pages/_app.tsx b/pages/_app.tsx
index 3e99414..3844bc2 100644
--- a/pages/_app.tsx
+++ b/pages/_app.tsx
@@ -20,7 +20,7 @@ import { StyledFooter } from "../app/components/Layout/components/Footer/footer.
 import { config } from "../app/config/config";
 import { mergeAppTheme } from "../app/theme/theme";
 
-const DEFAULT_ENTITY_LIST_TYPE = "organisms";
+const DEFAULT_ENTITY_LIST_TYPE = "genomes";
 
 export interface PageProps extends AzulEntitiesStaticResponse {
   pageTitle?: string;
diff --git a/routes/constants.ts b/routes/constants.ts
index c44740a..05eb80a 100644
--- a/routes/constants.ts
+++ b/routes/constants.ts
@@ -1,5 +1,5 @@
 export const ROUTES = {
   ABOUT: "/about",
-  ORGANISMS: "/data/organisms",
+  GENOMES: "/data/genomes",
   ROADMAP: "/roadmap",
 };
diff --git a/site-config/brc-analytics/local/config.ts b/site-config/brc-analytics/local/config.ts
index 5d6e907..781a54a 100644
--- a/site-config/brc-analytics/local/config.ts
+++ b/site-config/brc-analytics/local/config.ts
@@ -68,7 +68,7 @@ export function makeConfig(browserUrl: string, gitHubUrl: string): SiteConfig {
           undefined,
           [
             { label: "About", url: ROUTES.ABOUT },
-            { label: "Datasets", url: ROUTES.ORGANISMS },
+            { label: "Datasets", url: ROUTES.GENOMES },
             { label: "Roadmap", url: ROUTES.ROADMAP },
           ],
           undefined,
diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
index cc61338..42d2bf5 100644
--- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts
+++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
@@ -80,10 +80,10 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
     ],
   },
   exploreMode: EXPLORE_MODE.CS_FETCH_CS_FILTERING,
-  explorerTitle: "Organisms",
+  explorerTitle: "Genomes",
   getId: getGenomeId,
   getTitle: getGenomeTitle,
-  label: "Organisms",
+  label: "Genomes",
   list: {
     columns: [
       {
@@ -226,6 +226,6 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
     enableTab: false,
     listHero,
   },
-  route: "organisms",
+  route: "genomes",
   staticLoadFile: "files/out/genomes.json",
 };

From 8e7ccc3a16f572c34a71673d62e683040c274d49 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Sat, 16 Nov 2024 17:35:55 -0800
Subject: [PATCH 04/19] feat: rename "organism" to "taxon" (#177)

---
 .../brc-analytics-catalog/common/entities.ts  |  2 +-
 .../brc-analytics-catalog/common/utils.ts     |  2 +-
 .../common/viewModelBuilders.ts               | 10 ++---
 files/build-catalog.ts                        |  2 +-
 files/out/genomes.json                        | 40 +++++++++----------
 site-config/brc-analytics/category.ts         |  4 +-
 .../local/index/genomeEntityConfig.ts         | 12 +++---
 7 files changed, 36 insertions(+), 36 deletions(-)

diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
index 3087c32..28d0b20 100644
--- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts
+++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
@@ -20,10 +20,10 @@ export interface BRCDataCatalogGenome {
   length: number;
   level: string;
   ncbiTaxonomyId: string;
-  organism: string;
   scaffoldCount: number;
   scaffoldL50: number;
   scaffoldN50: number;
+  taxon: string;
   ucscBrowserUrl: string | null;
 }
 
diff --git a/app/apis/catalog/brc-analytics-catalog/common/utils.ts b/app/apis/catalog/brc-analytics-catalog/common/utils.ts
index 935fde0..0baded0 100644
--- a/app/apis/catalog/brc-analytics-catalog/common/utils.ts
+++ b/app/apis/catalog/brc-analytics-catalog/common/utils.ts
@@ -6,7 +6,7 @@ export function getGenomeId(genome: BRCDataCatalogGenome): string {
 
 export function getGenomeTitle(genome?: BRCDataCatalogGenome): string {
   if (!genome) return "";
-  return `${genome.organism}`;
+  return `${genome.taxon}`;
 }
 
 export function sanitizeEntityId(entityId?: string): string {
diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
index c364d2c..d960147 100644
--- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
+++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -150,15 +150,15 @@ export const buildLevel = (
 };
 
 /**
- * Build props for the organism cell.
+ * Build props for the taxon cell.
  * @param genome - Genome entity.
  * @returns Props to be used for the cell.
  */
-export const buildOrganism = (
+export const buildTaxon = (
   genome: BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: genome.organism,
+    value: genome.taxon,
   };
 };
 
@@ -289,7 +289,7 @@ export const buildGenomeDetails = (
   keyValuePairs.set(
     "Taxon",
     C.Link({
-      label: genome.organism,
+      label: genome.taxon,
       url: `https://www.ncbi.nlm.nih.gov/datasets/taxonomy/${encodeURIComponent(
         genome.ncbiTaxonomyId
       )}/`,
@@ -321,7 +321,7 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs(
 ): Breadcrumb[] {
   return [
     { path: ROUTES.GENOMES, text: "Genomes" },
-    { path: "", text: `${genome.organism}` },
+    { path: "", text: `${genome.taxon}` },
     { path: "", text: "Choose Analysis Methods" },
   ];
 }
diff --git a/files/build-catalog.ts b/files/build-catalog.ts
index 3576b9b..ff24ba7 100644
--- a/files/build-catalog.ts
+++ b/files/build-catalog.ts
@@ -30,10 +30,10 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
       length: parseNumber(row.length),
       level: row.level,
       ncbiTaxonomyId: row.taxonomyId,
-      organism: row.taxon,
       scaffoldCount: parseNumber(row.scaffoldCount),
       scaffoldL50: parseNumber(row.scaffoldL50),
       scaffoldN50: parseNumber(row.scaffoldN50),
+      taxon: row.taxon,
       ucscBrowserUrl: parseStringOrNull(row.ucscBrowser),
     })
   );
diff --git a/files/out/genomes.json b/files/out/genomes.json
index 203502b..771cac1 100644
--- a/files/out/genomes.json
+++ b/files/out/genomes.json
@@ -10,10 +10,10 @@
     "length": 27007701,
     "level": "Chromosome",
     "ncbiTaxonomyId": "5855",
-    "organism": "Plasmodium vivax",
     "scaffoldCount": 2747,
     "scaffoldL50": 6,
     "scaffoldN50": 1678596,
+    "taxon": "Plasmodium vivax",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2"
   },
   {
@@ -27,10 +27,10 @@
     "length": 26075494,
     "level": "Chromosome",
     "ncbiTaxonomyId": "185431",
-    "organism": "Trypanosoma brucei brucei TREU927",
     "scaffoldCount": 12,
     "scaffoldL50": 4,
     "scaffoldN50": 2481190,
+    "taxon": "Trypanosoma brucei brucei TREU927",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2"
   },
   {
@@ -44,10 +44,10 @@
     "length": 32855089,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "347515",
-    "organism": "Leishmania major strain Friedlin",
     "scaffoldCount": 36,
     "scaffoldL50": 11,
     "scaffoldN50": 1091540,
+    "taxon": "Leishmania major strain Friedlin",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2"
   },
   {
@@ -61,10 +61,10 @@
     "length": 23292622,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "36329",
-    "organism": "Plasmodium falciparum 3D7",
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 1687656,
+    "taxon": "Plasmodium falciparum 3D7",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.5"
   },
   {
@@ -78,10 +78,10 @@
     "length": 32068771,
     "level": "Chromosome",
     "ncbiTaxonomyId": "420245",
-    "organism": "Leishmania braziliensis MHOM/BR/75/M2904",
     "scaffoldCount": 138,
     "scaffoldL50": 11,
     "scaffoldN50": 992961,
+    "taxon": "Leishmania braziliensis MHOM/BR/75/M2904",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002845.2"
   },
   {
@@ -95,10 +95,10 @@
     "length": 65633124,
     "level": "Chromosome",
     "ncbiTaxonomyId": "508771",
-    "organism": "Toxoplasma gondii ME49",
     "scaffoldCount": 2276,
     "scaffoldL50": 6,
     "scaffoldN50": 4973582,
+    "taxon": "Toxoplasma gondii ME49",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006565.2"
   },
   {
@@ -112,10 +112,10 @@
     "length": 28947925,
     "level": "Scaffold",
     "ncbiTaxonomyId": "246410",
-    "organism": "Coccidioides immitis RS",
     "scaffoldCount": 6,
     "scaffoldL50": 3,
     "scaffoldN50": 4323945,
+    "taxon": "Coccidioides immitis RS",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149335.2"
   },
   {
@@ -129,10 +129,10 @@
     "length": 4411532,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "83332",
-    "organism": "Mycobacterium tuberculosis H37Rv",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4411532,
+    "taxon": "Mycobacterium tuberculosis H37Rv",
     "ucscBrowserUrl": null
   },
   {
@@ -146,10 +146,10 @@
     "length": 89937456,
     "level": "Scaffold",
     "ncbiTaxonomyId": "5693",
-    "organism": "Trypanosoma cruzi",
     "scaffoldCount": 29495,
     "scaffoldL50": 212,
     "scaffoldN50": 88624,
+    "taxon": "Trypanosoma cruzi",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209065.1"
   },
   {
@@ -163,10 +163,10 @@
     "length": 32444968,
     "level": "Chromosome",
     "ncbiTaxonomyId": "5661",
-    "organism": "Leishmania donovani",
     "scaffoldCount": 36,
     "scaffoldL50": 11,
     "scaffoldN50": 1024085,
+    "taxon": "Leishmania donovani",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000227135.1"
   },
   {
@@ -180,10 +180,10 @@
     "length": 4411709,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "83332",
-    "organism": "Mycobacterium tuberculosis H37Rv",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4411709,
+    "taxon": "Mycobacterium tuberculosis H37Rv",
     "ucscBrowserUrl": null
   },
   {
@@ -197,10 +197,10 @@
     "length": 196858,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "10244",
-    "organism": "Monkeypox virus",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 196858,
+    "taxon": "Monkeypox virus",
     "ucscBrowserUrl": null
   },
   {
@@ -214,10 +214,10 @@
     "length": 29903,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "2697049",
-    "organism": "Severe acute respiratory syndrome coronavirus 2",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 29903,
+    "taxon": "Severe acute respiratory syndrome coronavirus 2",
     "ucscBrowserUrl": null
   },
   {
@@ -231,10 +231,10 @@
     "length": 566339288,
     "level": "Chromosome",
     "ncbiTaxonomyId": "42434",
-    "organism": "Culex pipiens pallens",
     "scaffoldCount": 289,
     "scaffoldL50": 2,
     "scaffoldN50": 186194774,
+    "taxon": "Culex pipiens pallens",
     "ucscBrowserUrl": null
   },
   {
@@ -248,10 +248,10 @@
     "length": 28193268,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "443226",
-    "organism": "Coccidioides posadasii str. Silveira",
     "scaffoldCount": 9,
     "scaffoldL50": 2,
     "scaffoldN50": 8079863,
+    "taxon": "Coccidioides posadasii str. Silveira",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018416015.2"
   },
   {
@@ -265,10 +265,10 @@
     "length": 4516435,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "1773",
-    "organism": "Mycobacterium tuberculosis",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4516435,
+    "taxon": "Mycobacterium tuberculosis",
     "ucscBrowserUrl": null
   },
   {
@@ -282,10 +282,10 @@
     "length": 23043114,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "5861",
-    "organism": "Plasmodium yoelii",
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 2046250,
+    "taxon": "Plasmodium yoelii",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900002385.2"
   },
   {
@@ -299,10 +299,10 @@
     "length": 18338688,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "54757",
-    "organism": "Plasmodium vinckei vinckei",
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 1692345,
+    "taxon": "Plasmodium vinckei vinckei",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900681995.1"
   },
   {
@@ -316,10 +316,10 @@
     "length": 264451381,
     "level": "Chromosome",
     "ncbiTaxonomyId": "7165",
-    "organism": "Anopheles gambiae",
     "scaffoldCount": 190,
     "scaffoldL50": 2,
     "scaffoldN50": 99149756,
+    "taxon": "Anopheles gambiae",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2"
   },
   {
@@ -333,10 +333,10 @@
     "length": 4469156,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "1773",
-    "organism": "Mycobacterium tuberculosis",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4469156,
+    "taxon": "Mycobacterium tuberculosis",
     "ucscBrowserUrl": null
   }
 ]
diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts
index 7a4519f..92fc0f1 100644
--- a/site-config/brc-analytics/category.ts
+++ b/site-config/brc-analytics/category.ts
@@ -8,10 +8,10 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = {
   IS_REF: "isRef",
   LENGTH: "length",
   LEVEL: "level",
-  ORGANISM: "organism",
   SCAFFOLD_COUNT: "scaffoldCount",
   SCAFFOLD_L50: "scaffoldL50",
   SCAFFOLD_N50: "scaffoldN50",
+  TAXON: "taxon",
   TAXONOMY_ID: "ncbiTaxonomyId",
   UCSC_BROWSER_URL: "ucscBrowserUrl",
 };
@@ -26,10 +26,10 @@ export const BRC_DATA_CATALOG_CATEGORY_LABEL = {
   IS_REF: "Is Reference",
   LENGTH: "Length",
   LEVEL: "Level",
-  ORGANISM: "Organism",
   SCAFFOLD_COUNT: "Scaffolds",
   SCAFFOLD_L50: "Scaffold L50",
   SCAFFOLD_N50: "Scaffold N50",
+  TAXON: "Taxon",
   TAXONOMY_ID: "Taxonomy ID",
   UCSC_BROWSER_URL: "UCSC Browser",
 };
diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
index 42d2bf5..208d2a9 100644
--- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts
+++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
@@ -30,8 +30,8 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
       {
         categoryConfigs: [
           {
-            key: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM,
-            label: BRC_DATA_CATALOG_CATEGORY_LABEL.ORGANISM,
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON,
           },
           {
             key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID,
@@ -99,10 +99,10 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
       {
         componentConfig: {
           component: C.BasicCell,
-          viewBuilder: V.buildOrganism,
+          viewBuilder: V.buildTaxon,
         } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
-        header: BRC_DATA_CATALOG_CATEGORY_LABEL.ORGANISM,
-        id: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
         width: { max: "1fr", min: "284px" },
       },
       {
@@ -217,7 +217,7 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
     ],
     defaultSort: {
       desc: SORT_DIRECTION.ASCENDING,
-      id: BRC_DATA_CATALOG_CATEGORY_KEY.ORGANISM,
+      id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
     },
   } as ListConfig<BRCDataCatalogGenome>,
   listView: {

From 325a209e94d8a584aa104bcd4d1b4d9834c7b9c3 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Sun, 17 Nov 2024 18:33:14 -0800
Subject: [PATCH 05/19] feat: add tags to genome list (#177)

---
 .../brc-analytics-catalog/common/entities.ts  |  1 +
 app/components/index.ts                       |  1 +
 .../common/viewModelBuilders.ts               | 14 +++++++
 files/build-catalog.ts                        | 19 +++++++---
 files/entities.ts                             |  7 ++++
 files/out/genomes.json                        | 38 +++++++++++++++++++
 site-config/brc-analytics/category.ts         |  2 +
 .../local/index/genomeEntityConfig.ts         | 13 +++++++
 8 files changed, 90 insertions(+), 5 deletions(-)

diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
index 28d0b20..e61b319 100644
--- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts
+++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
@@ -23,6 +23,7 @@ export interface BRCDataCatalogGenome {
   scaffoldCount: number;
   scaffoldL50: number;
   scaffoldN50: number;
+  tags: string[];
   taxon: string;
   ucscBrowserUrl: string | null;
 }
diff --git a/app/components/index.ts b/app/components/index.ts
index 53ec783..4a868b3 100644
--- a/app/components/index.ts
+++ b/app/components/index.ts
@@ -22,6 +22,7 @@ export {
 export { Logo } from "@databiosphere/findable-ui/lib/components/Layout/components/Header/components/Content/components/Logo/logo";
 export { Link } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link";
 export { BasicCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/BasicCell/basicCell";
+export { NTagCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/NTagCell/nTagCell";
 export { CopyText } from "./common/CopyText/copyText";
 export { AnalysisMethod } from "./Entity/components/AnalysisMethod/analysisMethod";
 export { AnalysisMethods } from "./Entity/components/AnalysisMethods/analysisMethods";
diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
index d960147..72b346f 100644
--- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
+++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -201,6 +201,20 @@ export const buildScaffoldN50 = (
   };
 };
 
+/**
+ * Build props for the tags cell.
+ * @param genome - Genome entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildTags = (
+  genome: BRCDataCatalogGenome
+): ComponentProps<typeof C.NTagCell> => {
+  return {
+    label: "Tags",
+    values: genome.tags,
+  };
+};
+
 /**
  * Build props for the taxonomy ID cell.
  * @param genome - Genome entity.
diff --git a/files/build-catalog.ts b/files/build-catalog.ts
index ff24ba7..4c8a323 100644
--- a/files/build-catalog.ts
+++ b/files/build-catalog.ts
@@ -1,8 +1,9 @@
 import { parse as parseCsv } from "csv-parse/sync";
 import fsp from "fs/promises";
 import { BRCDataCatalogGenome } from "../app/apis/catalog/brc-analytics-catalog/common/entities";
-import { SourceGenome } from "./entities";
+import { SourceGenome, SourceOrganism } from "./entities";
 
+const SOURCE_PATH_ORGANISMS = "files/source/organisms-from-ncbi.tsv";
 const SOURCE_PATH_GENOMES = "files/source/genomes-from-ncbi.tsv";
 
 buildCatalog();
@@ -17,9 +18,16 @@ async function buildCatalog(): Promise<void> {
 }
 
 async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
+  const sourceOrganismRows = await readValuesFile<SourceOrganism>(
+    SOURCE_PATH_ORGANISMS
+  );
+  const sourceOrganismsByTaxon = new Map(
+    sourceOrganismRows.map((row) => [row.taxon, row])
+  );
   const sourceRows = await readValuesFile<SourceGenome>(SOURCE_PATH_GENOMES);
-  const mappedRows = sourceRows.map(
-    (row): BRCDataCatalogGenome => ({
+  const mappedRows = sourceRows.map((row): BRCDataCatalogGenome => {
+    const tagsString = sourceOrganismsByTaxon.get(row.taxon)?.CustomTags;
+    return {
       accession: row.accession,
       annotationStatus: parseStringOrNull(row.annotationStatus),
       chromosomes: parseNumberOrNull(row.chromosomeCount),
@@ -33,10 +41,11 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
       scaffoldCount: parseNumber(row.scaffoldCount),
       scaffoldL50: parseNumber(row.scaffoldL50),
       scaffoldN50: parseNumber(row.scaffoldN50),
+      tags: tagsString ? [tagsString] : [],
       taxon: row.taxon,
       ucscBrowserUrl: parseStringOrNull(row.ucscBrowser),
-    })
-  );
+    };
+  });
   return mappedRows.sort((a, b) => a.accession.localeCompare(b.accession));
 }
 
diff --git a/files/entities.ts b/files/entities.ts
index 3aa6edd..40c1774 100644
--- a/files/entities.ts
+++ b/files/entities.ts
@@ -15,3 +15,10 @@ export interface SourceGenome {
   taxonomyId: string;
   ucscBrowser: string;
 }
+
+export interface SourceOrganism {
+  assemblyCount: string;
+  CustomTags: string;
+  taxon: string;
+  taxonomyId: string;
+}
diff --git a/files/out/genomes.json b/files/out/genomes.json
index 771cac1..b8c9c76 100644
--- a/files/out/genomes.json
+++ b/files/out/genomes.json
@@ -13,6 +13,9 @@
     "scaffoldCount": 2747,
     "scaffoldL50": 6,
     "scaffoldN50": 1678596,
+    "tags": [
+      "VEuPathDb"
+    ],
     "taxon": "Plasmodium vivax",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2"
   },
@@ -30,6 +33,7 @@
     "scaffoldCount": 12,
     "scaffoldL50": 4,
     "scaffoldN50": 2481190,
+    "tags": [],
     "taxon": "Trypanosoma brucei brucei TREU927",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2"
   },
@@ -47,6 +51,7 @@
     "scaffoldCount": 36,
     "scaffoldL50": 11,
     "scaffoldN50": 1091540,
+    "tags": [],
     "taxon": "Leishmania major strain Friedlin",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2"
   },
@@ -64,6 +69,7 @@
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 1687656,
+    "tags": [],
     "taxon": "Plasmodium falciparum 3D7",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.5"
   },
@@ -81,6 +87,7 @@
     "scaffoldCount": 138,
     "scaffoldL50": 11,
     "scaffoldN50": 992961,
+    "tags": [],
     "taxon": "Leishmania braziliensis MHOM/BR/75/M2904",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002845.2"
   },
@@ -98,6 +105,7 @@
     "scaffoldCount": 2276,
     "scaffoldL50": 6,
     "scaffoldN50": 4973582,
+    "tags": [],
     "taxon": "Toxoplasma gondii ME49",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006565.2"
   },
@@ -115,6 +123,7 @@
     "scaffoldCount": 6,
     "scaffoldL50": 3,
     "scaffoldN50": 4323945,
+    "tags": [],
     "taxon": "Coccidioides immitis RS",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149335.2"
   },
@@ -132,6 +141,7 @@
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4411532,
+    "tags": [],
     "taxon": "Mycobacterium tuberculosis H37Rv",
     "ucscBrowserUrl": null
   },
@@ -149,6 +159,9 @@
     "scaffoldCount": 29495,
     "scaffoldL50": 212,
     "scaffoldN50": 88624,
+    "tags": [
+      "VEuPathDb"
+    ],
     "taxon": "Trypanosoma cruzi",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209065.1"
   },
@@ -166,6 +179,9 @@
     "scaffoldCount": 36,
     "scaffoldL50": 11,
     "scaffoldN50": 1024085,
+    "tags": [
+      "VEuPathDb"
+    ],
     "taxon": "Leishmania donovani",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000227135.1"
   },
@@ -183,6 +199,7 @@
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4411709,
+    "tags": [],
     "taxon": "Mycobacterium tuberculosis H37Rv",
     "ucscBrowserUrl": null
   },
@@ -200,6 +217,9 @@
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 196858,
+    "tags": [
+      "Virus"
+    ],
     "taxon": "Monkeypox virus",
     "ucscBrowserUrl": null
   },
@@ -217,6 +237,9 @@
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 29903,
+    "tags": [
+      "Virus"
+    ],
     "taxon": "Severe acute respiratory syndrome coronavirus 2",
     "ucscBrowserUrl": null
   },
@@ -234,6 +257,7 @@
     "scaffoldCount": 289,
     "scaffoldL50": 2,
     "scaffoldN50": 186194774,
+    "tags": [],
     "taxon": "Culex pipiens pallens",
     "ucscBrowserUrl": null
   },
@@ -251,6 +275,7 @@
     "scaffoldCount": 9,
     "scaffoldL50": 2,
     "scaffoldN50": 8079863,
+    "tags": [],
     "taxon": "Coccidioides posadasii str. Silveira",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018416015.2"
   },
@@ -268,6 +293,9 @@
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4516435,
+    "tags": [
+      "Bact"
+    ],
     "taxon": "Mycobacterium tuberculosis",
     "ucscBrowserUrl": null
   },
@@ -285,6 +313,9 @@
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 2046250,
+    "tags": [
+      "VEuPathDb"
+    ],
     "taxon": "Plasmodium yoelii",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900002385.2"
   },
@@ -302,6 +333,7 @@
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 1692345,
+    "tags": [],
     "taxon": "Plasmodium vinckei vinckei",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900681995.1"
   },
@@ -319,6 +351,9 @@
     "scaffoldCount": 190,
     "scaffoldL50": 2,
     "scaffoldN50": 99149756,
+    "tags": [
+      "VEuPathDb"
+    ],
     "taxon": "Anopheles gambiae",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2"
   },
@@ -336,6 +371,9 @@
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4469156,
+    "tags": [
+      "Bact"
+    ],
     "taxon": "Mycobacterium tuberculosis",
     "ucscBrowserUrl": null
   }
diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts
index 92fc0f1..edca097 100644
--- a/site-config/brc-analytics/category.ts
+++ b/site-config/brc-analytics/category.ts
@@ -11,6 +11,7 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = {
   SCAFFOLD_COUNT: "scaffoldCount",
   SCAFFOLD_L50: "scaffoldL50",
   SCAFFOLD_N50: "scaffoldN50",
+  TAGS: "tags",
   TAXON: "taxon",
   TAXONOMY_ID: "ncbiTaxonomyId",
   UCSC_BROWSER_URL: "ucscBrowserUrl",
@@ -29,6 +30,7 @@ export const BRC_DATA_CATALOG_CATEGORY_LABEL = {
   SCAFFOLD_COUNT: "Scaffolds",
   SCAFFOLD_L50: "Scaffold L50",
   SCAFFOLD_N50: "Scaffold N50",
+  TAGS: "Tags",
   TAXON: "Taxon",
   TAXONOMY_ID: "Taxonomy ID",
   UCSC_BROWSER_URL: "UCSC Browser",
diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
index 208d2a9..612e3be 100644
--- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts
+++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
@@ -61,6 +61,10 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
             key: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS,
             label: BRC_DATA_CATALOG_CATEGORY_LABEL.ANNOTATION_STATUS,
           },
+          {
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS,
+          },
         ],
       },
     ],
@@ -214,6 +218,15 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
         id: BRC_DATA_CATALOG_CATEGORY_KEY.ANNOTATION_STATUS,
         width: { max: "0.5fr", min: "142px" },
       },
+      {
+        componentConfig: {
+          component: C.NTagCell,
+          viewBuilder: V.buildTags,
+        } as ComponentConfig<typeof C.NTagCell, BRCDataCatalogGenome>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS,
+        width: { max: "0.5fr", min: "142px" },
+      },
     ],
     defaultSort: {
       desc: SORT_DIRECTION.ASCENDING,

From df266dea3394893e921209c436a383ea77e47a89 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Mon, 18 Nov 2024 18:15:31 -0800
Subject: [PATCH 06/19] feat: add organism list (#177)

---
 .../brc-analytics-catalog/common/entities.ts  |   7 +
 .../brc-analytics-catalog/common/utils.ts     |   6 +-
 .../common/viewModelBuilders.ts               |  24 +++-
 files/build-catalog.ts                        |  40 ++++--
 files/out/organisms.json                      | 136 ++++++++++++++++++
 routes/constants.ts                           |   1 +
 site-config/brc-analytics/category.ts         |   2 +
 site-config/brc-analytics/local/config.ts     |  14 +-
 .../local/index/organismEntityConfig.ts       | 102 +++++++++++++
 9 files changed, 316 insertions(+), 16 deletions(-)
 create mode 100644 files/out/organisms.json
 create mode 100644 site-config/brc-analytics/local/index/organismEntityConfig.ts

diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
index e61b319..7e713f5 100644
--- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts
+++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
@@ -28,6 +28,13 @@ export interface BRCDataCatalogGenome {
   ucscBrowserUrl: string | null;
 }
 
+export interface BRCDataCatalogOrganism {
+  assemblyCount: number;
+  ncbiTaxonomyId: string;
+  tags: string[];
+  taxon: string;
+}
+
 export interface EntitiesResponse<R> {
   hits: R[];
   pagination: EntitiesResponsePagination;
diff --git a/app/apis/catalog/brc-analytics-catalog/common/utils.ts b/app/apis/catalog/brc-analytics-catalog/common/utils.ts
index 0baded0..45fc474 100644
--- a/app/apis/catalog/brc-analytics-catalog/common/utils.ts
+++ b/app/apis/catalog/brc-analytics-catalog/common/utils.ts
@@ -1,4 +1,4 @@
-import { BRCDataCatalogGenome } from "./entities";
+import { BRCDataCatalogGenome, BRCDataCatalogOrganism } from "./entities";
 
 export function getGenomeId(genome: BRCDataCatalogGenome): string {
   return sanitizeEntityId(genome.accession);
@@ -9,6 +9,10 @@ export function getGenomeTitle(genome?: BRCDataCatalogGenome): string {
   return `${genome.taxon}`;
 }
 
+export function getOrganismId(organism: BRCDataCatalogOrganism): string {
+  return sanitizeEntityId(organism.ncbiTaxonomyId);
+}
+
 export function sanitizeEntityId(entityId?: string): string {
   if (!entityId) return "";
   return entityId.replace(/\./g, "_");
diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
index 72b346f..b7f6e85 100644
--- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
+++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -6,7 +6,10 @@ import {
 import { ViewContext } from "@databiosphere/findable-ui/lib/config/entities";
 import { ComponentProps } from "react";
 import { ROUTES } from "../../../../../routes/constants";
-import { BRCDataCatalogGenome } from "../../../../apis/catalog/brc-analytics-catalog/common/entities";
+import {
+  BRCDataCatalogGenome,
+  BRCDataCatalogOrganism,
+} from "../../../../apis/catalog/brc-analytics-catalog/common/entities";
 import * as C from "../../../../components";
 import { GENOME_BROWSER, NCBI_DATASETS_URL } from "./constants";
 
@@ -71,6 +74,19 @@ export const buildAnnotationStatus = (
   };
 };
 
+/**
+ * Build props for the assemblies cell.
+ * @param organism - Genome entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildAssemblyCount = (
+  organism: BRCDataCatalogOrganism
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: organism.assemblyCount,
+  };
+};
+
 /**
  * Build props for the chromosomes cell.
  * @param genome - Genome entity.
@@ -155,7 +171,7 @@ export const buildLevel = (
  * @returns Props to be used for the cell.
  */
 export const buildTaxon = (
-  genome: BRCDataCatalogGenome
+  genome: BRCDataCatalogOrganism | BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
     value: genome.taxon,
@@ -207,7 +223,7 @@ export const buildScaffoldN50 = (
  * @returns Props to be used for the cell.
  */
 export const buildTags = (
-  genome: BRCDataCatalogGenome
+  genome: BRCDataCatalogOrganism | BRCDataCatalogGenome
 ): ComponentProps<typeof C.NTagCell> => {
   return {
     label: "Tags",
@@ -221,7 +237,7 @@ export const buildTags = (
  * @returns Props to be used for the cell.
  */
 export const buildTaxonomyId = (
-  genome: BRCDataCatalogGenome
+  genome: BRCDataCatalogOrganism | BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
     value: genome.ncbiTaxonomyId,
diff --git a/files/build-catalog.ts b/files/build-catalog.ts
index 4c8a323..6c881f2 100644
--- a/files/build-catalog.ts
+++ b/files/build-catalog.ts
@@ -1,6 +1,9 @@
 import { parse as parseCsv } from "csv-parse/sync";
 import fsp from "fs/promises";
-import { BRCDataCatalogGenome } from "../app/apis/catalog/brc-analytics-catalog/common/entities";
+import {
+  BRCDataCatalogGenome,
+  BRCDataCatalogOrganism,
+} from "../app/apis/catalog/brc-analytics-catalog/common/entities";
 import { SourceGenome, SourceOrganism } from "./entities";
 
 const SOURCE_PATH_ORGANISMS = "files/source/organisms-from-ncbi.tsv";
@@ -9,7 +12,16 @@ const SOURCE_PATH_GENOMES = "files/source/genomes-from-ncbi.tsv";
 buildCatalog();
 
 async function buildCatalog(): Promise<void> {
-  const genomes = await buildGenomes();
+  const organisms = await buildOrganisms();
+
+  const organismsByTaxon = new Map(
+    organisms.map((organism) => [organism.taxon, organism])
+  );
+
+  const genomes = await buildGenomes(organismsByTaxon);
+
+  console.log("Organisms:", genomes.length);
+  await saveJson("files/out/organisms.json", organisms);
 
   console.log("Genomes:", genomes.length);
   await saveJson("files/out/genomes.json", genomes);
@@ -17,16 +29,28 @@ async function buildCatalog(): Promise<void> {
   console.log("Done");
 }
 
-async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
-  const sourceOrganismRows = await readValuesFile<SourceOrganism>(
+async function buildOrganisms(): Promise<BRCDataCatalogOrganism[]> {
+  const sourceRows = await readValuesFile<SourceOrganism>(
     SOURCE_PATH_ORGANISMS
   );
-  const sourceOrganismsByTaxon = new Map(
-    sourceOrganismRows.map((row) => [row.taxon, row])
+  const mappedRows = sourceRows.map((row): BRCDataCatalogOrganism => {
+    return {
+      assemblyCount: parseNumber(row.assemblyCount),
+      ncbiTaxonomyId: row.taxonomyId,
+      tags: row.CustomTags ? [row.CustomTags] : [],
+      taxon: row.taxon,
+    };
+  });
+  return mappedRows.sort((a, b) =>
+    a.ncbiTaxonomyId.localeCompare(b.ncbiTaxonomyId)
   );
+}
+
+async function buildGenomes(
+  organismsByTaxon: Map<string, BRCDataCatalogOrganism>
+): Promise<BRCDataCatalogGenome[]> {
   const sourceRows = await readValuesFile<SourceGenome>(SOURCE_PATH_GENOMES);
   const mappedRows = sourceRows.map((row): BRCDataCatalogGenome => {
-    const tagsString = sourceOrganismsByTaxon.get(row.taxon)?.CustomTags;
     return {
       accession: row.accession,
       annotationStatus: parseStringOrNull(row.annotationStatus),
@@ -41,7 +65,7 @@ async function buildGenomes(): Promise<BRCDataCatalogGenome[]> {
       scaffoldCount: parseNumber(row.scaffoldCount),
       scaffoldL50: parseNumber(row.scaffoldL50),
       scaffoldN50: parseNumber(row.scaffoldN50),
-      tags: tagsString ? [tagsString] : [],
+      tags: organismsByTaxon.get(row.taxon)?.tags ?? [],
       taxon: row.taxon,
       ucscBrowserUrl: parseStringOrNull(row.ucscBrowser),
     };
diff --git a/files/out/organisms.json b/files/out/organisms.json
new file mode 100644
index 0000000..4ceb6ba
--- /dev/null
+++ b/files/out/organisms.json
@@ -0,0 +1,136 @@
+[
+  {
+    "assemblyCount": 6911,
+    "ncbiTaxonomyId": "10244",
+    "tags": [
+      "Virus"
+    ],
+    "taxon": "Monkeypox virus"
+  },
+  {
+    "assemblyCount": 7823,
+    "ncbiTaxonomyId": "1773",
+    "tags": [
+      "Bact"
+    ],
+    "taxon": "Mycobacterium tuberculosis"
+  },
+  {
+    "assemblyCount": 13,
+    "ncbiTaxonomyId": "199306",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Coccidioides posadasii"
+  },
+  {
+    "assemblyCount": 92,
+    "ncbiTaxonomyId": "2697049",
+    "tags": [
+      "Virus"
+    ],
+    "taxon": "Severe acute respiratory syndrome coronavirus 2"
+  },
+  {
+    "assemblyCount": 5,
+    "ncbiTaxonomyId": "5501",
+    "tags": [],
+    "taxon": "Coccidioides immitis"
+  },
+  {
+    "assemblyCount": 11,
+    "ncbiTaxonomyId": "5660",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Leishmania braziliensis"
+  },
+  {
+    "assemblyCount": 12,
+    "ncbiTaxonomyId": "5661",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Leishmania donovani"
+  },
+  {
+    "assemblyCount": 7,
+    "ncbiTaxonomyId": "5664",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Leishmania major"
+  },
+  {
+    "assemblyCount": 5,
+    "ncbiTaxonomyId": "5691",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Trypanosoma brucei"
+  },
+  {
+    "assemblyCount": 44,
+    "ncbiTaxonomyId": "5693",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Trypanosoma cruzi"
+  },
+  {
+    "assemblyCount": 29,
+    "ncbiTaxonomyId": "5811",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Toxoplasma gondii"
+  },
+  {
+    "assemblyCount": 67,
+    "ncbiTaxonomyId": "5833",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Plasmodium falciparum"
+  },
+  {
+    "assemblyCount": 19,
+    "ncbiTaxonomyId": "5855",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Plasmodium vivax"
+  },
+  {
+    "assemblyCount": 10,
+    "ncbiTaxonomyId": "5860",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Plasmodium vinckei"
+  },
+  {
+    "assemblyCount": 15,
+    "ncbiTaxonomyId": "5861",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Plasmodium yoelii"
+  },
+  {
+    "assemblyCount": 7,
+    "ncbiTaxonomyId": "7165",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Anopheles gambiae"
+  },
+  {
+    "assemblyCount": 5,
+    "ncbiTaxonomyId": "7175",
+    "tags": [
+      "VEuPathDb"
+    ],
+    "taxon": "Culex pipiens"
+  }
+]
diff --git a/routes/constants.ts b/routes/constants.ts
index 05eb80a..b1f6088 100644
--- a/routes/constants.ts
+++ b/routes/constants.ts
@@ -1,5 +1,6 @@
 export const ROUTES = {
   ABOUT: "/about",
   GENOMES: "/data/genomes",
+  ORGANISMS: "/data/organisms",
   ROADMAP: "/roadmap",
 };
diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts
index edca097..122bf19 100644
--- a/site-config/brc-analytics/category.ts
+++ b/site-config/brc-analytics/category.ts
@@ -2,6 +2,7 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = {
   ACCESSION: "accession",
   ANALYZE_GENOME: "analyzeGenome",
   ANNOTATION_STATUS: "annotationStatus",
+  ASSEMBLY_COUNT: "assemblyCount",
   CHROMOSOMES: "chromosomes",
   COVERAGE: "coverage",
   GC_PERCENT: "gcPercent",
@@ -21,6 +22,7 @@ export const BRC_DATA_CATALOG_CATEGORY_LABEL = {
   ACCESSION: "Accession",
   ANALYZE_GENOME: "Action",
   ANNOTATION_STATUS: "Annotation Status",
+  ASSEMBLY_COUNT: "Assemblies",
   CHROMOSOMES: "Chromosomes",
   COVERAGE: "Coverage",
   GC_PERCENT: "GC%",
diff --git a/site-config/brc-analytics/local/config.ts b/site-config/brc-analytics/local/config.ts
index 781a54a..627af71 100644
--- a/site-config/brc-analytics/local/config.ts
+++ b/site-config/brc-analytics/local/config.ts
@@ -1,11 +1,15 @@
 import { ANCHOR_TARGET } from "@databiosphere/findable-ui/lib/components/Links/common/entities";
 import { SiteConfig } from "@databiosphere/findable-ui/lib/config/entities";
 import { EntityConfig } from "@databiosphere/findable-ui/src/config/entities";
-import { BRCDataCatalogGenome } from "../../../app/apis/catalog/brc-analytics-catalog/common/entities";
+import {
+  BRCDataCatalogGenome,
+  BRCDataCatalogOrganism,
+} from "../../../app/apis/catalog/brc-analytics-catalog/common/entities";
 import * as C from "../../../app/components";
 import { ROUTES } from "../../../routes/constants";
 import { floating } from "./floating/floating";
 import { genomeEntityConfig } from "./index/genomeEntityConfig";
+import { organismEntityConfig } from "./index/organismEntityConfig";
 import { socialMedia } from "./socialMedia";
 
 const LOCALHOST = "http://localhost:3000";
@@ -35,7 +39,10 @@ export function makeConfig(browserUrl: string, gitHubUrl: string): SiteConfig {
     dataSource: {
       url: "",
     },
-    entities: [genomeEntityConfig as EntityConfig<BRCDataCatalogGenome>],
+    entities: [
+      organismEntityConfig as EntityConfig<BRCDataCatalogOrganism>,
+      genomeEntityConfig as EntityConfig<BRCDataCatalogGenome>,
+    ],
     explorerTitle: APP_TITLE,
     gitHubUrl,
     layout: {
@@ -68,7 +75,8 @@ export function makeConfig(browserUrl: string, gitHubUrl: string): SiteConfig {
           undefined,
           [
             { label: "About", url: ROUTES.ABOUT },
-            { label: "Datasets", url: ROUTES.GENOMES },
+            { label: "Organisms", url: ROUTES.ORGANISMS },
+            { label: "Genomes", url: ROUTES.GENOMES },
             { label: "Roadmap", url: ROUTES.ROADMAP },
           ],
           undefined,
diff --git a/site-config/brc-analytics/local/index/organismEntityConfig.ts b/site-config/brc-analytics/local/index/organismEntityConfig.ts
new file mode 100644
index 0000000..1a39944
--- /dev/null
+++ b/site-config/brc-analytics/local/index/organismEntityConfig.ts
@@ -0,0 +1,102 @@
+import {
+  ComponentConfig,
+  ListConfig,
+  SORT_DIRECTION,
+} from "@databiosphere/findable-ui/lib/config/entities";
+import { EXPLORE_MODE } from "@databiosphere/findable-ui/lib/hooks/useExploreMode";
+import { BRCDataCatalogOrganism } from "../../../../app/apis/catalog/brc-analytics-catalog/common/entities";
+import { getOrganismId } from "../../../../app/apis/catalog/brc-analytics-catalog/common/utils";
+import * as C from "../../../../app/components";
+import * as V from "../../../../app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders";
+import { BRCEntityConfig } from "../../../common/entities";
+import {
+  BRC_DATA_CATALOG_CATEGORY_KEY,
+  BRC_DATA_CATALOG_CATEGORY_LABEL,
+} from "../../category";
+
+/**
+ * Entity config object responsible to config anything related to the /genomes route.
+ */
+export const organismEntityConfig: BRCEntityConfig<BRCDataCatalogOrganism> = {
+  categoryGroupConfig: {
+    categoryGroups: [
+      {
+        categoryConfigs: [
+          {
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON,
+          },
+          {
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID,
+          },
+          {
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS,
+          },
+        ],
+      },
+    ],
+    key: "organisms",
+  },
+  detail: {
+    detailOverviews: [],
+    staticLoad: true,
+    tabs: [],
+  },
+  exploreMode: EXPLORE_MODE.CS_FETCH_CS_FILTERING,
+  explorerTitle: "Organisms",
+  getId: getOrganismId,
+  label: "Organisms",
+  list: {
+    columns: [
+      {
+        componentConfig: {
+          component: C.BasicCell,
+          viewBuilder: V.buildTaxon,
+        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogOrganism>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
+        width: "auto",
+      },
+      {
+        componentConfig: {
+          component: C.BasicCell,
+          viewBuilder: V.buildTaxonomyId,
+        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogOrganism>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID,
+        width: { max: "0.5fr", min: "164px" },
+      },
+      {
+        componentConfig: {
+          component: C.BasicCell,
+          viewBuilder: V.buildAssemblyCount,
+        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogOrganism>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.ASSEMBLY_COUNT,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.ASSEMBLY_COUNT,
+        width: { max: "0.5fr", min: "164px" },
+      },
+      {
+        componentConfig: {
+          component: C.NTagCell,
+          viewBuilder: V.buildTags,
+        } as ComponentConfig<typeof C.NTagCell, BRCDataCatalogOrganism>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAGS,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.TAGS,
+        width: { max: "0.5fr", min: "142px" },
+      },
+    ],
+    defaultSort: {
+      desc: SORT_DIRECTION.ASCENDING,
+      id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
+    },
+  } as ListConfig<BRCDataCatalogOrganism>,
+  listView: {
+    disablePagination: true,
+    enableDownload: true,
+    enableTab: false,
+  },
+  route: "organisms",
+  staticLoadFile: "files/out/organisms.json",
+};

From 4541d15a4c57e101d707112364fe55e3544ec6ec Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Thu, 5 Dec 2024 00:36:40 -0800
Subject: [PATCH 07/19] fix: make `isRef` a string to avoid error when
 searching filters (#177)

---
 .../brc-analytics-catalog/common/entities.ts  |  2 +-
 .../common/viewModelBuilders.ts               |  2 +-
 files/build-catalog.ts                        |  4 +-
 files/out/genomes.json                        | 40 +++++++++----------
 4 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
index 7e713f5..1998a66 100644
--- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts
+++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
@@ -16,7 +16,7 @@ export interface BRCDataCatalogGenome {
   coverage: string | null;
   gcPercent: number;
   geneModelUrl: string | null;
-  isRef: boolean;
+  isRef: string;
   length: number;
   level: string;
   ncbiTaxonomyId: string;
diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
index b7f6e85..6968b98 100644
--- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
+++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -135,7 +135,7 @@ export const buildIsRef = (
   genome: BRCDataCatalogGenome
 ): ComponentProps<typeof C.BasicCell> => {
   return {
-    value: genome.isRef ? "Yes" : "No",
+    value: genome.isRef,
   };
 };
 
diff --git a/files/build-catalog.ts b/files/build-catalog.ts
index 6c881f2..ee6029e 100644
--- a/files/build-catalog.ts
+++ b/files/build-catalog.ts
@@ -106,6 +106,6 @@ function parseNumber(value: string): number {
   return n;
 }
 
-function parseBoolean(value: string): boolean {
-  return value[0].toLowerCase() === "t";
+function parseBoolean(value: string): string {
+  return value[0].toLowerCase() === "t" ? "Yes" : "No";
 }
diff --git a/files/out/genomes.json b/files/out/genomes.json
index b8c9c76..474a330 100644
--- a/files/out/genomes.json
+++ b/files/out/genomes.json
@@ -6,7 +6,7 @@
     "coverage": null,
     "gcPercent": 42.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 27007701,
     "level": "Chromosome",
     "ncbiTaxonomyId": "5855",
@@ -26,7 +26,7 @@
     "coverage": null,
     "gcPercent": 46.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 26075494,
     "level": "Chromosome",
     "ncbiTaxonomyId": "185431",
@@ -44,7 +44,7 @@
     "coverage": null,
     "gcPercent": 59.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 32855089,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "347515",
@@ -62,7 +62,7 @@
     "coverage": "100.0x",
     "gcPercent": 19.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 23292622,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "36329",
@@ -80,7 +80,7 @@
     "coverage": null,
     "gcPercent": 58,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 32068771,
     "level": "Chromosome",
     "ncbiTaxonomyId": "420245",
@@ -98,7 +98,7 @@
     "coverage": "26.5x",
     "gcPercent": 52.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 65633124,
     "level": "Chromosome",
     "ncbiTaxonomyId": "508771",
@@ -116,7 +116,7 @@
     "coverage": null,
     "gcPercent": 46,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 28947925,
     "level": "Scaffold",
     "ncbiTaxonomyId": "246410",
@@ -134,7 +134,7 @@
     "coverage": null,
     "gcPercent": 65.5,
     "geneModelUrl": null,
-    "isRef": true,
+    "isRef": "Yes",
     "length": 4411532,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "83332",
@@ -152,7 +152,7 @@
     "coverage": null,
     "gcPercent": 51.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 89937456,
     "level": "Scaffold",
     "ncbiTaxonomyId": "5693",
@@ -172,7 +172,7 @@
     "coverage": null,
     "gcPercent": 59.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 32444968,
     "level": "Chromosome",
     "ncbiTaxonomyId": "5661",
@@ -192,7 +192,7 @@
     "coverage": null,
     "gcPercent": 65.5,
     "geneModelUrl": null,
-    "isRef": false,
+    "isRef": "No",
     "length": 4411709,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "83332",
@@ -210,7 +210,7 @@
     "coverage": null,
     "gcPercent": 33,
     "geneModelUrl": null,
-    "isRef": false,
+    "isRef": "No",
     "length": 196858,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "10244",
@@ -230,7 +230,7 @@
     "coverage": null,
     "gcPercent": 38,
     "geneModelUrl": null,
-    "isRef": false,
+    "isRef": "No",
     "length": 29903,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "2697049",
@@ -250,7 +250,7 @@
     "coverage": "250.0x",
     "gcPercent": 37,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 566339288,
     "level": "Chromosome",
     "ncbiTaxonomyId": "42434",
@@ -268,7 +268,7 @@
     "coverage": "475.0x",
     "gcPercent": 46.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 28193268,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "443226",
@@ -286,7 +286,7 @@
     "coverage": "20.0x",
     "gcPercent": 65.5,
     "geneModelUrl": null,
-    "isRef": false,
+    "isRef": "No",
     "length": 4516435,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "1773",
@@ -306,7 +306,7 @@
     "coverage": "100.0x",
     "gcPercent": 21.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 23043114,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "5861",
@@ -326,7 +326,7 @@
     "coverage": "155.0x",
     "gcPercent": 23,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 18338688,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "54757",
@@ -344,7 +344,7 @@
     "coverage": "54.0x",
     "gcPercent": 44.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz",
-    "isRef": true,
+    "isRef": "Yes",
     "length": 264451381,
     "level": "Chromosome",
     "ncbiTaxonomyId": "7165",
@@ -364,7 +364,7 @@
     "coverage": "100.0x",
     "gcPercent": 65.5,
     "geneModelUrl": null,
-    "isRef": false,
+    "isRef": "No",
     "length": 4469156,
     "level": "Complete Genome",
     "ncbiTaxonomyId": "1773",

From 841c25588a794f4799bc845a349e17192be76d3d Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Thu, 5 Dec 2024 15:32:53 -0800
Subject: [PATCH 08/19] feat: fix build from ncbi and report on accession
 matches (#177)

---
 files/build-files-from-ncbi.py       | 33 +++++++++++++++++++++++-----
 files/source/genomes-from-ncbi.tsv   | 24 ++++++++++----------
 files/source/organisms-from-ncbi.tsv |  6 ++---
 3 files changed, 44 insertions(+), 19 deletions(-)

diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py
index 0690d18..0c2c112 100644
--- a/files/build-files-from-ncbi.py
+++ b/files/build-files-from-ncbi.py
@@ -15,15 +15,21 @@
 def build_taxonomy_request_body(taxa):
   return {"taxons": taxa, "children": False, "ranks": ["genus"]}
 
-def get_organism_row(organism_taxonomy):
+def get_organism_row(organism_info):
+  if len(organism_info.get("errors", [])) > 0:
+    raise Exception(organism_info)
+
+  organism_taxonomy = organism_info["taxonomy"]
+
   return {
     "taxon": organism_taxonomy["current_scientific_name"]["name"],
-    "taxonomyId": organism_taxonomy["tax_id"],
+    "taxonomyId": str(organism_taxonomy["tax_id"]),
     "assemblyCount": next(count["count"] for count in organism_taxonomy["counts"] if count["type"] == "COUNT_TYPE_ASSEMBLY"),
   }
 
 def get_organisms_df(taxa):
-  return pd.DataFrame([get_organism_row(organism_info["taxonomy"]) for organism_info in requests.post(TAXONOMY_URL, json=build_taxonomy_request_body(taxa)).json()["reports"]])
+  organisms_info = requests.post(TAXONOMY_URL, json=build_taxonomy_request_body(taxa)).json()["reports"]
+  return pd.DataFrame([get_organism_row(organism_info) for organism_info in organisms_info])
 
 def get_tax_ids(organisms_df):
   return list(organisms_df["taxonomyId"])
@@ -53,6 +59,22 @@ def get_genome_row(genome_info):
 def get_genomes_df(tax_ids):
   return pd.DataFrame(data=[get_genome_row(genome_info) for genome_info in requests.get(build_genomes_url(tax_ids)).json()["reports"]])
 
+def print_column_match_summary(from_df, in_df, from_column, in_column, important=True):
+  unmatched_values = from_df[from_column][~(from_df[from_column].isin(in_df[in_column]))]
+  message = (
+    f"No values from {from_column} absent in {in_column}" if len(unmatched_values) == 0
+    else f"{len(unmatched_values)} values from {from_column} absent in {in_column}: {", ".join(unmatched_values)}"
+  )
+  if not important:
+    message = "(" + message + ")"
+  print(message)
+
+def print_accession_match_summaries(genomes_source_df, assemblies_df):
+  print_column_match_summary(genomes_source_df, assemblies_df, "pairedAccession", "genBank")
+  print_column_match_summary(genomes_source_df, assemblies_df, "pairedAccession", "refSeq", False)
+  print_column_match_summary(genomes_source_df, assemblies_df, "accession", "genBank", False)
+  print_column_match_summary(genomes_source_df, assemblies_df, "accession", "refSeq")
+
 def _id_to_gene_model_url(asm_id):
   hubs_url = "https://hgdownload.soe.ucsc.edu/hubs/"
   components = [asm_id[0:3], asm_id[4:7], asm_id[7:10], asm_id[10:13], asm_id, "genes"]
@@ -81,7 +103,6 @@ def _id_to_gene_model_url(asm_id):
   # No match, I guess that's OK ?
   return None
 
-
 def add_gene_model_url(genomes_df: pd.DataFrame):
   return pd.concat([genomes_df, genomes_df["accession"].apply(_id_to_gene_model_url).rename("geneModelUrl")], axis="columns")
 
@@ -90,7 +111,7 @@ def build_files():
 
   taxa_df = pd.read_csv(TAXA_URL, keep_default_na=False)
 
-  organisms_source_df = get_organisms_df(list(taxa_df["Name"]))
+  organisms_source_df = get_organisms_df([taxon for taxon in taxa_df["Name"] if taxon])
 
   organisms_df = organisms_source_df.merge(taxa_df[["TaxId", "CustomTags"]], how="left", left_on="taxonomyId", right_on="TaxId").drop(columns=["TaxId"])
 
@@ -104,6 +125,8 @@ def build_files():
   gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="pairedAccession", right_on="genBank")
   ref_seq_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="refSeq")
 
+  print_accession_match_summaries(genomes_source_df, assemblies_df)
+
   genomes_df = add_gene_model_url(gen_bank_merge_df.combine_first(ref_seq_merge_df))
 
   genomes_df.to_csv(GENOMES_OUTPUT_PATH, index=False, sep="\t")
diff --git a/files/source/genomes-from-ncbi.tsv b/files/source/genomes-from-ncbi.tsv
index 79d5b1b..24926e2 100644
--- a/files/source/genomes-from-ncbi.tsv
+++ b/files/source/genomes-from-ncbi.tsv
@@ -1,21 +1,23 @@
 taxon	taxonomyId	accession	isRef	level	chromosomeCount	length	scaffoldCount	scaffoldN50	scaffoldL50	coverage	gcPercent	annotationStatus	pairedAccession	ucscBrowser	genBank	refSeq	geneModelUrl
-Mycobacterium tuberculosis H37Rv	83332	GCF_000195955.2	True	Complete Genome	1.0	4411532	1	4411532	1		65.5		GCA_000195955.2				
+Mycobacterium tuberculosis H37Rv	83332	GCF_000195955.2	True	Complete Genome	1.0	4411532	1	4411532	1		65.5		GCA_000195955.2	https://genome.ucsc.edu/h/GCF_000195955.2	GCA_000195955.2	GCF_000195955.2	
 Plasmodium falciparum 3D7	36329	GCF_000002765.6	True	Complete Genome	14.0	23292622	14	1687656	5	100.0x	19.5	Full annotation	GCA_000002765.3	https://genome.ucsc.edu/h/GCF_000002765.5	GCA_000002765.3	GCF_000002765.5	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz
-Leishmania major strain Friedlin	347515	GCF_000002725.2	True	Complete Genome	36.0	32855089	36	1091540	11		59.5	Full annotation	GCA_000002725.2	https://genome.ucsc.edu/h/GCF_000002725.2	GCA_000002725.2	GCF_000002725.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz
+Plasmodium falciparum 3D7	36329	GCF_000002765.6	True	Complete Genome	14.0	23292622	14	1687656	5	100.0x	19.5	Full annotation	GCA_000002765.3	https://genome.ucsc.edu/h/GCF_000002765.6	GCA_000002765.3	GCF_000002765.6	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz
+Leishmania major strain Friedlin	347515	GCF_000002725.2	True	Complete Genome	36.0	32855089	36	1091540	11	100.0x	59.5	Full annotation	GCA_000002725.2	https://genome.ucsc.edu/h/GCF_000002725.2	GCA_000002725.2	GCF_000002725.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz
 Plasmodium yoelii	5861	GCF_900002385.2	True	Complete Genome	14.0	23043114	14	2046250	5	100.0x	21.5	Full annotation	GCA_900002385.2	https://genome.ucsc.edu/h/GCF_900002385.2	GCA_900002385.2	GCF_900002385.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz
 Coccidioides posadasii str. Silveira	443226	GCF_018416015.2	True	Complete Genome	9.0	28193268	9	8079863	2	475.0x	46.5	Full annotation	GCA_018416015.2	https://genome.ucsc.edu/h/GCA_018416015.2	GCA_018416015.2	GCF_018416015.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz
-Plasmodium vinckei vinckei	54757	GCF_900681995.1	True	Complete Genome	14.0	18338688	14	1692345	5	155.0x	23.0	Full annotation	GCA_900681995.1	https://genome.ucsc.edu/h/GCF_900681995.1	GCA_900681995.1	GCF_900681995.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz
+Coccidioides posadasii str. Silveira	443226	GCF_018416015.2	True	Complete Genome	9.0	28193268	9	8079863	2	475.0x	46.5	Full annotation	GCA_018416015.2	https://genome.ucsc.edu/h/GCF_018416015.2	GCA_018416015.2	GCF_018416015.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz
+Plasmodium vinckei vinckei	54757	GCF_900681995.1	True	Chromosome	14.0	18338688	14	1692345	5	155.0x	23.0	Full annotation	GCA_900681995.1	https://genome.ucsc.edu/h/GCF_900681995.1	GCA_900681995.1	GCF_900681995.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz
 Leishmania donovani	5661	GCF_000227135.1	True	Chromosome	36.0	32444968	36	1024085	11		59.5	Full annotation	GCA_000227135.2	https://genome.ucsc.edu/h/GCF_000227135.1	GCA_000227135.2	GCF_000227135.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz
-Toxoplasma gondii ME49	508771	GCF_000006565.2	True	Chromosome	14.0	65633124	2276	4973582	6	26.5x	52.5		GCA_000006565.2	https://genome.ucsc.edu/h/GCF_000006565.2	GCA_000006565.2	GCF_000006565.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz
+Toxoplasma gondii ME49	508771	GCF_000006565.2	True	Chromosome	14.0	65633124	2276	4973582	6	26.5x	52.5	Full annotation	GCA_000006565.2	https://genome.ucsc.edu/h/GCF_000006565.2	GCA_000006565.2	GCF_000006565.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz
 Trypanosoma brucei brucei TREU927	185431	GCF_000002445.2	True	Chromosome	11.0	26075494	12	2481190	4		46.5	Full annotation	GCA_000002445.1	https://genome.ucsc.edu/h/GCF_000002445.2	GCA_000002445.1	GCF_000002445.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz
 Anopheles gambiae	7165	GCF_943734735.2	True	Chromosome	3.0	264451381	190	99149756	2	54.0x	44.5	Full annotation	GCA_943734735.2	https://genome.ucsc.edu/h/GCF_943734735.2	GCA_943734735.2	GCF_943734735.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz
 Plasmodium vivax	5855	GCF_000002415.2	True	Chromosome	14.0	27007701	2747	1678596	6		42.5	Full annotation	GCA_000002415.2	https://genome.ucsc.edu/h/GCF_000002415.2	GCA_000002415.2	GCF_000002415.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz
-Culex pipiens pallens	42434	GCF_016801865.2	True	Chromosome	3.0	566339288	289	186194774	2	250.0x	37.0	Full annotation	GCA_016801865.2				https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz
-Leishmania braziliensis MHOM/BR/75/M2904	420245	GCF_000002845.2	True	Chromosome	35.0	32068771	138	992961	11		58.0		GCA_000002845.2	https://genome.ucsc.edu/h/GCF_000002845.2	GCA_000002845.2	GCF_000002845.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz
-Trypanosoma cruzi	5693	GCF_000209065.1	True	Scaffold		89937456	29495	88624	212		51.5	Full annotation	GCA_000209065.1	https://genome.ucsc.edu/h/GCF_000209065.1	GCA_000209065.1	GCF_000209065.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz
-Coccidioides immitis RS	246410	GCF_000149335.2	True	Scaffold		28947925	6	4323945	3		46.0	Full annotation	GCA_000149335.2	https://genome.ucsc.edu/h/GCF_000149335.2	GCA_000149335.2	GCF_000149335.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz
-Mycobacterium tuberculosis H37Rv	83332	GCF_000277735.2	False	Complete Genome	1.0	4411709	1	4411709	1		65.5		GCA_000277735.2				
-Severe acute respiratory syndrome coronavirus 2	2697049	GCF_009858895.2	False	Complete Genome	1.0	29903	1	29903	1		38.0		GCA_009858895.3				
-Monkeypox virus	10244	GCF_000857045.1	False	Complete Genome	1.0	196858	1	196858	1		33.0		GCA_000857045.1				
+Culex pipiens pallens	42434	GCF_016801865.2	True	Chromosome	3.0	566339288	289	186194774	2	250.0x	37.0	Full annotation	GCA_016801865.2	https://genome.ucsc.edu/h/GCF_016801865.2	GCA_016801865.2	GCF_016801865.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz
+Leishmania braziliensis MHOM/BR/75/M2904	420245	GCF_000002845.2	True	Chromosome	35.0	32068771	138	992961	11		58.0	Full annotation	GCA_000002845.2	https://genome.ucsc.edu/h/GCF_000002845.2	GCA_000002845.2	GCF_000002845.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz
+Trypanosoma cruzi	5693	GCF_000209065.1	True	Scaffold	1.0	89937456	29495	88624	212		51.5	Full annotation	GCA_000209065.1	https://genome.ucsc.edu/h/GCF_000209065.1	GCA_000209065.1	GCF_000209065.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz
+Coccidioides immitis RS	246410	GCF_000149335.2	True	Scaffold	1.0	28947925	6	4323945	3		46.0	Full annotation	GCA_000149335.2	https://genome.ucsc.edu/h/GCF_000149335.2	GCA_000149335.2	GCF_000149335.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz
+Mycobacterium tuberculosis H37Rv	83332	GCF_000277735.2	False	Complete Genome	1.0	4411709	1	4411709	1		65.5		GCA_000277735.2	https://genome.ucsc.edu/h/GCF_000857045.1	GCA_000857045.1	GCF_000857045.1	
+Severe acute respiratory syndrome coronavirus 2	2697049	GCF_009858895.2	False	Complete Genome	1.0	29903	1	29903	1	20.0x	38.0		GCA_009858895.3	https://genome.ucsc.edu/h/GCF_009858895.2	GCA_009858895.3	GCF_009858895.2	
+Monkeypox virus	10244	GCF_000857045.1	False	Complete Genome	1.0	196858	1	196858	1	100.0x	33.0		GCA_000857045.1	https://genome.ucsc.edu/h/GCF_000857045.1	GCA_000857045.1	GCF_000857045.1	
 Mycobacterium tuberculosis	1773	GCF_030566675.1	False	Complete Genome	1.0	4516435	1	4516435	1	20.0x	65.5		GCA_030566675.1				
 Mycobacterium tuberculosis	1773	GCF_963525475.1	False	Complete Genome	1.0	4469156	1	4469156	1	100.0x	65.5		GCA_963525475.1				
diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv
index 6686f92..499eae1 100644
--- a/files/source/organisms-from-ncbi.tsv
+++ b/files/source/organisms-from-ncbi.tsv
@@ -7,12 +7,12 @@ Leishmania braziliensis	5660	11	VEuPathDb
 Leishmania donovani	5661	12	VEuPathDb
 Leishmania major	5664	7	VEuPathDb
 Monkeypox virus	10244	6911	Virus
-Mycobacterium tuberculosis	1773	7823	Bact
+Mycobacterium tuberculosis	1773	7829	Bact
 Plasmodium falciparum	5833	67	VEuPathDb
 Plasmodium vinckei	5860	10	VEuPathDb
 Plasmodium vivax	5855	19	VEuPathDb
 Plasmodium yoelii	5861	15	VEuPathDb
-Severe acute respiratory syndrome coronavirus 2	2697049	92	Virus
+Severe acute respiratory syndrome coronavirus 2	2697049	12408	Virus
 Toxoplasma gondii	5811	29	VEuPathDb
-Trypanosoma brucei	5691	5	VEuPathDb
+Trypanosoma brucei	5691	6	VEuPathDb
 Trypanosoma cruzi	5693	44	VEuPathDb

From c6996201b4f31b52dade77b84dca7cd00ab109cd Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Thu, 5 Dec 2024 15:33:07 -0800
Subject: [PATCH 09/19] feat: build catalog (#177)

---
 files/out/genomes.json   | 62 +++++++++++++++++++++++++++++++---------
 files/out/organisms.json |  6 ++--
 2 files changed, 52 insertions(+), 16 deletions(-)

diff --git a/files/out/genomes.json b/files/out/genomes.json
index 474a330..d7bec9c 100644
--- a/files/out/genomes.json
+++ b/files/out/genomes.json
@@ -41,7 +41,7 @@
     "accession": "GCF_000002725.2",
     "annotationStatus": "Full annotation",
     "chromosomes": 36,
-    "coverage": null,
+    "coverage": "100.0x",
     "gcPercent": 59.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz",
     "isRef": "Yes",
@@ -73,9 +73,27 @@
     "taxon": "Plasmodium falciparum 3D7",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.5"
   },
+  {
+    "accession": "GCF_000002765.6",
+    "annotationStatus": "Full annotation",
+    "chromosomes": 14,
+    "coverage": "100.0x",
+    "gcPercent": 19.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz",
+    "isRef": "Yes",
+    "length": 23292622,
+    "level": "Complete Genome",
+    "ncbiTaxonomyId": "36329",
+    "scaffoldCount": 14,
+    "scaffoldL50": 5,
+    "scaffoldN50": 1687656,
+    "tags": [],
+    "taxon": "Plasmodium falciparum 3D7",
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.6"
+  },
   {
     "accession": "GCF_000002845.2",
-    "annotationStatus": null,
+    "annotationStatus": "Full annotation",
     "chromosomes": 35,
     "coverage": null,
     "gcPercent": 58,
@@ -93,7 +111,7 @@
   },
   {
     "accession": "GCF_000006565.2",
-    "annotationStatus": null,
+    "annotationStatus": "Full annotation",
     "chromosomes": 14,
     "coverage": "26.5x",
     "gcPercent": 52.5,
@@ -112,7 +130,7 @@
   {
     "accession": "GCF_000149335.2",
     "annotationStatus": "Full annotation",
-    "chromosomes": null,
+    "chromosomes": 1,
     "coverage": null,
     "gcPercent": 46,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz",
@@ -143,12 +161,12 @@
     "scaffoldN50": 4411532,
     "tags": [],
     "taxon": "Mycobacterium tuberculosis H37Rv",
-    "ucscBrowserUrl": null
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000195955.2"
   },
   {
     "accession": "GCF_000209065.1",
     "annotationStatus": "Full annotation",
-    "chromosomes": null,
+    "chromosomes": 1,
     "coverage": null,
     "gcPercent": 51.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz",
@@ -201,13 +219,13 @@
     "scaffoldN50": 4411709,
     "tags": [],
     "taxon": "Mycobacterium tuberculosis H37Rv",
-    "ucscBrowserUrl": null
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000857045.1"
   },
   {
     "accession": "GCF_000857045.1",
     "annotationStatus": null,
     "chromosomes": 1,
-    "coverage": null,
+    "coverage": "100.0x",
     "gcPercent": 33,
     "geneModelUrl": null,
     "isRef": "No",
@@ -221,13 +239,13 @@
       "Virus"
     ],
     "taxon": "Monkeypox virus",
-    "ucscBrowserUrl": null
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000857045.1"
   },
   {
     "accession": "GCF_009858895.2",
     "annotationStatus": null,
     "chromosomes": 1,
-    "coverage": null,
+    "coverage": "20.0x",
     "gcPercent": 38,
     "geneModelUrl": null,
     "isRef": "No",
@@ -241,7 +259,7 @@
       "Virus"
     ],
     "taxon": "Severe acute respiratory syndrome coronavirus 2",
-    "ucscBrowserUrl": null
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_009858895.2"
   },
   {
     "accession": "GCF_016801865.2",
@@ -259,7 +277,7 @@
     "scaffoldN50": 186194774,
     "tags": [],
     "taxon": "Culex pipiens pallens",
-    "ucscBrowserUrl": null
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_016801865.2"
   },
   {
     "accession": "GCF_018416015.2",
@@ -279,6 +297,24 @@
     "taxon": "Coccidioides posadasii str. Silveira",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018416015.2"
   },
+  {
+    "accession": "GCF_018416015.2",
+    "annotationStatus": "Full annotation",
+    "chromosomes": 9,
+    "coverage": "475.0x",
+    "gcPercent": 46.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz",
+    "isRef": "Yes",
+    "length": 28193268,
+    "level": "Complete Genome",
+    "ncbiTaxonomyId": "443226",
+    "scaffoldCount": 9,
+    "scaffoldL50": 2,
+    "scaffoldN50": 8079863,
+    "tags": [],
+    "taxon": "Coccidioides posadasii str. Silveira",
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_018416015.2"
+  },
   {
     "accession": "GCF_030566675.1",
     "annotationStatus": null,
@@ -328,7 +364,7 @@
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz",
     "isRef": "Yes",
     "length": 18338688,
-    "level": "Complete Genome",
+    "level": "Chromosome",
     "ncbiTaxonomyId": "54757",
     "scaffoldCount": 14,
     "scaffoldL50": 5,
diff --git a/files/out/organisms.json b/files/out/organisms.json
index 4ceb6ba..54db9de 100644
--- a/files/out/organisms.json
+++ b/files/out/organisms.json
@@ -8,7 +8,7 @@
     "taxon": "Monkeypox virus"
   },
   {
-    "assemblyCount": 7823,
+    "assemblyCount": 7829,
     "ncbiTaxonomyId": "1773",
     "tags": [
       "Bact"
@@ -24,7 +24,7 @@
     "taxon": "Coccidioides posadasii"
   },
   {
-    "assemblyCount": 92,
+    "assemblyCount": 12408,
     "ncbiTaxonomyId": "2697049",
     "tags": [
       "Virus"
@@ -62,7 +62,7 @@
     "taxon": "Leishmania major"
   },
   {
-    "assemblyCount": 5,
+    "assemblyCount": 6,
     "ncbiTaxonomyId": "5691",
     "tags": [
       "VEuPathDb"

From a1fc72c90c0aff06e5d4a21aae963cc76de112c1 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Thu, 5 Dec 2024 23:11:05 -0800
Subject: [PATCH 10/19] feat: match only `accession` with both `genBank` and
 `refSeq` (#177)

---
 files/build-files-from-ncbi.py     | 22 +++----------
 files/out/genomes.json             | 52 +++++-------------------------
 files/source/genomes-from-ncbi.tsv | 18 +++++------
 3 files changed, 20 insertions(+), 72 deletions(-)

diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py
index 0c2c112..1b8da76 100644
--- a/files/build-files-from-ncbi.py
+++ b/files/build-files-from-ncbi.py
@@ -59,22 +59,6 @@ def get_genome_row(genome_info):
 def get_genomes_df(tax_ids):
   return pd.DataFrame(data=[get_genome_row(genome_info) for genome_info in requests.get(build_genomes_url(tax_ids)).json()["reports"]])
 
-def print_column_match_summary(from_df, in_df, from_column, in_column, important=True):
-  unmatched_values = from_df[from_column][~(from_df[from_column].isin(in_df[in_column]))]
-  message = (
-    f"No values from {from_column} absent in {in_column}" if len(unmatched_values) == 0
-    else f"{len(unmatched_values)} values from {from_column} absent in {in_column}: {", ".join(unmatched_values)}"
-  )
-  if not important:
-    message = "(" + message + ")"
-  print(message)
-
-def print_accession_match_summaries(genomes_source_df, assemblies_df):
-  print_column_match_summary(genomes_source_df, assemblies_df, "pairedAccession", "genBank")
-  print_column_match_summary(genomes_source_df, assemblies_df, "pairedAccession", "refSeq", False)
-  print_column_match_summary(genomes_source_df, assemblies_df, "accession", "genBank", False)
-  print_column_match_summary(genomes_source_df, assemblies_df, "accession", "refSeq")
-
 def _id_to_gene_model_url(asm_id):
   hubs_url = "https://hgdownload.soe.ucsc.edu/hubs/"
   components = [asm_id[0:3], asm_id[4:7], asm_id[7:10], asm_id[10:13], asm_id, "genes"]
@@ -122,10 +106,12 @@ def build_files():
   genomes_source_df = get_genomes_df(get_tax_ids(organisms_df))
   assemblies_df = pd.DataFrame(requests.get(ASSEMBLIES_URL).json()["data"])[["ucscBrowser", "genBank", "refSeq"]]
 
-  gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="pairedAccession", right_on="genBank")
+  gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="genBank")
   ref_seq_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="refSeq")
 
-  print_accession_match_summaries(genomes_source_df, assemblies_df)
+  unmatched_accessions = genomes_source_df["accession"][~(genomes_source_df["accession"].isin(assemblies_df["genBank"]) | genomes_source_df["accession"].isin(assemblies_df["refSeq"]))]
+  if len(unmatched_accessions) > 0:
+    print(f"{len(unmatched_accessions)} accessions had no match in assembly list: {", ".join(unmatched_accessions)}")
 
   genomes_df = add_gene_model_url(gen_bank_merge_df.combine_first(ref_seq_merge_df))
 
diff --git a/files/out/genomes.json b/files/out/genomes.json
index d7bec9c..be5dfaf 100644
--- a/files/out/genomes.json
+++ b/files/out/genomes.json
@@ -41,7 +41,7 @@
     "accession": "GCF_000002725.2",
     "annotationStatus": "Full annotation",
     "chromosomes": 36,
-    "coverage": "100.0x",
+    "coverage": null,
     "gcPercent": 59.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz",
     "isRef": "Yes",
@@ -55,24 +55,6 @@
     "taxon": "Leishmania major strain Friedlin",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2"
   },
-  {
-    "accession": "GCF_000002765.6",
-    "annotationStatus": "Full annotation",
-    "chromosomes": 14,
-    "coverage": "100.0x",
-    "gcPercent": 19.5,
-    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz",
-    "isRef": "Yes",
-    "length": 23292622,
-    "level": "Complete Genome",
-    "ncbiTaxonomyId": "36329",
-    "scaffoldCount": 14,
-    "scaffoldL50": 5,
-    "scaffoldN50": 1687656,
-    "tags": [],
-    "taxon": "Plasmodium falciparum 3D7",
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.5"
-  },
   {
     "accession": "GCF_000002765.6",
     "annotationStatus": "Full annotation",
@@ -93,7 +75,7 @@
   },
   {
     "accession": "GCF_000002845.2",
-    "annotationStatus": "Full annotation",
+    "annotationStatus": null,
     "chromosomes": 35,
     "coverage": null,
     "gcPercent": 58,
@@ -111,7 +93,7 @@
   },
   {
     "accession": "GCF_000006565.2",
-    "annotationStatus": "Full annotation",
+    "annotationStatus": null,
     "chromosomes": 14,
     "coverage": "26.5x",
     "gcPercent": 52.5,
@@ -130,7 +112,7 @@
   {
     "accession": "GCF_000149335.2",
     "annotationStatus": "Full annotation",
-    "chromosomes": 1,
+    "chromosomes": null,
     "coverage": null,
     "gcPercent": 46,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz",
@@ -166,7 +148,7 @@
   {
     "accession": "GCF_000209065.1",
     "annotationStatus": "Full annotation",
-    "chromosomes": 1,
+    "chromosomes": null,
     "coverage": null,
     "gcPercent": 51.5,
     "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz",
@@ -219,13 +201,13 @@
     "scaffoldN50": 4411709,
     "tags": [],
     "taxon": "Mycobacterium tuberculosis H37Rv",
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000857045.1"
+    "ucscBrowserUrl": null
   },
   {
     "accession": "GCF_000857045.1",
     "annotationStatus": null,
     "chromosomes": 1,
-    "coverage": "100.0x",
+    "coverage": null,
     "gcPercent": 33,
     "geneModelUrl": null,
     "isRef": "No",
@@ -245,7 +227,7 @@
     "accession": "GCF_009858895.2",
     "annotationStatus": null,
     "chromosomes": 1,
-    "coverage": "20.0x",
+    "coverage": null,
     "gcPercent": 38,
     "geneModelUrl": null,
     "isRef": "No",
@@ -279,24 +261,6 @@
     "taxon": "Culex pipiens pallens",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_016801865.2"
   },
-  {
-    "accession": "GCF_018416015.2",
-    "annotationStatus": "Full annotation",
-    "chromosomes": 9,
-    "coverage": "475.0x",
-    "gcPercent": 46.5,
-    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz",
-    "isRef": "Yes",
-    "length": 28193268,
-    "level": "Complete Genome",
-    "ncbiTaxonomyId": "443226",
-    "scaffoldCount": 9,
-    "scaffoldL50": 2,
-    "scaffoldN50": 8079863,
-    "tags": [],
-    "taxon": "Coccidioides posadasii str. Silveira",
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCA_018416015.2"
-  },
   {
     "accession": "GCF_018416015.2",
     "annotationStatus": "Full annotation",
diff --git a/files/source/genomes-from-ncbi.tsv b/files/source/genomes-from-ncbi.tsv
index 24926e2..a0f918b 100644
--- a/files/source/genomes-from-ncbi.tsv
+++ b/files/source/genomes-from-ncbi.tsv
@@ -1,23 +1,21 @@
 taxon	taxonomyId	accession	isRef	level	chromosomeCount	length	scaffoldCount	scaffoldN50	scaffoldL50	coverage	gcPercent	annotationStatus	pairedAccession	ucscBrowser	genBank	refSeq	geneModelUrl
 Mycobacterium tuberculosis H37Rv	83332	GCF_000195955.2	True	Complete Genome	1.0	4411532	1	4411532	1		65.5		GCA_000195955.2	https://genome.ucsc.edu/h/GCF_000195955.2	GCA_000195955.2	GCF_000195955.2	
-Plasmodium falciparum 3D7	36329	GCF_000002765.6	True	Complete Genome	14.0	23292622	14	1687656	5	100.0x	19.5	Full annotation	GCA_000002765.3	https://genome.ucsc.edu/h/GCF_000002765.5	GCA_000002765.3	GCF_000002765.5	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz
 Plasmodium falciparum 3D7	36329	GCF_000002765.6	True	Complete Genome	14.0	23292622	14	1687656	5	100.0x	19.5	Full annotation	GCA_000002765.3	https://genome.ucsc.edu/h/GCF_000002765.6	GCA_000002765.3	GCF_000002765.6	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz
-Leishmania major strain Friedlin	347515	GCF_000002725.2	True	Complete Genome	36.0	32855089	36	1091540	11	100.0x	59.5	Full annotation	GCA_000002725.2	https://genome.ucsc.edu/h/GCF_000002725.2	GCA_000002725.2	GCF_000002725.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz
+Leishmania major strain Friedlin	347515	GCF_000002725.2	True	Complete Genome	36.0	32855089	36	1091540	11		59.5	Full annotation	GCA_000002725.2	https://genome.ucsc.edu/h/GCF_000002725.2	GCA_000002725.2	GCF_000002725.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz
 Plasmodium yoelii	5861	GCF_900002385.2	True	Complete Genome	14.0	23043114	14	2046250	5	100.0x	21.5	Full annotation	GCA_900002385.2	https://genome.ucsc.edu/h/GCF_900002385.2	GCA_900002385.2	GCF_900002385.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz
-Coccidioides posadasii str. Silveira	443226	GCF_018416015.2	True	Complete Genome	9.0	28193268	9	8079863	2	475.0x	46.5	Full annotation	GCA_018416015.2	https://genome.ucsc.edu/h/GCA_018416015.2	GCA_018416015.2	GCF_018416015.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz
 Coccidioides posadasii str. Silveira	443226	GCF_018416015.2	True	Complete Genome	9.0	28193268	9	8079863	2	475.0x	46.5	Full annotation	GCA_018416015.2	https://genome.ucsc.edu/h/GCF_018416015.2	GCA_018416015.2	GCF_018416015.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz
 Plasmodium vinckei vinckei	54757	GCF_900681995.1	True	Chromosome	14.0	18338688	14	1692345	5	155.0x	23.0	Full annotation	GCA_900681995.1	https://genome.ucsc.edu/h/GCF_900681995.1	GCA_900681995.1	GCF_900681995.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz
 Leishmania donovani	5661	GCF_000227135.1	True	Chromosome	36.0	32444968	36	1024085	11		59.5	Full annotation	GCA_000227135.2	https://genome.ucsc.edu/h/GCF_000227135.1	GCA_000227135.2	GCF_000227135.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz
-Toxoplasma gondii ME49	508771	GCF_000006565.2	True	Chromosome	14.0	65633124	2276	4973582	6	26.5x	52.5	Full annotation	GCA_000006565.2	https://genome.ucsc.edu/h/GCF_000006565.2	GCA_000006565.2	GCF_000006565.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz
+Toxoplasma gondii ME49	508771	GCF_000006565.2	True	Chromosome	14.0	65633124	2276	4973582	6	26.5x	52.5		GCA_000006565.2	https://genome.ucsc.edu/h/GCF_000006565.2	GCA_000006565.2	GCF_000006565.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz
 Trypanosoma brucei brucei TREU927	185431	GCF_000002445.2	True	Chromosome	11.0	26075494	12	2481190	4		46.5	Full annotation	GCA_000002445.1	https://genome.ucsc.edu/h/GCF_000002445.2	GCA_000002445.1	GCF_000002445.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz
 Anopheles gambiae	7165	GCF_943734735.2	True	Chromosome	3.0	264451381	190	99149756	2	54.0x	44.5	Full annotation	GCA_943734735.2	https://genome.ucsc.edu/h/GCF_943734735.2	GCA_943734735.2	GCF_943734735.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz
 Plasmodium vivax	5855	GCF_000002415.2	True	Chromosome	14.0	27007701	2747	1678596	6		42.5	Full annotation	GCA_000002415.2	https://genome.ucsc.edu/h/GCF_000002415.2	GCA_000002415.2	GCF_000002415.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz
 Culex pipiens pallens	42434	GCF_016801865.2	True	Chromosome	3.0	566339288	289	186194774	2	250.0x	37.0	Full annotation	GCA_016801865.2	https://genome.ucsc.edu/h/GCF_016801865.2	GCA_016801865.2	GCF_016801865.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz
-Leishmania braziliensis MHOM/BR/75/M2904	420245	GCF_000002845.2	True	Chromosome	35.0	32068771	138	992961	11		58.0	Full annotation	GCA_000002845.2	https://genome.ucsc.edu/h/GCF_000002845.2	GCA_000002845.2	GCF_000002845.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz
-Trypanosoma cruzi	5693	GCF_000209065.1	True	Scaffold	1.0	89937456	29495	88624	212		51.5	Full annotation	GCA_000209065.1	https://genome.ucsc.edu/h/GCF_000209065.1	GCA_000209065.1	GCF_000209065.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz
-Coccidioides immitis RS	246410	GCF_000149335.2	True	Scaffold	1.0	28947925	6	4323945	3		46.0	Full annotation	GCA_000149335.2	https://genome.ucsc.edu/h/GCF_000149335.2	GCA_000149335.2	GCF_000149335.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz
-Mycobacterium tuberculosis H37Rv	83332	GCF_000277735.2	False	Complete Genome	1.0	4411709	1	4411709	1		65.5		GCA_000277735.2	https://genome.ucsc.edu/h/GCF_000857045.1	GCA_000857045.1	GCF_000857045.1	
-Severe acute respiratory syndrome coronavirus 2	2697049	GCF_009858895.2	False	Complete Genome	1.0	29903	1	29903	1	20.0x	38.0		GCA_009858895.3	https://genome.ucsc.edu/h/GCF_009858895.2	GCA_009858895.3	GCF_009858895.2	
-Monkeypox virus	10244	GCF_000857045.1	False	Complete Genome	1.0	196858	1	196858	1	100.0x	33.0		GCA_000857045.1	https://genome.ucsc.edu/h/GCF_000857045.1	GCA_000857045.1	GCF_000857045.1	
+Leishmania braziliensis MHOM/BR/75/M2904	420245	GCF_000002845.2	True	Chromosome	35.0	32068771	138	992961	11		58.0		GCA_000002845.2	https://genome.ucsc.edu/h/GCF_000002845.2	GCA_000002845.2	GCF_000002845.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz
+Trypanosoma cruzi	5693	GCF_000209065.1	True	Scaffold		89937456	29495	88624	212		51.5	Full annotation	GCA_000209065.1	https://genome.ucsc.edu/h/GCF_000209065.1	GCA_000209065.1	GCF_000209065.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz
+Coccidioides immitis RS	246410	GCF_000149335.2	True	Scaffold		28947925	6	4323945	3		46.0	Full annotation	GCA_000149335.2	https://genome.ucsc.edu/h/GCF_000149335.2	GCA_000149335.2	GCF_000149335.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz
+Mycobacterium tuberculosis H37Rv	83332	GCF_000277735.2	False	Complete Genome	1.0	4411709	1	4411709	1		65.5		GCA_000277735.2				
+Severe acute respiratory syndrome coronavirus 2	2697049	GCF_009858895.2	False	Complete Genome	1.0	29903	1	29903	1		38.0		GCA_009858895.3	https://genome.ucsc.edu/h/GCF_009858895.2	GCA_009858895.3	GCF_009858895.2	
+Monkeypox virus	10244	GCF_000857045.1	False	Complete Genome	1.0	196858	1	196858	1		33.0		GCA_000857045.1	https://genome.ucsc.edu/h/GCF_000857045.1	GCA_000857045.1	GCF_000857045.1	
 Mycobacterium tuberculosis	1773	GCF_030566675.1	False	Complete Genome	1.0	4516435	1	4516435	1	20.0x	65.5		GCA_030566675.1				
 Mycobacterium tuberculosis	1773	GCF_963525475.1	False	Complete Genome	1.0	4469156	1	4469156	1	100.0x	65.5		GCA_963525475.1				

From 2a51095728a74709bb0147eec0a4eacd21f4f90f Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Fri, 6 Dec 2024 15:08:39 -0800
Subject: [PATCH 11/19] fix: "is ref" filter labels (#177)

---
 site-config/brc-analytics/local/index/genomeEntityConfig.ts | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
index 612e3be..27b0a9d 100644
--- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts
+++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
@@ -44,10 +44,6 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
           {
             key: BRC_DATA_CATALOG_CATEGORY_KEY.IS_REF,
             label: BRC_DATA_CATALOG_CATEGORY_LABEL.IS_REF,
-            mapSelectCategoryValue: (value) => ({
-              ...value,
-              label: value.label ? "Yes" : "No",
-            }),
           },
           {
             key: BRC_DATA_CATALOG_CATEGORY_KEY.LEVEL,

From 021f70ae54b8db6db0ff9ad4d608acafb77d7260 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Tue, 10 Dec 2024 23:49:29 -0800
Subject: [PATCH 12/19] chore: build catalog (#177)

---
 files/build-files-from-ncbi.py       |   2 +-
 files/out/genomes.json               | 158 +++++++++++++--------------
 files/out/organisms.json             |  56 +++++++---
 files/source/genomes-from-ncbi.tsv   |  10 +-
 files/source/organisms-from-ncbi.tsv |  30 ++---
 5 files changed, 139 insertions(+), 117 deletions(-)

diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py
index 1b8da76..3cb9562 100644
--- a/files/build-files-from-ncbi.py
+++ b/files/build-files-from-ncbi.py
@@ -95,7 +95,7 @@ def build_files():
 
   taxa_df = pd.read_csv(TAXA_URL, keep_default_na=False)
 
-  organisms_source_df = get_organisms_df([taxon for taxon in taxa_df["Name"] if taxon])
+  organisms_source_df = get_organisms_df([taxon.strip() for taxon in taxa_df["Name"] if taxon])
 
   organisms_df = organisms_source_df.merge(taxa_df[["TaxId", "CustomTags"]], how="left", left_on="taxonomyId", right_on="TaxId").drop(columns=["TaxId"])
 
diff --git a/files/out/genomes.json b/files/out/genomes.json
index be5dfaf..e8ab3b0 100644
--- a/files/out/genomes.json
+++ b/files/out/genomes.json
@@ -14,7 +14,7 @@
     "scaffoldL50": 6,
     "scaffoldN50": 1678596,
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Plasmodium vivax",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002415.2"
@@ -37,6 +37,24 @@
     "taxon": "Trypanosoma brucei brucei TREU927",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2"
   },
+  {
+    "accession": "GCF_000002655.1",
+    "annotationStatus": "Full annotation",
+    "chromosomes": 8,
+    "coverage": null,
+    "gcPercent": 50,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/genes/GCF_000002655.1_ASM265v1.ncbiRefSeq.gtf.gz",
+    "isRef": "Yes",
+    "length": 29384958,
+    "level": "Chromosome",
+    "ncbiTaxonomyId": "330879",
+    "scaffoldCount": 8,
+    "scaffoldL50": 4,
+    "scaffoldN50": 3948441,
+    "tags": [],
+    "taxon": "Aspergillus fumigatus Af293",
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002655.1"
+  },
   {
     "accession": "GCF_000002725.2",
     "annotationStatus": "Full annotation",
@@ -109,6 +127,24 @@
     "taxon": "Toxoplasma gondii ME49",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006565.2"
   },
+  {
+    "accession": "GCF_000091045.1",
+    "annotationStatus": "Full annotation",
+    "chromosomes": 14,
+    "coverage": null,
+    "gcPercent": 48.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/091/045/GCF_000091045.1/genes/GCF_000091045.1_ASM9104v1.ncbiRefSeq.gtf.gz",
+    "isRef": "Yes",
+    "length": 19051922,
+    "level": "Chromosome",
+    "ncbiTaxonomyId": "214684",
+    "scaffoldCount": 14,
+    "scaffoldL50": 6,
+    "scaffoldN50": 1438950,
+    "tags": [],
+    "taxon": "Cryptococcus neoformans var. neoformans JEC21",
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000091045.1"
+  },
   {
     "accession": "GCF_000149335.2",
     "annotationStatus": "Full annotation",
@@ -127,6 +163,24 @@
     "taxon": "Coccidioides immitis RS",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149335.2"
   },
+  {
+    "accession": "GCF_000182965.3",
+    "annotationStatus": "Full annotation",
+    "chromosomes": 8,
+    "coverage": "700.0x",
+    "gcPercent": 33.5,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/182/965/GCF_000182965.3/genes/GCF_000182965.3_ASM18296v3.ncbiRefSeq.gtf.gz",
+    "isRef": "Yes",
+    "length": 14282666,
+    "level": "Chromosome",
+    "ncbiTaxonomyId": "237561",
+    "scaffoldCount": 8,
+    "scaffoldL50": 3,
+    "scaffoldN50": 2231883,
+    "tags": [],
+    "taxon": "Candida albicans SC5314",
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182965.3"
+  },
   {
     "accession": "GCF_000195955.2",
     "annotationStatus": null,
@@ -160,7 +214,7 @@
     "scaffoldL50": 212,
     "scaffoldN50": 88624,
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Trypanosoma cruzi",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000209065.1"
@@ -180,7 +234,7 @@
     "scaffoldL50": 11,
     "scaffoldN50": 1024085,
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Leishmania donovani",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000227135.1"
@@ -201,47 +255,27 @@
     "scaffoldN50": 4411709,
     "tags": [],
     "taxon": "Mycobacterium tuberculosis H37Rv",
-    "ucscBrowserUrl": null
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000277735.2"
   },
   {
-    "accession": "GCF_000857045.1",
-    "annotationStatus": null,
-    "chromosomes": 1,
-    "coverage": null,
-    "gcPercent": 33,
-    "geneModelUrl": null,
-    "isRef": "No",
-    "length": 196858,
-    "level": "Complete Genome",
-    "ncbiTaxonomyId": "10244",
-    "scaffoldCount": 1,
-    "scaffoldL50": 1,
-    "scaffoldN50": 196858,
-    "tags": [
-      "Virus"
-    ],
-    "taxon": "Monkeypox virus",
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000857045.1"
-  },
-  {
-    "accession": "GCF_009858895.2",
-    "annotationStatus": null,
-    "chromosomes": 1,
-    "coverage": null,
-    "gcPercent": 38,
-    "geneModelUrl": null,
-    "isRef": "No",
-    "length": 29903,
-    "level": "Complete Genome",
-    "ncbiTaxonomyId": "2697049",
-    "scaffoldCount": 1,
-    "scaffoldL50": 1,
-    "scaffoldN50": 29903,
+    "accession": "GCF_015732765.1",
+    "annotationStatus": "Full annotation",
+    "chromosomes": 3,
+    "coverage": "76.0x",
+    "gcPercent": 37,
+    "geneModelUrl": "https://hgdownload.soe.ucsc.edu/hubs/GCF/015/732/765/GCF_015732765.1/genes/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal.ncbiRefSeq.gtf.gz",
+    "isRef": "Yes",
+    "length": 573214445,
+    "level": "Chromosome",
+    "ncbiTaxonomyId": "7176",
+    "scaffoldCount": 56,
+    "scaffoldL50": 2,
+    "scaffoldN50": 201550677,
     "tags": [
-      "Virus"
+      "VEuPathDB"
     ],
-    "taxon": "Severe acute respiratory syndrome coronavirus 2",
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_009858895.2"
+    "taxon": "Culex quinquefasciatus",
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_015732765.1"
   },
   {
     "accession": "GCF_016801865.2",
@@ -279,26 +313,6 @@
     "taxon": "Coccidioides posadasii str. Silveira",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_018416015.2"
   },
-  {
-    "accession": "GCF_030566675.1",
-    "annotationStatus": null,
-    "chromosomes": 1,
-    "coverage": "20.0x",
-    "gcPercent": 65.5,
-    "geneModelUrl": null,
-    "isRef": "No",
-    "length": 4516435,
-    "level": "Complete Genome",
-    "ncbiTaxonomyId": "1773",
-    "scaffoldCount": 1,
-    "scaffoldL50": 1,
-    "scaffoldN50": 4516435,
-    "tags": [
-      "Bact"
-    ],
-    "taxon": "Mycobacterium tuberculosis",
-    "ucscBrowserUrl": null
-  },
   {
     "accession": "GCF_900002385.2",
     "annotationStatus": "Full annotation",
@@ -314,7 +328,7 @@
     "scaffoldL50": 5,
     "scaffoldN50": 2046250,
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Plasmodium yoelii",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900002385.2"
@@ -352,29 +366,9 @@
     "scaffoldL50": 2,
     "scaffoldN50": 99149756,
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Anopheles gambiae",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_943734735.2"
-  },
-  {
-    "accession": "GCF_963525475.1",
-    "annotationStatus": null,
-    "chromosomes": 1,
-    "coverage": "100.0x",
-    "gcPercent": 65.5,
-    "geneModelUrl": null,
-    "isRef": "No",
-    "length": 4469156,
-    "level": "Complete Genome",
-    "ncbiTaxonomyId": "1773",
-    "scaffoldCount": 1,
-    "scaffoldL50": 1,
-    "scaffoldN50": 4469156,
-    "tags": [
-      "Bact"
-    ],
-    "taxon": "Mycobacterium tuberculosis",
-    "ucscBrowserUrl": null
   }
 ]
diff --git a/files/out/organisms.json b/files/out/organisms.json
index 54db9de..1bf4697 100644
--- a/files/out/organisms.json
+++ b/files/out/organisms.json
@@ -19,7 +19,7 @@
     "assemblyCount": 13,
     "ncbiTaxonomyId": "199306",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Coccidioides posadasii"
   },
@@ -31,6 +31,24 @@
     ],
     "taxon": "Severe acute respiratory syndrome coronavirus 2"
   },
+  {
+    "assemblyCount": 1,
+    "ncbiTaxonomyId": "42434",
+    "tags": [],
+    "taxon": "Culex pipiens pallens"
+  },
+  {
+    "assemblyCount": 183,
+    "ncbiTaxonomyId": "5207",
+    "tags": [],
+    "taxon": "Cryptococcus neoformans"
+  },
+  {
+    "assemblyCount": 117,
+    "ncbiTaxonomyId": "5476",
+    "tags": [],
+    "taxon": "Candida albicans"
+  },
   {
     "assemblyCount": 5,
     "ncbiTaxonomyId": "5501",
@@ -41,7 +59,7 @@
     "assemblyCount": 11,
     "ncbiTaxonomyId": "5660",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Leishmania braziliensis"
   },
@@ -49,7 +67,7 @@
     "assemblyCount": 12,
     "ncbiTaxonomyId": "5661",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Leishmania donovani"
   },
@@ -57,7 +75,7 @@
     "assemblyCount": 7,
     "ncbiTaxonomyId": "5664",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Leishmania major"
   },
@@ -65,7 +83,7 @@
     "assemblyCount": 6,
     "ncbiTaxonomyId": "5691",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Trypanosoma brucei"
   },
@@ -73,7 +91,7 @@
     "assemblyCount": 44,
     "ncbiTaxonomyId": "5693",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Trypanosoma cruzi"
   },
@@ -81,7 +99,7 @@
     "assemblyCount": 29,
     "ncbiTaxonomyId": "5811",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Toxoplasma gondii"
   },
@@ -89,7 +107,7 @@
     "assemblyCount": 67,
     "ncbiTaxonomyId": "5833",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Plasmodium falciparum"
   },
@@ -97,7 +115,7 @@
     "assemblyCount": 19,
     "ncbiTaxonomyId": "5855",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Plasmodium vivax"
   },
@@ -105,7 +123,7 @@
     "assemblyCount": 10,
     "ncbiTaxonomyId": "5860",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Plasmodium vinckei"
   },
@@ -113,7 +131,7 @@
     "assemblyCount": 15,
     "ncbiTaxonomyId": "5861",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Plasmodium yoelii"
   },
@@ -121,16 +139,22 @@
     "assemblyCount": 7,
     "ncbiTaxonomyId": "7165",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
     "taxon": "Anopheles gambiae"
   },
   {
-    "assemblyCount": 5,
-    "ncbiTaxonomyId": "7175",
+    "assemblyCount": 3,
+    "ncbiTaxonomyId": "7176",
     "tags": [
-      "VEuPathDb"
+      "VEuPathDB"
     ],
-    "taxon": "Culex pipiens"
+    "taxon": "Culex quinquefasciatus"
+  },
+  {
+    "assemblyCount": 352,
+    "ncbiTaxonomyId": "746128",
+    "tags": [],
+    "taxon": "Aspergillus fumigatus"
   }
 ]
diff --git a/files/source/genomes-from-ncbi.tsv b/files/source/genomes-from-ncbi.tsv
index a0f918b..468f878 100644
--- a/files/source/genomes-from-ncbi.tsv
+++ b/files/source/genomes-from-ncbi.tsv
@@ -5,17 +5,17 @@ Leishmania major strain Friedlin	347515	GCF_000002725.2	True	Complete Genome	36.
 Plasmodium yoelii	5861	GCF_900002385.2	True	Complete Genome	14.0	23043114	14	2046250	5	100.0x	21.5	Full annotation	GCA_900002385.2	https://genome.ucsc.edu/h/GCF_900002385.2	GCA_900002385.2	GCF_900002385.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz
 Coccidioides posadasii str. Silveira	443226	GCF_018416015.2	True	Complete Genome	9.0	28193268	9	8079863	2	475.0x	46.5	Full annotation	GCA_018416015.2	https://genome.ucsc.edu/h/GCF_018416015.2	GCA_018416015.2	GCF_018416015.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz
 Plasmodium vinckei vinckei	54757	GCF_900681995.1	True	Chromosome	14.0	18338688	14	1692345	5	155.0x	23.0	Full annotation	GCA_900681995.1	https://genome.ucsc.edu/h/GCF_900681995.1	GCA_900681995.1	GCF_900681995.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz
+Candida albicans SC5314	237561	GCF_000182965.3	True	Chromosome	8.0	14282666	8	2231883	3	700.0x	33.5	Full annotation	GCA_000182965.3	https://genome.ucsc.edu/h/GCF_000182965.3	GCA_000182965.3	GCF_000182965.3	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/182/965/GCF_000182965.3/genes/GCF_000182965.3_ASM18296v3.ncbiRefSeq.gtf.gz
+Cryptococcus neoformans var. neoformans JEC21	214684	GCF_000091045.1	True	Chromosome	14.0	19051922	14	1438950	6		48.5	Full annotation	GCA_000091045.1	https://genome.ucsc.edu/h/GCF_000091045.1	GCA_000091045.1	GCF_000091045.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/091/045/GCF_000091045.1/genes/GCF_000091045.1_ASM9104v1.ncbiRefSeq.gtf.gz
 Leishmania donovani	5661	GCF_000227135.1	True	Chromosome	36.0	32444968	36	1024085	11		59.5	Full annotation	GCA_000227135.2	https://genome.ucsc.edu/h/GCF_000227135.1	GCA_000227135.2	GCF_000227135.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz
+Aspergillus fumigatus Af293	330879	GCF_000002655.1	True	Chromosome	8.0	29384958	8	3948441	4		50.0	Full annotation	GCA_000002655.1	https://genome.ucsc.edu/h/GCF_000002655.1	GCA_000002655.1	GCF_000002655.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/genes/GCF_000002655.1_ASM265v1.ncbiRefSeq.gtf.gz
 Toxoplasma gondii ME49	508771	GCF_000006565.2	True	Chromosome	14.0	65633124	2276	4973582	6	26.5x	52.5		GCA_000006565.2	https://genome.ucsc.edu/h/GCF_000006565.2	GCA_000006565.2	GCF_000006565.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz
 Trypanosoma brucei brucei TREU927	185431	GCF_000002445.2	True	Chromosome	11.0	26075494	12	2481190	4		46.5	Full annotation	GCA_000002445.1	https://genome.ucsc.edu/h/GCF_000002445.2	GCA_000002445.1	GCF_000002445.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz
 Anopheles gambiae	7165	GCF_943734735.2	True	Chromosome	3.0	264451381	190	99149756	2	54.0x	44.5	Full annotation	GCA_943734735.2	https://genome.ucsc.edu/h/GCF_943734735.2	GCA_943734735.2	GCF_943734735.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz
 Plasmodium vivax	5855	GCF_000002415.2	True	Chromosome	14.0	27007701	2747	1678596	6		42.5	Full annotation	GCA_000002415.2	https://genome.ucsc.edu/h/GCF_000002415.2	GCA_000002415.2	GCF_000002415.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz
+Culex quinquefasciatus	7176	GCF_015732765.1	True	Chromosome	3.0	573214445	56	201550677	2	76.0x	37.0	Full annotation	GCA_015732765.1	https://genome.ucsc.edu/h/GCF_015732765.1	GCA_015732765.1	GCF_015732765.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/015/732/765/GCF_015732765.1/genes/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal.ncbiRefSeq.gtf.gz
 Culex pipiens pallens	42434	GCF_016801865.2	True	Chromosome	3.0	566339288	289	186194774	2	250.0x	37.0	Full annotation	GCA_016801865.2	https://genome.ucsc.edu/h/GCF_016801865.2	GCA_016801865.2	GCF_016801865.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz
 Leishmania braziliensis MHOM/BR/75/M2904	420245	GCF_000002845.2	True	Chromosome	35.0	32068771	138	992961	11		58.0		GCA_000002845.2	https://genome.ucsc.edu/h/GCF_000002845.2	GCA_000002845.2	GCF_000002845.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz
 Trypanosoma cruzi	5693	GCF_000209065.1	True	Scaffold		89937456	29495	88624	212		51.5	Full annotation	GCA_000209065.1	https://genome.ucsc.edu/h/GCF_000209065.1	GCA_000209065.1	GCF_000209065.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz
 Coccidioides immitis RS	246410	GCF_000149335.2	True	Scaffold		28947925	6	4323945	3		46.0	Full annotation	GCA_000149335.2	https://genome.ucsc.edu/h/GCF_000149335.2	GCA_000149335.2	GCF_000149335.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz
-Mycobacterium tuberculosis H37Rv	83332	GCF_000277735.2	False	Complete Genome	1.0	4411709	1	4411709	1		65.5		GCA_000277735.2				
-Severe acute respiratory syndrome coronavirus 2	2697049	GCF_009858895.2	False	Complete Genome	1.0	29903	1	29903	1		38.0		GCA_009858895.3	https://genome.ucsc.edu/h/GCF_009858895.2	GCA_009858895.3	GCF_009858895.2	
-Monkeypox virus	10244	GCF_000857045.1	False	Complete Genome	1.0	196858	1	196858	1		33.0		GCA_000857045.1	https://genome.ucsc.edu/h/GCF_000857045.1	GCA_000857045.1	GCF_000857045.1	
-Mycobacterium tuberculosis	1773	GCF_030566675.1	False	Complete Genome	1.0	4516435	1	4516435	1	20.0x	65.5		GCA_030566675.1				
-Mycobacterium tuberculosis	1773	GCF_963525475.1	False	Complete Genome	1.0	4469156	1	4469156	1	100.0x	65.5		GCA_963525475.1				
+Mycobacterium tuberculosis H37Rv	83332	GCF_000277735.2	False	Complete Genome	1.0	4411709	1	4411709	1		65.5		GCA_000277735.2	https://genome.ucsc.edu/h/GCF_000277735.2	GCA_000277735.2	GCF_000277735.2	
diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv
index 499eae1..eb42060 100644
--- a/files/source/organisms-from-ncbi.tsv
+++ b/files/source/organisms-from-ncbi.tsv
@@ -1,18 +1,22 @@
 taxon	taxonomyId	assemblyCount	CustomTags
-Anopheles gambiae	7165	7	VEuPathDb
+Anopheles gambiae	7165	7	VEuPathDB
+Aspergillus fumigatus	746128	352	
+Candida albicans	5476	117	
 Coccidioides immitis	5501	5	
-Coccidioides posadasii	199306	13	VEuPathDb
-Culex pipiens	7175	5	VEuPathDb
-Leishmania braziliensis	5660	11	VEuPathDb
-Leishmania donovani	5661	12	VEuPathDb
-Leishmania major	5664	7	VEuPathDb
+Coccidioides posadasii	199306	13	VEuPathDB
+Cryptococcus neoformans	5207	183	
+Culex pipiens pallens	42434	1	
+Culex quinquefasciatus	7176	3	VEuPathDB
+Leishmania braziliensis	5660	11	VEuPathDB
+Leishmania donovani	5661	12	VEuPathDB
+Leishmania major	5664	7	VEuPathDB
 Monkeypox virus	10244	6911	Virus
 Mycobacterium tuberculosis	1773	7829	Bact
-Plasmodium falciparum	5833	67	VEuPathDb
-Plasmodium vinckei	5860	10	VEuPathDb
-Plasmodium vivax	5855	19	VEuPathDb
-Plasmodium yoelii	5861	15	VEuPathDb
+Plasmodium falciparum	5833	67	VEuPathDB
+Plasmodium vinckei	5860	10	VEuPathDB
+Plasmodium vivax	5855	19	VEuPathDB
+Plasmodium yoelii	5861	15	VEuPathDB
 Severe acute respiratory syndrome coronavirus 2	2697049	12408	Virus
-Toxoplasma gondii	5811	29	VEuPathDb
-Trypanosoma brucei	5691	6	VEuPathDb
-Trypanosoma cruzi	5693	44	VEuPathDb
+Toxoplasma gondii	5811	29	VEuPathDB
+Trypanosoma brucei	5691	6	VEuPathDB
+Trypanosoma cruzi	5693	44	VEuPathDB

From fb0ccf1cb0c64b698721df835b92b0500ded5cd9 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Wed, 11 Dec 2024 22:32:58 -0800
Subject: [PATCH 13/19] feat: make genome taxa the same as organism taxa and
 add strain field (#177)

---
 .../brc-analytics-catalog/common/entities.ts  |   1 +
 files/build-catalog.ts                        |   1 +
 files/build-files-from-ncbi.py                |  26 ++--
 files/entities.ts                             |   1 +
 files/out/genomes.json                        | 115 +++++++++++++-----
 files/source/genomes-from-ncbi.tsv            |  43 +++----
 files/source/organisms-from-ncbi.tsv          |  44 +++----
 7 files changed, 150 insertions(+), 81 deletions(-)

diff --git a/app/apis/catalog/brc-analytics-catalog/common/entities.ts b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
index 1998a66..fb529c2 100644
--- a/app/apis/catalog/brc-analytics-catalog/common/entities.ts
+++ b/app/apis/catalog/brc-analytics-catalog/common/entities.ts
@@ -23,6 +23,7 @@ export interface BRCDataCatalogGenome {
   scaffoldCount: number;
   scaffoldL50: number;
   scaffoldN50: number;
+  strain: string | null;
   tags: string[];
   taxon: string;
   ucscBrowserUrl: string | null;
diff --git a/files/build-catalog.ts b/files/build-catalog.ts
index ee6029e..e3f7b88 100644
--- a/files/build-catalog.ts
+++ b/files/build-catalog.ts
@@ -65,6 +65,7 @@ async function buildGenomes(
       scaffoldCount: parseNumber(row.scaffoldCount),
       scaffoldL50: parseNumber(row.scaffoldL50),
       scaffoldN50: parseNumber(row.scaffoldN50),
+      strain: parseStringOrNull(row.strain),
       tags: organismsByTaxon.get(row.taxon)?.tags ?? [],
       taxon: row.taxon,
       ucscBrowserUrl: parseStringOrNull(row.ucscBrowser),
diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py
index 3cb9562..190f188 100644
--- a/files/build-files-from-ncbi.py
+++ b/files/build-files-from-ncbi.py
@@ -15,7 +15,7 @@
 def build_taxonomy_request_body(taxa):
   return {"taxons": taxa, "children": False, "ranks": ["genus"]}
 
-def get_organism_row(organism_info):
+def get_organism_row(organism_info, accession):
   if len(organism_info.get("errors", [])) > 0:
     raise Exception(organism_info)
 
@@ -25,11 +25,12 @@ def get_organism_row(organism_info):
     "taxon": organism_taxonomy["current_scientific_name"]["name"],
     "taxonomyId": str(organism_taxonomy["tax_id"]),
     "assemblyCount": next(count["count"] for count in organism_taxonomy["counts"] if count["type"] == "COUNT_TYPE_ASSEMBLY"),
+    "accession": accession,
   }
 
-def get_organisms_df(taxa):
-  organisms_info = requests.post(TAXONOMY_URL, json=build_taxonomy_request_body(taxa)).json()["reports"]
-  return pd.DataFrame([get_organism_row(organism_info) for organism_info in organisms_info])
+def get_organisms_df(taxa_with_accessions):
+  organisms_info_with_accessions = [(organism_info, accession) for taxon, accession in taxa_with_accessions for organism_info in requests.post(TAXONOMY_URL, json=build_taxonomy_request_body([taxon])).json()["reports"]]
+  return pd.DataFrame([get_organism_row(organism_info, accession) for organism_info, accession in organisms_info_with_accessions])
 
 def get_tax_ids(organisms_df):
   return list(organisms_df["taxonomyId"])
@@ -37,10 +38,11 @@ def get_tax_ids(organisms_df):
 def build_genomes_url(tax_ids):
   return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{urllib.parse.quote(",".join([str(id) for id in tax_ids]))}/dataset_report?filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome"
 
-def get_genome_row(genome_info):
+def get_genome_row(genome_info, taxon):
   refseq_category = genome_info["assembly_info"].get("refseq_category")
   return {
-    "taxon": genome_info["organism"]["organism_name"],
+    "taxon": taxon,
+    "strain": genome_info["organism"].get("infraspecific_names", {}).get("strain", ""),
     "taxonomyId": genome_info["organism"]["tax_id"],
     "accession": genome_info["accession"],
     "isRef": refseq_category == "reference genome",
@@ -56,8 +58,12 @@ def get_genome_row(genome_info):
     "pairedAccession": genome_info["paired_accession"],
   }
 
-def get_genomes_df(tax_ids):
-  return pd.DataFrame(data=[get_genome_row(genome_info) for genome_info in requests.get(build_genomes_url(tax_ids)).json()["reports"]])
+def get_organism_genomes(tax_id, accession):
+  return [genome_info for genome_info in requests.get(build_genomes_url([tax_id])).json()["reports"] if genome_info["accession"] == accession]
+
+def get_genomes_df(organism_ids):
+  genomes_info_with_organisms = [(genome_info, taxon) for tax_id, taxon, accession in organism_ids for genome_info in get_organism_genomes(tax_id, accession)]
+  return pd.DataFrame(data=[get_genome_row(*info) for info in genomes_info_with_organisms])
 
 def _id_to_gene_model_url(asm_id):
   hubs_url = "https://hgdownload.soe.ucsc.edu/hubs/"
@@ -95,7 +101,7 @@ def build_files():
 
   taxa_df = pd.read_csv(TAXA_URL, keep_default_na=False)
 
-  organisms_source_df = get_organisms_df([taxon.strip() for taxon in taxa_df["Name"] if taxon])
+  organisms_source_df = get_organisms_df([(taxon.strip(), accession.strip()) for taxon, accession in zip(taxa_df["Name"], taxa_df["RefSeq Accession"]) if taxon])
 
   organisms_df = organisms_source_df.merge(taxa_df[["TaxId", "CustomTags"]], how="left", left_on="taxonomyId", right_on="TaxId").drop(columns=["TaxId"])
 
@@ -103,7 +109,7 @@ def build_files():
 
   print(f"Wrote to {ORGANISMS_OUTPUT_PATH}")
 
-  genomes_source_df = get_genomes_df(get_tax_ids(organisms_df))
+  genomes_source_df = get_genomes_df(zip(organisms_df["taxonomyId"], organisms_df["taxon"], organisms_df["accession"]))
   assemblies_df = pd.DataFrame(requests.get(ASSEMBLIES_URL).json()["data"])[["ucscBrowser", "genBank", "refSeq"]]
 
   gen_bank_merge_df = genomes_source_df.merge(assemblies_df, how="left", left_on="accession", right_on="genBank")
diff --git a/files/entities.ts b/files/entities.ts
index 40c1774..a96f44f 100644
--- a/files/entities.ts
+++ b/files/entities.ts
@@ -11,6 +11,7 @@ export interface SourceGenome {
   scaffoldCount: string;
   scaffoldL50: string;
   scaffoldN50: string;
+  strain: string;
   taxon: string;
   taxonomyId: string;
   ucscBrowser: string;
diff --git a/files/out/genomes.json b/files/out/genomes.json
index e8ab3b0..7fe173d 100644
--- a/files/out/genomes.json
+++ b/files/out/genomes.json
@@ -13,6 +13,7 @@
     "scaffoldCount": 2747,
     "scaffoldL50": 6,
     "scaffoldN50": 1678596,
+    "strain": "Salvador I",
     "tags": [
       "VEuPathDB"
     ],
@@ -33,8 +34,11 @@
     "scaffoldCount": 12,
     "scaffoldL50": 4,
     "scaffoldN50": 2481190,
-    "tags": [],
-    "taxon": "Trypanosoma brucei brucei TREU927",
+    "strain": null,
+    "tags": [
+      "VEuPathDB"
+    ],
+    "taxon": "Trypanosoma brucei",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002445.2"
   },
   {
@@ -51,8 +55,9 @@
     "scaffoldCount": 8,
     "scaffoldL50": 4,
     "scaffoldN50": 3948441,
+    "strain": "Af293",
     "tags": [],
-    "taxon": "Aspergillus fumigatus Af293",
+    "taxon": "Aspergillus fumigatus",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002655.1"
   },
   {
@@ -69,8 +74,11 @@
     "scaffoldCount": 36,
     "scaffoldL50": 11,
     "scaffoldN50": 1091540,
-    "tags": [],
-    "taxon": "Leishmania major strain Friedlin",
+    "strain": "Friedlin",
+    "tags": [
+      "VEuPathDB"
+    ],
+    "taxon": "Leishmania major",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002725.2"
   },
   {
@@ -87,8 +95,11 @@
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 1687656,
-    "tags": [],
-    "taxon": "Plasmodium falciparum 3D7",
+    "strain": null,
+    "tags": [
+      "VEuPathDB"
+    ],
+    "taxon": "Plasmodium falciparum",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002765.6"
   },
   {
@@ -105,8 +116,11 @@
     "scaffoldCount": 138,
     "scaffoldL50": 11,
     "scaffoldN50": 992961,
-    "tags": [],
-    "taxon": "Leishmania braziliensis MHOM/BR/75/M2904",
+    "strain": "MHOM/BR/75/M2904",
+    "tags": [
+      "VEuPathDB"
+    ],
+    "taxon": "Leishmania braziliensis",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000002845.2"
   },
   {
@@ -123,8 +137,11 @@
     "scaffoldCount": 2276,
     "scaffoldL50": 6,
     "scaffoldN50": 4973582,
-    "tags": [],
-    "taxon": "Toxoplasma gondii ME49",
+    "strain": "ME49",
+    "tags": [
+      "VEuPathDB"
+    ],
+    "taxon": "Toxoplasma gondii",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000006565.2"
   },
   {
@@ -141,8 +158,9 @@
     "scaffoldCount": 14,
     "scaffoldL50": 6,
     "scaffoldN50": 1438950,
+    "strain": "JEC21",
     "tags": [],
-    "taxon": "Cryptococcus neoformans var. neoformans JEC21",
+    "taxon": "Cryptococcus neoformans",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000091045.1"
   },
   {
@@ -159,8 +177,9 @@
     "scaffoldCount": 6,
     "scaffoldL50": 3,
     "scaffoldN50": 4323945,
+    "strain": "RS",
     "tags": [],
-    "taxon": "Coccidioides immitis RS",
+    "taxon": "Coccidioides immitis",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000149335.2"
   },
   {
@@ -177,8 +196,9 @@
     "scaffoldCount": 8,
     "scaffoldL50": 3,
     "scaffoldN50": 2231883,
+    "strain": "SC5314",
     "tags": [],
-    "taxon": "Candida albicans SC5314",
+    "taxon": "Candida albicans",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000182965.3"
   },
   {
@@ -195,8 +215,11 @@
     "scaffoldCount": 1,
     "scaffoldL50": 1,
     "scaffoldN50": 4411532,
-    "tags": [],
-    "taxon": "Mycobacterium tuberculosis H37Rv",
+    "strain": "H37Rv",
+    "tags": [
+      "Bact"
+    ],
+    "taxon": "Mycobacterium tuberculosis",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000195955.2"
   },
   {
@@ -213,6 +236,7 @@
     "scaffoldCount": 29495,
     "scaffoldL50": 212,
     "scaffoldN50": 88624,
+    "strain": "CL Brener",
     "tags": [
       "VEuPathDB"
     ],
@@ -233,6 +257,7 @@
     "scaffoldCount": 36,
     "scaffoldL50": 11,
     "scaffoldN50": 1024085,
+    "strain": "BPK282A1",
     "tags": [
       "VEuPathDB"
     ],
@@ -240,22 +265,46 @@
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000227135.1"
   },
   {
-    "accession": "GCF_000277735.2",
+    "accession": "GCF_000857045.1",
     "annotationStatus": null,
     "chromosomes": 1,
     "coverage": null,
-    "gcPercent": 65.5,
+    "gcPercent": 33,
     "geneModelUrl": null,
     "isRef": "No",
-    "length": 4411709,
+    "length": 196858,
     "level": "Complete Genome",
-    "ncbiTaxonomyId": "83332",
+    "ncbiTaxonomyId": "10244",
     "scaffoldCount": 1,
     "scaffoldL50": 1,
-    "scaffoldN50": 4411709,
-    "tags": [],
-    "taxon": "Mycobacterium tuberculosis H37Rv",
-    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000277735.2"
+    "scaffoldN50": 196858,
+    "strain": "Zaire-96-I-16",
+    "tags": [
+      "Virus"
+    ],
+    "taxon": "Monkeypox virus",
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_000857045.1"
+  },
+  {
+    "accession": "GCF_009858895.2",
+    "annotationStatus": null,
+    "chromosomes": 1,
+    "coverage": null,
+    "gcPercent": 38,
+    "geneModelUrl": null,
+    "isRef": "No",
+    "length": 29903,
+    "level": "Complete Genome",
+    "ncbiTaxonomyId": "2697049",
+    "scaffoldCount": 1,
+    "scaffoldL50": 1,
+    "scaffoldN50": 29903,
+    "strain": null,
+    "tags": [
+      "Virus"
+    ],
+    "taxon": "Severe acute respiratory syndrome coronavirus 2",
+    "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_009858895.2"
   },
   {
     "accession": "GCF_015732765.1",
@@ -271,6 +320,7 @@
     "scaffoldCount": 56,
     "scaffoldL50": 2,
     "scaffoldN50": 201550677,
+    "strain": "JHB",
     "tags": [
       "VEuPathDB"
     ],
@@ -291,6 +341,7 @@
     "scaffoldCount": 289,
     "scaffoldL50": 2,
     "scaffoldN50": 186194774,
+    "strain": null,
     "tags": [],
     "taxon": "Culex pipiens pallens",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_016801865.2"
@@ -309,8 +360,11 @@
     "scaffoldCount": 9,
     "scaffoldL50": 2,
     "scaffoldN50": 8079863,
-    "tags": [],
-    "taxon": "Coccidioides posadasii str. Silveira",
+    "strain": "Silveira",
+    "tags": [
+      "VEuPathDB"
+    ],
+    "taxon": "Coccidioides posadasii",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_018416015.2"
   },
   {
@@ -327,6 +381,7 @@
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 2046250,
+    "strain": "17X",
     "tags": [
       "VEuPathDB"
     ],
@@ -347,8 +402,11 @@
     "scaffoldCount": 14,
     "scaffoldL50": 5,
     "scaffoldN50": 1692345,
-    "tags": [],
-    "taxon": "Plasmodium vinckei vinckei",
+    "strain": null,
+    "tags": [
+      "VEuPathDB"
+    ],
+    "taxon": "Plasmodium vinckei",
     "ucscBrowserUrl": "https://genome.ucsc.edu/h/GCF_900681995.1"
   },
   {
@@ -365,6 +423,7 @@
     "scaffoldCount": 190,
     "scaffoldL50": 2,
     "scaffoldN50": 99149756,
+    "strain": null,
     "tags": [
       "VEuPathDB"
     ],
diff --git a/files/source/genomes-from-ncbi.tsv b/files/source/genomes-from-ncbi.tsv
index 468f878..5b137dc 100644
--- a/files/source/genomes-from-ncbi.tsv
+++ b/files/source/genomes-from-ncbi.tsv
@@ -1,21 +1,22 @@
-taxon	taxonomyId	accession	isRef	level	chromosomeCount	length	scaffoldCount	scaffoldN50	scaffoldL50	coverage	gcPercent	annotationStatus	pairedAccession	ucscBrowser	genBank	refSeq	geneModelUrl
-Mycobacterium tuberculosis H37Rv	83332	GCF_000195955.2	True	Complete Genome	1.0	4411532	1	4411532	1		65.5		GCA_000195955.2	https://genome.ucsc.edu/h/GCF_000195955.2	GCA_000195955.2	GCF_000195955.2	
-Plasmodium falciparum 3D7	36329	GCF_000002765.6	True	Complete Genome	14.0	23292622	14	1687656	5	100.0x	19.5	Full annotation	GCA_000002765.3	https://genome.ucsc.edu/h/GCF_000002765.6	GCA_000002765.3	GCF_000002765.6	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz
-Leishmania major strain Friedlin	347515	GCF_000002725.2	True	Complete Genome	36.0	32855089	36	1091540	11		59.5	Full annotation	GCA_000002725.2	https://genome.ucsc.edu/h/GCF_000002725.2	GCA_000002725.2	GCF_000002725.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz
-Plasmodium yoelii	5861	GCF_900002385.2	True	Complete Genome	14.0	23043114	14	2046250	5	100.0x	21.5	Full annotation	GCA_900002385.2	https://genome.ucsc.edu/h/GCF_900002385.2	GCA_900002385.2	GCF_900002385.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz
-Coccidioides posadasii str. Silveira	443226	GCF_018416015.2	True	Complete Genome	9.0	28193268	9	8079863	2	475.0x	46.5	Full annotation	GCA_018416015.2	https://genome.ucsc.edu/h/GCF_018416015.2	GCA_018416015.2	GCF_018416015.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz
-Plasmodium vinckei vinckei	54757	GCF_900681995.1	True	Chromosome	14.0	18338688	14	1692345	5	155.0x	23.0	Full annotation	GCA_900681995.1	https://genome.ucsc.edu/h/GCF_900681995.1	GCA_900681995.1	GCF_900681995.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz
-Candida albicans SC5314	237561	GCF_000182965.3	True	Chromosome	8.0	14282666	8	2231883	3	700.0x	33.5	Full annotation	GCA_000182965.3	https://genome.ucsc.edu/h/GCF_000182965.3	GCA_000182965.3	GCF_000182965.3	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/182/965/GCF_000182965.3/genes/GCF_000182965.3_ASM18296v3.ncbiRefSeq.gtf.gz
-Cryptococcus neoformans var. neoformans JEC21	214684	GCF_000091045.1	True	Chromosome	14.0	19051922	14	1438950	6		48.5	Full annotation	GCA_000091045.1	https://genome.ucsc.edu/h/GCF_000091045.1	GCA_000091045.1	GCF_000091045.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/091/045/GCF_000091045.1/genes/GCF_000091045.1_ASM9104v1.ncbiRefSeq.gtf.gz
-Leishmania donovani	5661	GCF_000227135.1	True	Chromosome	36.0	32444968	36	1024085	11		59.5	Full annotation	GCA_000227135.2	https://genome.ucsc.edu/h/GCF_000227135.1	GCA_000227135.2	GCF_000227135.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz
-Aspergillus fumigatus Af293	330879	GCF_000002655.1	True	Chromosome	8.0	29384958	8	3948441	4		50.0	Full annotation	GCA_000002655.1	https://genome.ucsc.edu/h/GCF_000002655.1	GCA_000002655.1	GCF_000002655.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/genes/GCF_000002655.1_ASM265v1.ncbiRefSeq.gtf.gz
-Toxoplasma gondii ME49	508771	GCF_000006565.2	True	Chromosome	14.0	65633124	2276	4973582	6	26.5x	52.5		GCA_000006565.2	https://genome.ucsc.edu/h/GCF_000006565.2	GCA_000006565.2	GCF_000006565.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz
-Trypanosoma brucei brucei TREU927	185431	GCF_000002445.2	True	Chromosome	11.0	26075494	12	2481190	4		46.5	Full annotation	GCA_000002445.1	https://genome.ucsc.edu/h/GCF_000002445.2	GCA_000002445.1	GCF_000002445.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz
-Anopheles gambiae	7165	GCF_943734735.2	True	Chromosome	3.0	264451381	190	99149756	2	54.0x	44.5	Full annotation	GCA_943734735.2	https://genome.ucsc.edu/h/GCF_943734735.2	GCA_943734735.2	GCF_943734735.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz
-Plasmodium vivax	5855	GCF_000002415.2	True	Chromosome	14.0	27007701	2747	1678596	6		42.5	Full annotation	GCA_000002415.2	https://genome.ucsc.edu/h/GCF_000002415.2	GCA_000002415.2	GCF_000002415.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz
-Culex quinquefasciatus	7176	GCF_015732765.1	True	Chromosome	3.0	573214445	56	201550677	2	76.0x	37.0	Full annotation	GCA_015732765.1	https://genome.ucsc.edu/h/GCF_015732765.1	GCA_015732765.1	GCF_015732765.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/015/732/765/GCF_015732765.1/genes/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal.ncbiRefSeq.gtf.gz
-Culex pipiens pallens	42434	GCF_016801865.2	True	Chromosome	3.0	566339288	289	186194774	2	250.0x	37.0	Full annotation	GCA_016801865.2	https://genome.ucsc.edu/h/GCF_016801865.2	GCA_016801865.2	GCF_016801865.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz
-Leishmania braziliensis MHOM/BR/75/M2904	420245	GCF_000002845.2	True	Chromosome	35.0	32068771	138	992961	11		58.0		GCA_000002845.2	https://genome.ucsc.edu/h/GCF_000002845.2	GCA_000002845.2	GCF_000002845.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz
-Trypanosoma cruzi	5693	GCF_000209065.1	True	Scaffold		89937456	29495	88624	212		51.5	Full annotation	GCA_000209065.1	https://genome.ucsc.edu/h/GCF_000209065.1	GCA_000209065.1	GCF_000209065.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz
-Coccidioides immitis RS	246410	GCF_000149335.2	True	Scaffold		28947925	6	4323945	3		46.0	Full annotation	GCA_000149335.2	https://genome.ucsc.edu/h/GCF_000149335.2	GCA_000149335.2	GCF_000149335.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz
-Mycobacterium tuberculosis H37Rv	83332	GCF_000277735.2	False	Complete Genome	1.0	4411709	1	4411709	1		65.5		GCA_000277735.2	https://genome.ucsc.edu/h/GCF_000277735.2	GCA_000277735.2	GCF_000277735.2	
+taxon	strain	taxonomyId	accession	isRef	level	chromosomeCount	length	scaffoldCount	scaffoldN50	scaffoldL50	coverage	gcPercent	annotationStatus	pairedAccession	ucscBrowser	genBank	refSeq	geneModelUrl
+Plasmodium falciparum		36329	GCF_000002765.6	True	Complete Genome	14.0	23292622	14	1687656	5	100.0x	19.5	Full annotation	GCA_000002765.3	https://genome.ucsc.edu/h/GCF_000002765.6	GCA_000002765.3	GCF_000002765.6	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/765/GCF_000002765.6/genes/GCF_000002765.6_GCA_000002765.ncbiRefSeq.gtf.gz
+Plasmodium vivax	Salvador I	5855	GCF_000002415.2	True	Chromosome	14.0	27007701	2747	1678596	6		42.5	Full annotation	GCA_000002415.2	https://genome.ucsc.edu/h/GCF_000002415.2	GCA_000002415.2	GCF_000002415.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/415/GCF_000002415.2/genes/GCF_000002415.2_ASM241v2.ncbiRefSeq.gtf.gz
+Plasmodium yoelii	17X	5861	GCF_900002385.2	True	Complete Genome	14.0	23043114	14	2046250	5	100.0x	21.5	Full annotation	GCA_900002385.2	https://genome.ucsc.edu/h/GCF_900002385.2	GCA_900002385.2	GCF_900002385.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/002/385/GCF_900002385.2/genes/GCF_900002385.2_GCA_900002385.ncbiRefSeq.gtf.gz
+Plasmodium vinckei		54757	GCF_900681995.1	True	Chromosome	14.0	18338688	14	1692345	5	155.0x	23.0	Full annotation	GCA_900681995.1	https://genome.ucsc.edu/h/GCF_900681995.1	GCA_900681995.1	GCF_900681995.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/900/681/995/GCF_900681995.1/genes/GCF_900681995.1_PVVCY_v1.ncbiRefSeq.gtf.gz
+Culex pipiens pallens		42434	GCF_016801865.2	True	Chromosome	3.0	566339288	289	186194774	2	250.0x	37.0	Full annotation	GCA_016801865.2	https://genome.ucsc.edu/h/GCF_016801865.2	GCA_016801865.2	GCF_016801865.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/016/801/865/GCF_016801865.2/genes/GCF_016801865.2_TS_CPP_V2.ncbiRefSeq.gtf.gz
+Culex quinquefasciatus	JHB	7176	GCF_015732765.1	True	Chromosome	3.0	573214445	56	201550677	2	76.0x	37.0	Full annotation	GCA_015732765.1	https://genome.ucsc.edu/h/GCF_015732765.1	GCA_015732765.1	GCF_015732765.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/015/732/765/GCF_015732765.1/genes/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal.ncbiRefSeq.gtf.gz
+Anopheles gambiae		7165	GCF_943734735.2	True	Chromosome	3.0	264451381	190	99149756	2	54.0x	44.5	Full annotation	GCA_943734735.2	https://genome.ucsc.edu/h/GCF_943734735.2	GCA_943734735.2	GCF_943734735.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/943/734/735/GCF_943734735.2/genes/GCF_943734735.2_idAnoGambNW_F1_1.ncbiRefSeq.gtf.gz
+Toxoplasma gondii	ME49	508771	GCF_000006565.2	True	Chromosome	14.0	65633124	2276	4973582	6	26.5x	52.5		GCA_000006565.2	https://genome.ucsc.edu/h/GCF_000006565.2	GCA_000006565.2	GCF_000006565.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/006/565/GCF_000006565.2/genes/GCF_000006565.2_TGA4.ncbiRefSeq.gtf.gz
+Mycobacterium tuberculosis	H37Rv	83332	GCF_000195955.2	True	Complete Genome	1.0	4411532	1	4411532	1		65.5		GCA_000195955.2	https://genome.ucsc.edu/h/GCF_000195955.2	GCA_000195955.2	GCF_000195955.2	
+Coccidioides posadasii	Silveira	443226	GCF_018416015.2	True	Complete Genome	9.0	28193268	9	8079863	2	475.0x	46.5	Full annotation	GCA_018416015.2	https://genome.ucsc.edu/h/GCF_018416015.2	GCA_018416015.2	GCF_018416015.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/018/416/015/GCF_018416015.2/genes/GCF_018416015.2_ASM1841601v2.ncbiRefSeq.gtf.gz
+Coccidioides immitis	RS	246410	GCF_000149335.2	True	Scaffold		28947925	6	4323945	3		46.0	Full annotation	GCA_000149335.2	https://genome.ucsc.edu/h/GCF_000149335.2	GCA_000149335.2	GCF_000149335.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/149/335/GCF_000149335.2/genes/GCF_000149335.2_ASM14933v2.ncbiRefSeq.gtf.gz
+Trypanosoma cruzi	CL Brener	5693	GCF_000209065.1	True	Scaffold		89937456	29495	88624	212		51.5	Full annotation	GCA_000209065.1	https://genome.ucsc.edu/h/GCF_000209065.1	GCA_000209065.1	GCF_000209065.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/209/065/GCF_000209065.1/genes/GCF_000209065.1_ASM20906v1.ncbiRefSeq.gtf.gz
+Trypanosoma brucei		185431	GCF_000002445.2	True	Chromosome	11.0	26075494	12	2481190	4		46.5	Full annotation	GCA_000002445.1	https://genome.ucsc.edu/h/GCF_000002445.2	GCA_000002445.1	GCF_000002445.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/445/GCF_000002445.2/genes/GCF_000002445.2_ASM244v1.ncbiRefSeq.gtf.gz
+Leishmania major	Friedlin	347515	GCF_000002725.2	True	Complete Genome	36.0	32855089	36	1091540	11		59.5	Full annotation	GCA_000002725.2	https://genome.ucsc.edu/h/GCF_000002725.2	GCA_000002725.2	GCF_000002725.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/725/GCF_000002725.2/genes/GCF_000002725.2_ASM272v2.ncbiRefSeq.gtf.gz
+Leishmania donovani	BPK282A1	5661	GCF_000227135.1	True	Chromosome	36.0	32444968	36	1024085	11		59.5	Full annotation	GCA_000227135.2	https://genome.ucsc.edu/h/GCF_000227135.1	GCA_000227135.2	GCF_000227135.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/227/135/GCF_000227135.1/genes/GCF_000227135.1_ASM22713v2.ncbiRefSeq.gtf.gz
+Leishmania braziliensis	MHOM/BR/75/M2904	420245	GCF_000002845.2	True	Chromosome	35.0	32068771	138	992961	11		58.0		GCA_000002845.2	https://genome.ucsc.edu/h/GCF_000002845.2	GCA_000002845.2	GCF_000002845.2	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/845/GCF_000002845.2/genes/GCF_000002845.2_ASM284v2.ncbiRefSeq.gtf.gz
+Severe acute respiratory syndrome coronavirus 2		2697049	GCF_009858895.2	False	Complete Genome	1.0	29903	1	29903	1		38.0		GCA_009858895.3	https://genome.ucsc.edu/h/GCF_009858895.2	GCA_009858895.3	GCF_009858895.2	
+Monkeypox virus	Zaire-96-I-16	10244	GCF_000857045.1	False	Complete Genome	1.0	196858	1	196858	1		33.0		GCA_000857045.1	https://genome.ucsc.edu/h/GCF_000857045.1	GCA_000857045.1	GCF_000857045.1	
+Aspergillus fumigatus	Af293	330879	GCF_000002655.1	True	Chromosome	8.0	29384958	8	3948441	4		50.0	Full annotation	GCA_000002655.1	https://genome.ucsc.edu/h/GCF_000002655.1	GCA_000002655.1	GCF_000002655.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/002/655/GCF_000002655.1/genes/GCF_000002655.1_ASM265v1.ncbiRefSeq.gtf.gz
+Candida albicans	SC5314	237561	GCF_000182965.3	True	Chromosome	8.0	14282666	8	2231883	3	700.0x	33.5	Full annotation	GCA_000182965.3	https://genome.ucsc.edu/h/GCF_000182965.3	GCA_000182965.3	GCF_000182965.3	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/182/965/GCF_000182965.3/genes/GCF_000182965.3_ASM18296v3.ncbiRefSeq.gtf.gz
+Cryptococcus neoformans	JEC21	214684	GCF_000091045.1	True	Chromosome	14.0	19051922	14	1438950	6		48.5	Full annotation	GCA_000091045.1	https://genome.ucsc.edu/h/GCF_000091045.1	GCA_000091045.1	GCF_000091045.1	https://hgdownload.soe.ucsc.edu/hubs/GCF/000/091/045/GCF_000091045.1/genes/GCF_000091045.1_ASM9104v1.ncbiRefSeq.gtf.gz
diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv
index eb42060..a7a0d3a 100644
--- a/files/source/organisms-from-ncbi.tsv
+++ b/files/source/organisms-from-ncbi.tsv
@@ -1,22 +1,22 @@
-taxon	taxonomyId	assemblyCount	CustomTags
-Anopheles gambiae	7165	7	VEuPathDB
-Aspergillus fumigatus	746128	352	
-Candida albicans	5476	117	
-Coccidioides immitis	5501	5	
-Coccidioides posadasii	199306	13	VEuPathDB
-Cryptococcus neoformans	5207	183	
-Culex pipiens pallens	42434	1	
-Culex quinquefasciatus	7176	3	VEuPathDB
-Leishmania braziliensis	5660	11	VEuPathDB
-Leishmania donovani	5661	12	VEuPathDB
-Leishmania major	5664	7	VEuPathDB
-Monkeypox virus	10244	6911	Virus
-Mycobacterium tuberculosis	1773	7829	Bact
-Plasmodium falciparum	5833	67	VEuPathDB
-Plasmodium vinckei	5860	10	VEuPathDB
-Plasmodium vivax	5855	19	VEuPathDB
-Plasmodium yoelii	5861	15	VEuPathDB
-Severe acute respiratory syndrome coronavirus 2	2697049	12408	Virus
-Toxoplasma gondii	5811	29	VEuPathDB
-Trypanosoma brucei	5691	6	VEuPathDB
-Trypanosoma cruzi	5693	44	VEuPathDB
+taxon	taxonomyId	assemblyCount	accession	CustomTags
+Plasmodium falciparum	5833	67	GCF_000002765.6	VEuPathDB
+Plasmodium vivax	5855	19	GCF_000002415.2	VEuPathDB
+Plasmodium yoelii	5861	15	GCF_900002385.2	VEuPathDB
+Plasmodium vinckei	5860	10	GCF_900681995.1	VEuPathDB
+Culex pipiens pallens	42434	1	GCF_016801865.2	
+Culex quinquefasciatus	7176	3	GCF_015732765.1	VEuPathDB
+Anopheles gambiae	7165	7	GCF_943734735.2	VEuPathDB
+Toxoplasma gondii	5811	29	GCF_000006565.2	VEuPathDB
+Mycobacterium tuberculosis	1773	7829	GCF_000195955.2	Bact
+Coccidioides posadasii	199306	13	GCF_018416015.2	VEuPathDB
+Coccidioides immitis	5501	5	GCF_000149335.2	
+Trypanosoma cruzi	5693	44	GCF_000209065.1	VEuPathDB
+Trypanosoma brucei	5691	6	GCF_000002445.2	VEuPathDB
+Leishmania major	5664	7	GCF_000002725.2	VEuPathDB
+Leishmania donovani	5661	12	GCF_000227135.1	VEuPathDB
+Leishmania braziliensis	5660	11	GCF_000002845.2	VEuPathDB
+Severe acute respiratory syndrome coronavirus 2	2697049	12408	GCF_009858895.2	Virus
+Monkeypox virus	10244	6911	GCF_000857045.1	Virus
+Aspergillus fumigatus	746128	352	GCF_000002655.1	
+Candida albicans	5476	117	GCF_000182965.3	
+Cryptococcus neoformans	5207	183	GCF_000091045.1	

From fed91145f055106104714e0d2cec8f0f4071624c Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Wed, 11 Dec 2024 22:34:27 -0800
Subject: [PATCH 14/19] chore: upgrade findable-ui (#177)

---
 package-lock.json | 8 ++++----
 package.json      | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index c62da75..f276898 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -8,7 +8,7 @@
       "name": "brc-analytics",
       "version": "0.0.0",
       "dependencies": {
-        "@databiosphere/findable-ui": "15.0.2",
+        "@databiosphere/findable-ui": "^16.1.0",
         "@emotion/react": "^11.13.3",
         "@emotion/styled": "^11.13.0",
         "@mdx-js/loader": "^3.0.1",
@@ -1383,9 +1383,9 @@
       }
     },
     "node_modules/@databiosphere/findable-ui": {
-      "version": "15.0.2",
-      "resolved": "https://registry.npmjs.org/@databiosphere/findable-ui/-/findable-ui-15.0.2.tgz",
-      "integrity": "sha512-q6ANGEVeYmF8XjCAAiXadIva6tYZ4sO29grgQYAdcewgw1B7BxbiP7OXlQ9jAhSVGILZelWH8jqgFIR09lCrBw==",
+      "version": "16.1.0",
+      "resolved": "https://registry.npmjs.org/@databiosphere/findable-ui/-/findable-ui-16.1.0.tgz",
+      "integrity": "sha512-qoU0mVsbqJz+Dl8kfJPiRP/vniESbDNeNz1rGLsi0vaC2z1TdRT3SQfmE0b8KYzMd2aOw3UiRBPQIKQvHrVVCg==",
       "engines": {
         "node": "20.10.0"
       },
diff --git a/package.json b/package.json
index 28ee298..779fb3c 100644
--- a/package.json
+++ b/package.json
@@ -14,7 +14,7 @@
     "build-brc-db": "esrun files/build-catalog.ts"
   },
   "dependencies": {
-    "@databiosphere/findable-ui": "15.0.2",
+    "@databiosphere/findable-ui": "^16.1.0",
     "@emotion/react": "^11.13.3",
     "@emotion/styled": "^11.13.0",
     "@mdx-js/loader": "^3.0.1",

From 1f4f3affc7f9b6bb224786e0136e55e25b7f4ec3 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Wed, 11 Dec 2024 22:36:30 -0800
Subject: [PATCH 15/19] feat: link to filtered genomes from organism list
 (#177)

---
 .../common/viewModelBuilders.ts               | 46 +++++++++++++++++--
 .../local/index/genomeEntityConfig.ts         |  2 +-
 .../local/index/organismEntityConfig.ts       |  6 +--
 3 files changed, 45 insertions(+), 9 deletions(-)

diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
index 6968b98..a17458f 100644
--- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
+++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -3,6 +3,7 @@ import {
   Key,
   Value,
 } from "@databiosphere/findable-ui/lib/components/common/KeyValuePairs/keyValuePairs";
+import { LinkProps } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link";
 import { ViewContext } from "@databiosphere/findable-ui/lib/config/entities";
 import { ComponentProps } from "react";
 import { ROUTES } from "../../../../../routes/constants";
@@ -126,6 +127,19 @@ export const buildGcPercent = (
   };
 };
 
+/**
+ * Build props for the taxon cell.
+ * @param genome - Genome entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildGenomeTaxon = (
+  genome: BRCDataCatalogGenome
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: genome.taxon,
+  };
+};
+
 /**
  * Build props for the "is ref" cell.
  * @param genome - Genome entity.
@@ -167,14 +181,15 @@ export const buildLevel = (
 
 /**
  * Build props for the taxon cell.
- * @param genome - Genome entity.
+ * @param organism - Organism entity.
  * @returns Props to be used for the cell.
  */
-export const buildTaxon = (
-  genome: BRCDataCatalogOrganism | BRCDataCatalogGenome
-): ComponentProps<typeof C.BasicCell> => {
+export const buildOrganismTaxon = (
+  organism: BRCDataCatalogOrganism
+): ComponentProps<typeof C.Link> => {
   return {
-    value: genome.taxon,
+    label: organism.taxon,
+    url: getTaxonGenomesUrlObject(organism.taxon),
   };
 };
 
@@ -355,3 +370,24 @@ function getGenomeEntityChooseAnalysisMethodBreadcrumbs(
     { path: "", text: "Choose Analysis Methods" },
   ];
 }
+
+/**
+ * Get URL object for genomes filtered by a given taxon.
+ * @param taxon - Taxon.
+ * @returns URL object.
+ */
+function getTaxonGenomesUrlObject(taxon: string): LinkProps["url"] {
+  return {
+    href: ROUTES.GENOMES,
+    query: encodeURIComponent(
+      JSON.stringify({
+        filter: [
+          {
+            categoryKey: "taxon",
+            value: [taxon],
+          },
+        ],
+      })
+    ),
+  };
+}
diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
index 27b0a9d..ca286b9 100644
--- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts
+++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
@@ -99,7 +99,7 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
       {
         componentConfig: {
           component: C.BasicCell,
-          viewBuilder: V.buildTaxon,
+          viewBuilder: V.buildGenomeTaxon,
         } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
         header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON,
         id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
diff --git a/site-config/brc-analytics/local/index/organismEntityConfig.ts b/site-config/brc-analytics/local/index/organismEntityConfig.ts
index 1a39944..8c70ac2 100644
--- a/site-config/brc-analytics/local/index/organismEntityConfig.ts
+++ b/site-config/brc-analytics/local/index/organismEntityConfig.ts
@@ -52,9 +52,9 @@ export const organismEntityConfig: BRCEntityConfig<BRCDataCatalogOrganism> = {
     columns: [
       {
         componentConfig: {
-          component: C.BasicCell,
-          viewBuilder: V.buildTaxon,
-        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogOrganism>,
+          component: C.Link,
+          viewBuilder: V.buildOrganismTaxon,
+        } as ComponentConfig<typeof C.Link, BRCDataCatalogOrganism>,
         header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON,
         id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
         width: "auto",

From 4f9dfd6183285e25d42c4965e2adc656f284f348 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Wed, 11 Dec 2024 22:46:26 -0800
Subject: [PATCH 16/19] feat: add strain to genomes list (#177)

---
 .../common/viewModelBuilders.ts                   | 13 +++++++++++++
 site-config/brc-analytics/category.ts             |  2 ++
 .../local/index/genomeEntityConfig.ts             | 15 ++++++++++++++-
 3 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
index a17458f..9b61ff8 100644
--- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
+++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -232,6 +232,19 @@ export const buildScaffoldN50 = (
   };
 };
 
+/**
+ * Build props for the strain cell.
+ * @param genome - Genome entity.
+ * @returns Props to be used for the cell.
+ */
+export const buildStrain = (
+  genome: BRCDataCatalogGenome
+): ComponentProps<typeof C.BasicCell> => {
+  return {
+    value: genome.strain,
+  };
+};
+
 /**
  * Build props for the tags cell.
  * @param genome - Genome entity.
diff --git a/site-config/brc-analytics/category.ts b/site-config/brc-analytics/category.ts
index 122bf19..6b11043 100644
--- a/site-config/brc-analytics/category.ts
+++ b/site-config/brc-analytics/category.ts
@@ -12,6 +12,7 @@ export const BRC_DATA_CATALOG_CATEGORY_KEY = {
   SCAFFOLD_COUNT: "scaffoldCount",
   SCAFFOLD_L50: "scaffoldL50",
   SCAFFOLD_N50: "scaffoldN50",
+  STRAIN: "strain",
   TAGS: "tags",
   TAXON: "taxon",
   TAXONOMY_ID: "ncbiTaxonomyId",
@@ -32,6 +33,7 @@ export const BRC_DATA_CATALOG_CATEGORY_LABEL = {
   SCAFFOLD_COUNT: "Scaffolds",
   SCAFFOLD_L50: "Scaffold L50",
   SCAFFOLD_N50: "Scaffold N50",
+  STRAIN: "Strain",
   TAGS: "Tags",
   TAXON: "Taxon",
   TAXONOMY_ID: "Taxonomy ID",
diff --git a/site-config/brc-analytics/local/index/genomeEntityConfig.ts b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
index ca286b9..1544144 100644
--- a/site-config/brc-analytics/local/index/genomeEntityConfig.ts
+++ b/site-config/brc-analytics/local/index/genomeEntityConfig.ts
@@ -33,6 +33,10 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
             key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
             label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON,
           },
+          {
+            key: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN,
+            label: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN,
+          },
           {
             key: BRC_DATA_CATALOG_CATEGORY_KEY.TAXONOMY_ID,
             label: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXONOMY_ID,
@@ -103,7 +107,16 @@ export const genomeEntityConfig: BRCEntityConfig<BRCDataCatalogGenome> = {
         } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
         header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON,
         id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
-        width: { max: "1fr", min: "284px" },
+        width: { max: "1fr", min: "240px" },
+      },
+      {
+        componentConfig: {
+          component: C.BasicCell,
+          viewBuilder: V.buildStrain,
+        } as ComponentConfig<typeof C.BasicCell, BRCDataCatalogGenome>,
+        header: BRC_DATA_CATALOG_CATEGORY_LABEL.STRAIN,
+        id: BRC_DATA_CATALOG_CATEGORY_KEY.STRAIN,
+        width: { max: "0.5fr", min: "180px" },
       },
       {
         componentConfig: {

From d326bb3efb6f8805b9efd8d413f66b2b668a94b7 Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Wed, 11 Dec 2024 22:55:04 -0800
Subject: [PATCH 17/19] feat: hardcode organism assembly count as 1 (#177)

---
 files/build-files-from-ncbi.py       |  2 +-
 files/out/organisms.json             | 40 ++++++++++++++--------------
 files/source/organisms-from-ncbi.tsv | 40 ++++++++++++++--------------
 3 files changed, 41 insertions(+), 41 deletions(-)

diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py
index 190f188..41a32f0 100644
--- a/files/build-files-from-ncbi.py
+++ b/files/build-files-from-ncbi.py
@@ -24,7 +24,7 @@ def get_organism_row(organism_info, accession):
   return {
     "taxon": organism_taxonomy["current_scientific_name"]["name"],
     "taxonomyId": str(organism_taxonomy["tax_id"]),
-    "assemblyCount": next(count["count"] for count in organism_taxonomy["counts"] if count["type"] == "COUNT_TYPE_ASSEMBLY"),
+    "assemblyCount": 1,
     "accession": accession,
   }
 
diff --git a/files/out/organisms.json b/files/out/organisms.json
index 1bf4697..6d29b69 100644
--- a/files/out/organisms.json
+++ b/files/out/organisms.json
@@ -1,6 +1,6 @@
 [
   {
-    "assemblyCount": 6911,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "10244",
     "tags": [
       "Virus"
@@ -8,7 +8,7 @@
     "taxon": "Monkeypox virus"
   },
   {
-    "assemblyCount": 7829,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "1773",
     "tags": [
       "Bact"
@@ -16,7 +16,7 @@
     "taxon": "Mycobacterium tuberculosis"
   },
   {
-    "assemblyCount": 13,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "199306",
     "tags": [
       "VEuPathDB"
@@ -24,7 +24,7 @@
     "taxon": "Coccidioides posadasii"
   },
   {
-    "assemblyCount": 12408,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "2697049",
     "tags": [
       "Virus"
@@ -38,25 +38,25 @@
     "taxon": "Culex pipiens pallens"
   },
   {
-    "assemblyCount": 183,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5207",
     "tags": [],
     "taxon": "Cryptococcus neoformans"
   },
   {
-    "assemblyCount": 117,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5476",
     "tags": [],
     "taxon": "Candida albicans"
   },
   {
-    "assemblyCount": 5,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5501",
     "tags": [],
     "taxon": "Coccidioides immitis"
   },
   {
-    "assemblyCount": 11,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5660",
     "tags": [
       "VEuPathDB"
@@ -64,7 +64,7 @@
     "taxon": "Leishmania braziliensis"
   },
   {
-    "assemblyCount": 12,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5661",
     "tags": [
       "VEuPathDB"
@@ -72,7 +72,7 @@
     "taxon": "Leishmania donovani"
   },
   {
-    "assemblyCount": 7,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5664",
     "tags": [
       "VEuPathDB"
@@ -80,7 +80,7 @@
     "taxon": "Leishmania major"
   },
   {
-    "assemblyCount": 6,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5691",
     "tags": [
       "VEuPathDB"
@@ -88,7 +88,7 @@
     "taxon": "Trypanosoma brucei"
   },
   {
-    "assemblyCount": 44,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5693",
     "tags": [
       "VEuPathDB"
@@ -96,7 +96,7 @@
     "taxon": "Trypanosoma cruzi"
   },
   {
-    "assemblyCount": 29,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5811",
     "tags": [
       "VEuPathDB"
@@ -104,7 +104,7 @@
     "taxon": "Toxoplasma gondii"
   },
   {
-    "assemblyCount": 67,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5833",
     "tags": [
       "VEuPathDB"
@@ -112,7 +112,7 @@
     "taxon": "Plasmodium falciparum"
   },
   {
-    "assemblyCount": 19,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5855",
     "tags": [
       "VEuPathDB"
@@ -120,7 +120,7 @@
     "taxon": "Plasmodium vivax"
   },
   {
-    "assemblyCount": 10,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5860",
     "tags": [
       "VEuPathDB"
@@ -128,7 +128,7 @@
     "taxon": "Plasmodium vinckei"
   },
   {
-    "assemblyCount": 15,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "5861",
     "tags": [
       "VEuPathDB"
@@ -136,7 +136,7 @@
     "taxon": "Plasmodium yoelii"
   },
   {
-    "assemblyCount": 7,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "7165",
     "tags": [
       "VEuPathDB"
@@ -144,7 +144,7 @@
     "taxon": "Anopheles gambiae"
   },
   {
-    "assemblyCount": 3,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "7176",
     "tags": [
       "VEuPathDB"
@@ -152,7 +152,7 @@
     "taxon": "Culex quinquefasciatus"
   },
   {
-    "assemblyCount": 352,
+    "assemblyCount": 1,
     "ncbiTaxonomyId": "746128",
     "tags": [],
     "taxon": "Aspergillus fumigatus"
diff --git a/files/source/organisms-from-ncbi.tsv b/files/source/organisms-from-ncbi.tsv
index a7a0d3a..0615f1a 100644
--- a/files/source/organisms-from-ncbi.tsv
+++ b/files/source/organisms-from-ncbi.tsv
@@ -1,22 +1,22 @@
 taxon	taxonomyId	assemblyCount	accession	CustomTags
-Plasmodium falciparum	5833	67	GCF_000002765.6	VEuPathDB
-Plasmodium vivax	5855	19	GCF_000002415.2	VEuPathDB
-Plasmodium yoelii	5861	15	GCF_900002385.2	VEuPathDB
-Plasmodium vinckei	5860	10	GCF_900681995.1	VEuPathDB
+Plasmodium falciparum	5833	1	GCF_000002765.6	VEuPathDB
+Plasmodium vivax	5855	1	GCF_000002415.2	VEuPathDB
+Plasmodium yoelii	5861	1	GCF_900002385.2	VEuPathDB
+Plasmodium vinckei	5860	1	GCF_900681995.1	VEuPathDB
 Culex pipiens pallens	42434	1	GCF_016801865.2	
-Culex quinquefasciatus	7176	3	GCF_015732765.1	VEuPathDB
-Anopheles gambiae	7165	7	GCF_943734735.2	VEuPathDB
-Toxoplasma gondii	5811	29	GCF_000006565.2	VEuPathDB
-Mycobacterium tuberculosis	1773	7829	GCF_000195955.2	Bact
-Coccidioides posadasii	199306	13	GCF_018416015.2	VEuPathDB
-Coccidioides immitis	5501	5	GCF_000149335.2	
-Trypanosoma cruzi	5693	44	GCF_000209065.1	VEuPathDB
-Trypanosoma brucei	5691	6	GCF_000002445.2	VEuPathDB
-Leishmania major	5664	7	GCF_000002725.2	VEuPathDB
-Leishmania donovani	5661	12	GCF_000227135.1	VEuPathDB
-Leishmania braziliensis	5660	11	GCF_000002845.2	VEuPathDB
-Severe acute respiratory syndrome coronavirus 2	2697049	12408	GCF_009858895.2	Virus
-Monkeypox virus	10244	6911	GCF_000857045.1	Virus
-Aspergillus fumigatus	746128	352	GCF_000002655.1	
-Candida albicans	5476	117	GCF_000182965.3	
-Cryptococcus neoformans	5207	183	GCF_000091045.1	
+Culex quinquefasciatus	7176	1	GCF_015732765.1	VEuPathDB
+Anopheles gambiae	7165	1	GCF_943734735.2	VEuPathDB
+Toxoplasma gondii	5811	1	GCF_000006565.2	VEuPathDB
+Mycobacterium tuberculosis	1773	1	GCF_000195955.2	Bact
+Coccidioides posadasii	199306	1	GCF_018416015.2	VEuPathDB
+Coccidioides immitis	5501	1	GCF_000149335.2	
+Trypanosoma cruzi	5693	1	GCF_000209065.1	VEuPathDB
+Trypanosoma brucei	5691	1	GCF_000002445.2	VEuPathDB
+Leishmania major	5664	1	GCF_000002725.2	VEuPathDB
+Leishmania donovani	5661	1	GCF_000227135.1	VEuPathDB
+Leishmania braziliensis	5660	1	GCF_000002845.2	VEuPathDB
+Severe acute respiratory syndrome coronavirus 2	2697049	1	GCF_009858895.2	Virus
+Monkeypox virus	10244	1	GCF_000857045.1	Virus
+Aspergillus fumigatus	746128	1	GCF_000002655.1	
+Candida albicans	5476	1	GCF_000182965.3	
+Cryptococcus neoformans	5207	1	GCF_000091045.1	

From be94f0c216c12c6f1382ef4d18a45a0c1ecd5e4d Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Wed, 11 Dec 2024 23:19:09 -0800
Subject: [PATCH 18/19] fix: account for pagination when getting genomes (#177)

---
 files/build-files-from-ncbi.py | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/files/build-files-from-ncbi.py b/files/build-files-from-ncbi.py
index 41a32f0..a882381 100644
--- a/files/build-files-from-ncbi.py
+++ b/files/build-files-from-ncbi.py
@@ -35,8 +35,8 @@ def get_organisms_df(taxa_with_accessions):
 def get_tax_ids(organisms_df):
   return list(organisms_df["taxonomyId"])
 
-def build_genomes_url(tax_ids):
-  return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{urllib.parse.quote(",".join([str(id) for id in tax_ids]))}/dataset_report?filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome"
+def build_genomes_url(tax_ids, next_page_token):
+  return f"https://api.ncbi.nlm.nih.gov/datasets/v2/genome/taxon/{urllib.parse.quote(",".join([str(id) for id in tax_ids]))}/dataset_report?page_size=1000{"&page_token=" + next_page_token if next_page_token else ""}&filters.assembly_source=refseq&filters.has_annotation=true&filters.exclude_paired_reports=true&filters.exclude_atypical=true&filters.assembly_level=scaffold&filters.assembly_level=chromosome&filters.assembly_level=complete_genome"
 
 def get_genome_row(genome_info, taxon):
   refseq_category = genome_info["assembly_info"].get("refseq_category")
@@ -58,8 +58,20 @@ def get_genome_row(genome_info, taxon):
     "pairedAccession": genome_info["paired_accession"],
   }
 
+def get_organism_genomes_results(tax_id):
+  page = 1
+  next_page_token = None
+  results = []
+  while next_page_token or page == 1:
+    print(f"Requesting page {page} of taxon {tax_id}")
+    page_data = requests.get(build_genomes_url([tax_id], next_page_token)).json()
+    results += page_data["reports"]
+    next_page_token = page_data.get("next_page_token")
+    page += 1
+  return results
+
 def get_organism_genomes(tax_id, accession):
-  return [genome_info for genome_info in requests.get(build_genomes_url([tax_id])).json()["reports"] if genome_info["accession"] == accession]
+  return [genome_info for genome_info in get_organism_genomes_results(tax_id) if genome_info["accession"] == accession]
 
 def get_genomes_df(organism_ids):
   genomes_info_with_organisms = [(genome_info, taxon) for tax_id, taxon, accession in organism_ids for genome_info in get_organism_genomes(tax_id, accession)]

From 6edb5d9e0550d2192b14f1e755a7af2a1c83856d Mon Sep 17 00:00:00 2001
From: hunterckx <118154470+hunterckx@users.noreply.github.com>
Date: Thu, 12 Dec 2024 02:06:40 -0800
Subject: [PATCH 19/19] feat: add underline to genome links in organisms list
 (#177)

---
 app/components/common/StyledLink/styledLink.styles.tsx      | 6 ++++++
 app/components/index.ts                                     | 1 +
 .../brc-analytics-catalog/common/viewModelBuilders.ts       | 2 +-
 .../brc-analytics/local/index/organismEntityConfig.ts       | 4 ++--
 4 files changed, 10 insertions(+), 3 deletions(-)
 create mode 100644 app/components/common/StyledLink/styledLink.styles.tsx

diff --git a/app/components/common/StyledLink/styledLink.styles.tsx b/app/components/common/StyledLink/styledLink.styles.tsx
new file mode 100644
index 0000000..c0e74c5
--- /dev/null
+++ b/app/components/common/StyledLink/styledLink.styles.tsx
@@ -0,0 +1,6 @@
+import { Link } from "@databiosphere/findable-ui/lib/components/Links/components/Link/link";
+import styled from "@emotion/styled";
+
+export const StyledLink = styled(Link)`
+  text-decoration: underline;
+`;
diff --git a/app/components/index.ts b/app/components/index.ts
index 4a868b3..88553d9 100644
--- a/app/components/index.ts
+++ b/app/components/index.ts
@@ -24,6 +24,7 @@ export { Link } from "@databiosphere/findable-ui/lib/components/Links/components
 export { BasicCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/BasicCell/basicCell";
 export { NTagCell } from "@databiosphere/findable-ui/lib/components/Table/components/TableCell/components/NTagCell/nTagCell";
 export { CopyText } from "./common/CopyText/copyText";
+export { StyledLink } from "./common/StyledLink/styledLink.styles";
 export { AnalysisMethod } from "./Entity/components/AnalysisMethod/analysisMethod";
 export { AnalysisMethods } from "./Entity/components/AnalysisMethods/analysisMethods";
 export { AnalysisMethodsTitle } from "./Entity/components/AnalysisMethodsTitle/analysisMethodsTitle";
diff --git a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
index 9b61ff8..cd0edbf 100644
--- a/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
+++ b/app/viewModelBuilders/catalog/brc-analytics-catalog/common/viewModelBuilders.ts
@@ -186,7 +186,7 @@ export const buildLevel = (
  */
 export const buildOrganismTaxon = (
   organism: BRCDataCatalogOrganism
-): ComponentProps<typeof C.Link> => {
+): ComponentProps<typeof C.StyledLink> => {
   return {
     label: organism.taxon,
     url: getTaxonGenomesUrlObject(organism.taxon),
diff --git a/site-config/brc-analytics/local/index/organismEntityConfig.ts b/site-config/brc-analytics/local/index/organismEntityConfig.ts
index 8c70ac2..6c007c0 100644
--- a/site-config/brc-analytics/local/index/organismEntityConfig.ts
+++ b/site-config/brc-analytics/local/index/organismEntityConfig.ts
@@ -52,9 +52,9 @@ export const organismEntityConfig: BRCEntityConfig<BRCDataCatalogOrganism> = {
     columns: [
       {
         componentConfig: {
-          component: C.Link,
+          component: C.StyledLink,
           viewBuilder: V.buildOrganismTaxon,
-        } as ComponentConfig<typeof C.Link, BRCDataCatalogOrganism>,
+        } as ComponentConfig<typeof C.StyledLink, BRCDataCatalogOrganism>,
         header: BRC_DATA_CATALOG_CATEGORY_LABEL.TAXON,
         id: BRC_DATA_CATALOG_CATEGORY_KEY.TAXON,
         width: "auto",