From a7a13ffec4905a850d37396260730884845c8add Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Thu, 16 Oct 2025 14:23:38 -0400 Subject: [PATCH 01/42] implementing gtars qc --- ui/package-lock.json | 15 +++++ ui/package.json | 6 +- ui/src/main.tsx | 5 ++ ui/src/pages/bed-analytics.tsx | 112 +++++++++++++++++++++++++++++++++ ui/src/utils.ts | 64 +++++++++++++++++++ 5 files changed, 200 insertions(+), 2 deletions(-) create mode 100644 ui/src/pages/bed-analytics.tsx diff --git a/ui/package-lock.json b/ui/package-lock.json index 8e03fbf4..cd99975a 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -19,7 +19,9 @@ "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", "framer-motion": "^11.0.20", + "gtars-js": "file:../../gtars/gtars-wasm/pkg", "js-yaml": "^4.1.0", + "pako": "^2.1.0", "react": "^18.2.0", "react-bootstrap": "^2.10.1", "react-chartjs-2": "^5.2.0", @@ -50,6 +52,10 @@ "vite": "^6.3.6" } }, + "../../gtars/gtars-wasm/pkg": { + "name": "gtars-js", + "version": "0.5.0" + }, "node_modules/@aashutoshrathi/word-wrap": { "version": "1.2.6", "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz", @@ -2832,6 +2838,10 @@ "integrity": "sha512-EtKwoO6kxCL9WO5xipiHTZlSzBm7WLT627TqC/uVRd0HKmq8NXyebnNYxDoBi7wt8eTWrUrKXCOVaFq9x1kgag==", "dev": true }, + "node_modules/gtars-js": { + "resolved": "../../gtars/gtars-wasm/pkg", + "link": true + }, "node_modules/hast-util-is-element": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/hast-util-is-element/-/hast-util-is-element-3.0.0.tgz", @@ -4090,6 +4100,11 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/pako": { + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/pako/-/pako-2.1.0.tgz", + "integrity": "sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug==" + }, "node_modules/parent-module": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/parent-module/-/parent-module-1.0.1.tgz", diff --git a/ui/package.json b/ui/package.json index 081c74b0..7ccc253f 100644 --- a/ui/package.json +++ b/ui/package.json @@ -23,7 +23,9 @@ "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", "framer-motion": "^11.0.20", + "gtars-js": "file:../../gtars/gtars-wasm/pkg", "js-yaml": "^4.1.0", + "pako": "^2.1.0", "react": "^18.2.0", "react-bootstrap": "^2.10.1", "react-chartjs-2": "^5.2.0", @@ -35,8 +37,8 @@ "react-markdown": "^9.0.1", "react-router-dom": "^7.5.2", "rehype-highlight": "^7.0.0", - "vega-embed": "^7.0.2", - "three": "^0.177.0" + "three": "^0.177.0", + "vega-embed": "^7.0.2" }, "devDependencies": { "@types/js-yaml": "^4.0.9", diff --git a/ui/src/main.tsx b/ui/src/main.tsx index df411949..929d43c3 100644 --- a/ui/src/main.tsx +++ b/ui/src/main.tsx @@ -9,6 +9,7 @@ import toast, { Toaster } from 'react-hot-toast'; import { Home } from './pages/home.tsx'; import { Metrics } from './pages/metrics.tsx'; import { UMAPGraph } from './pages/visualization.tsx'; +import { BEDAnalytics } from './pages/bed-analytics.tsx'; import { HelmetProvider } from 'react-helmet-async'; // css stuff @@ -79,6 +80,10 @@ const router = createBrowserRouter([ path: '/umap', element: , }, + { + path: '/qc', + element: , + }, ]); // entry point diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx new file mode 100644 index 00000000..c9e661eb --- /dev/null +++ b/ui/src/pages/bed-analytics.tsx @@ -0,0 +1,112 @@ +import { useState, useRef } from 'react'; +import { Layout } from '../components/layout.tsx'; +import { RegionSet } from 'gtars-js'; +import { handleBedFileInput, type BedEntry } from '../utils.ts'; + +export const BEDAnalytics = () => { + const [regionsetRegions, setregionsetRegions] = useState(null); + const [Rs, setRs] = useState(null); + const [loadingRS, setLoadingRS] = useState(false); + const regionsetFileInputRef = useRef(null); + + const initializeRegionSet = (regionsetRegions) => { + if (regionsetRegions) { + console.log('initializing regionset'); + console.log(regionsetRegions); + setLoadingRS(true); + const rs = new RegionSet(regionsetRegions); + setRs(rs); + setLoadingRS(false); + } else { + setLoadingRS(false); + } + }; + + return ( + +
+
+ + { + const input = e.target as HTMLInputElement; + const file = input.files?.[0]; + if (file) { + // @ts-expect-error its fine :) + handleBedFileInput(e, (entries) => { + setregionsetRegions(entries); + }); + } + }} + /> + {regionsetRegions && ( +

+ {regionsetRegions.length} regions in universe +

+ )} +
+ +
+ {Rs &&

RegionSet initialized with {Rs.get_phi} regions

} +
+ +
+ + +
+ +
+
+
+ + RegionSet ready + +
+
+ {Rs && ( +
+

Mean region width: {Rs.mean_region_width}

+

Total number of regions: {Rs.number_of_regions}

+

Total number of nucleotides: {Rs.total_nucleotides}

+
+ )} +
+
+
+ + ); +}; \ No newline at end of file diff --git a/ui/src/utils.ts b/ui/src/utils.ts index 4cc01e5b..9e32655d 100644 --- a/ui/src/utils.ts +++ b/ui/src/utils.ts @@ -1,3 +1,5 @@ +import * as pako from 'pako'; + type ObjectType = 'bed' | 'bedset'; export const makeHttpDownloadLink = (md5: string) => { @@ -135,3 +137,65 @@ export const convertStatusCodeToMessage = (statusCode: number | undefined) => { return 'Unknown Error'; } }; + +// gtars bedfile handler +export type BedEntry = [string, number, number, string]; + +export async function parseBedFile(file: File): Promise { + let text: string; + if (file.name.endsWith('.gz')) { + const arrayBuffer = await file.arrayBuffer(); + const decompressed = pako.ungzip(new Uint8Array(arrayBuffer), { to: 'string' }); + text = decompressed; + } else { + text = await file.text(); + } + const lines = text.split('\n'); + const bedEntries: BedEntry[] = []; + +// export async function parseBedFile(file: File): Promise { +// const text = await file.text(); +// const lines = text.split('\n'); +// const bedEntries: BedEntry[] = []; + + for (const line of lines) { + const trimmedLine = line.trim(); + + // skip! + if (!trimmedLine || trimmedLine.startsWith('#')) { + continue; + } + + const columns = trimmedLine.split('\t'); + + // check for at least 3 columns (chr, start, end) + if (columns.length >= 3) { + const chr = columns[0]; + const start = parseInt(columns[1], 10); + const end = parseInt(columns[2], 10); + const rest = columns.slice(3).join('\t'); // join remaining columns if any + + // Validate that start and end are valid numbers + if (!isNaN(start) && !isNaN(end)) { + bedEntries.push([chr, start, end, rest]); + } + } + } + + return bedEntries; +} + +// helper function to handle file input change event +export function handleBedFileInput( + event: Event, + callback: (entries: BedEntry[]) => void +): void { + const input = event.target as HTMLInputElement; + const file = input.files?.[0]; + + if (file) { + parseBedFile(file) + .then(callback) + .catch((error) => console.error('Error parsing BED file:', error)); + } +} From e5864cd82f7b7f62cd062ee206c1e04d6c9c2e35 Mon Sep 17 00:00:00 2001 From: Nathan LeRoy Date: Thu, 16 Oct 2025 15:42:03 -0400 Subject: [PATCH 02/42] update pkgs and files vite config --- ui/package-lock.json | 4773 +++++++++++++++++++++----------- ui/package.json | 6 +- ui/src/pages/bed-analytics.tsx | 2 +- ui/vite.config.ts | 12 +- 4 files changed, 3230 insertions(+), 1563 deletions(-) diff --git a/ui/package-lock.json b/ui/package-lock.json index cd99975a..55c99c46 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -8,6 +8,7 @@ "name": "bedhost-ui-2", "version": "0.0.0", "dependencies": { + "@databio/gtars": "file:../../gtars/gtars-wasm/pkg", "@tanstack/react-query": "^5.28.0", "@tanstack/react-query-devtools": "^5.28.0", "@tanstack/react-table": "^8.15.3", @@ -19,7 +20,6 @@ "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", "framer-motion": "^11.0.20", - "gtars-js": "file:../../gtars/gtars-wasm/pkg", "js-yaml": "^4.1.0", "pako": "^2.1.0", "react": "^18.2.0", @@ -34,7 +34,9 @@ "react-router-dom": "^7.5.2", "rehype-highlight": "^7.0.0", "three": "^0.177.0", - "vega-embed": "^7.0.2" + "vega-embed": "^7.0.2", + "vite-plugin-top-level-await": "^1.6.0", + "vite-plugin-wasm": "^3.5.0" }, "devDependencies": { "@types/js-yaml": "^4.0.9", @@ -53,51 +55,28 @@ } }, "../../gtars/gtars-wasm/pkg": { - "name": "gtars-js", + "name": "@databio/gtars", "version": "0.5.0" }, - "node_modules/@aashutoshrathi/word-wrap": { - "version": "1.2.6", - "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz", - "integrity": "sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA==", - "dev": true, - "engines": { - "node": ">=0.10.0" - } - }, - "node_modules/@ampproject/remapping": { - "version": "2.3.0", - "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz", - "integrity": "sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw==", - "dev": true, - "license": "Apache-2.0", - "dependencies": { - "@jridgewell/gen-mapping": "^0.3.5", - "@jridgewell/trace-mapping": "^0.3.24" - }, - "engines": { - "node": ">=6.0.0" - } - }, "node_modules/@babel/code-frame": { - "version": "7.26.2", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.26.2.tgz", - "integrity": "sha512-RJlIHRueQgwWitWgF8OdFYGZX328Ax5BCemNGlqHfplnRT9ESi8JkFlvaVYbS+UubVY6dpv87Fs2u5M29iNFVQ==", + "version": "7.27.1", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.27.1.tgz", + "integrity": "sha512-cjQ7ZlQ0Mv3b47hABuTevyTuYN4i+loJKGeV9flcCgIK37cCXRh+L1bd3iBHlynerhQ7BhCkn2BPbQUL+rGqFg==", "dev": true, "license": "MIT", "dependencies": { - "@babel/helper-validator-identifier": "^7.25.9", + "@babel/helper-validator-identifier": "^7.27.1", "js-tokens": "^4.0.0", - "picocolors": "^1.0.0" + "picocolors": "^1.1.1" }, "engines": { "node": ">=6.9.0" } }, "node_modules/@babel/compat-data": { - "version": "7.26.8", - "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.26.8.tgz", - "integrity": "sha512-oH5UPLMWR3L2wEFLnFJ1TZXqHufiTKAiLfqw5zkhS4dKXLJ10yVztfil/twG8EDTA4F/tvVNw9nOl4ZMslB8rQ==", + "version": "7.28.4", + "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.28.4.tgz", + "integrity": "sha512-YsmSKC29MJwf0gF8Rjjrg5LQCmyh+j/nD8/eP7f+BeoQTKYqs9RoWbjGOdy0+1Ekr68RJZMUOPVQaQisnIo4Rw==", "dev": true, "license": "MIT", "engines": { @@ -105,22 +84,22 @@ } }, "node_modules/@babel/core": { - "version": "7.26.10", - "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.26.10.tgz", - "integrity": "sha512-vMqyb7XCDMPvJFFOaT9kxtiRh42GwlZEg1/uIgtZshS5a/8OaduUfCi7kynKgc3Tw/6Uo2D+db9qBttghhmxwQ==", - "dev": true, - "license": "MIT", - "dependencies": { - "@ampproject/remapping": "^2.2.0", - "@babel/code-frame": "^7.26.2", - "@babel/generator": "^7.26.10", - "@babel/helper-compilation-targets": "^7.26.5", - "@babel/helper-module-transforms": "^7.26.0", - "@babel/helpers": "^7.26.10", - "@babel/parser": "^7.26.10", - "@babel/template": "^7.26.9", - "@babel/traverse": "^7.26.10", - "@babel/types": "^7.26.10", + "version": "7.28.4", + "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.28.4.tgz", + "integrity": "sha512-2BCOP7TN8M+gVDj7/ht3hsaO/B/n5oDbiAyyvnRlNOs+u1o+JWNYTQrmpuNp1/Wq2gcFrI01JAW+paEKDMx/CA==", + "dev": true, + "license": "MIT", + "dependencies": { + "@babel/code-frame": "^7.27.1", + "@babel/generator": "^7.28.3", + "@babel/helper-compilation-targets": "^7.27.2", + "@babel/helper-module-transforms": "^7.28.3", + "@babel/helpers": "^7.28.4", + "@babel/parser": "^7.28.4", + "@babel/template": "^7.27.2", + "@babel/traverse": "^7.28.4", + "@babel/types": "^7.28.4", + "@jridgewell/remapping": "^2.3.5", "convert-source-map": "^2.0.0", "debug": "^4.1.0", "gensync": "^1.0.0-beta.2", @@ -146,16 +125,16 @@ } }, "node_modules/@babel/generator": { - "version": "7.27.0", - "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.27.0.tgz", - "integrity": "sha512-VybsKvpiN1gU1sdMZIp7FcqphVVKEwcuj02x73uvcHE0PTihx1nlBcowYWhDwjpoAXRv43+gDzyggGnn1XZhVw==", + "version": "7.28.3", + "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.28.3.tgz", + "integrity": "sha512-3lSpxGgvnmZznmBkCRnVREPUFJv2wrv9iAoFDvADJc0ypmdOxdUtcLeBgBJ6zE0PMeTKnxeQzyk0xTBq4Ep7zw==", "dev": true, "license": "MIT", "dependencies": { - "@babel/parser": "^7.27.0", - "@babel/types": "^7.27.0", - "@jridgewell/gen-mapping": "^0.3.5", - "@jridgewell/trace-mapping": "^0.3.25", + "@babel/parser": "^7.28.3", + "@babel/types": "^7.28.2", + "@jridgewell/gen-mapping": "^0.3.12", + "@jridgewell/trace-mapping": "^0.3.28", "jsesc": "^3.0.2" }, "engines": { @@ -163,14 +142,14 @@ } }, "node_modules/@babel/helper-compilation-targets": { - "version": "7.27.0", - "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.27.0.tgz", - "integrity": "sha512-LVk7fbXml0H2xH34dFzKQ7TDZ2G4/rVTOrq9V+icbbadjbVxxeFeDsNHv2SrZeWoA+6ZiTyWYWtScEIW07EAcA==", + "version": "7.27.2", + "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.27.2.tgz", + "integrity": "sha512-2+1thGUUWWjLTYTHZWK1n8Yga0ijBz1XAhUXcKy81rd5g6yh7hGqMp45v7cadSbEHc9G3OTv45SyneRN3ps4DQ==", "dev": true, "license": "MIT", "dependencies": { - "@babel/compat-data": "^7.26.8", - "@babel/helper-validator-option": "^7.25.9", + "@babel/compat-data": "^7.27.2", + "@babel/helper-validator-option": "^7.27.1", "browserslist": "^4.24.0", "lru-cache": "^5.1.1", "semver": "^6.3.1" @@ -189,30 +168,40 @@ "semver": "bin/semver.js" } }, + "node_modules/@babel/helper-globals": { + "version": "7.28.0", + "resolved": "https://registry.npmjs.org/@babel/helper-globals/-/helper-globals-7.28.0.tgz", + "integrity": "sha512-+W6cISkXFa1jXsDEdYA8HeevQT/FULhxzR99pxphltZcVaugps53THCeiWA8SguxxpSp3gKPiuYfSWopkLQ4hw==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=6.9.0" + } + }, "node_modules/@babel/helper-module-imports": { - "version": "7.25.9", - "resolved": "https://registry.npmjs.org/@babel/helper-module-imports/-/helper-module-imports-7.25.9.tgz", - "integrity": "sha512-tnUA4RsrmflIM6W6RFTLFSXITtl0wKjgpnLgXyowocVPrbYrLUXSBXDgTs8BlbmIzIdlBySRQjINYs2BAkiLtw==", + "version": "7.27.1", + "resolved": "https://registry.npmjs.org/@babel/helper-module-imports/-/helper-module-imports-7.27.1.tgz", + "integrity": "sha512-0gSFWUPNXNopqtIPQvlD5WgXYI5GY2kP2cCvoT8kczjbfcfuIljTbcWrulD1CIPIX2gt1wghbDy08yE1p+/r3w==", "dev": true, "license": "MIT", "dependencies": { - "@babel/traverse": "^7.25.9", - "@babel/types": "^7.25.9" + "@babel/traverse": "^7.27.1", + "@babel/types": "^7.27.1" }, "engines": { "node": ">=6.9.0" } }, "node_modules/@babel/helper-module-transforms": { - "version": "7.26.0", - "resolved": "https://registry.npmjs.org/@babel/helper-module-transforms/-/helper-module-transforms-7.26.0.tgz", - "integrity": "sha512-xO+xu6B5K2czEnQye6BHA7DolFFmS3LB7stHZFaOLb1pAwO1HWLS8fXA+eh0A2yIvltPVmx3eNNDBJA2SLHXFw==", + "version": "7.28.3", + "resolved": "https://registry.npmjs.org/@babel/helper-module-transforms/-/helper-module-transforms-7.28.3.tgz", + "integrity": "sha512-gytXUbs8k2sXS9PnQptz5o0QnpLL51SwASIORY6XaBKF88nsOT0Zw9szLqlSGQDP/4TljBAD5y98p2U1fqkdsw==", "dev": true, "license": "MIT", "dependencies": { - "@babel/helper-module-imports": "^7.25.9", - "@babel/helper-validator-identifier": "^7.25.9", - "@babel/traverse": "^7.25.9" + "@babel/helper-module-imports": "^7.27.1", + "@babel/helper-validator-identifier": "^7.27.1", + "@babel/traverse": "^7.28.3" }, "engines": { "node": ">=6.9.0" @@ -222,9 +211,9 @@ } }, "node_modules/@babel/helper-plugin-utils": { - "version": "7.26.5", - "resolved": "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.26.5.tgz", - "integrity": "sha512-RS+jZcRdZdRFzMyr+wcsaqOmld1/EqTghfaBGQQd/WnRdzdlvSZ//kF7U8VQTxf1ynZ4cjUcYgjVGx13ewNPMg==", + "version": "7.27.1", + "resolved": "https://registry.npmjs.org/@babel/helper-plugin-utils/-/helper-plugin-utils-7.27.1.tgz", + "integrity": "sha512-1gn1Up5YXka3YYAHGKpbideQ5Yjf1tDa9qYcgysz+cNCXukyLl6DjPXhD3VRwSb8c0J9tA4b2+rHEZtc6R0tlw==", "dev": true, "license": "MIT", "engines": { @@ -232,9 +221,9 @@ } }, "node_modules/@babel/helper-string-parser": { - "version": "7.25.9", - "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.25.9.tgz", - "integrity": "sha512-4A/SCr/2KLd5jrtOMFzaKjVtAei3+2r/NChoBNoZ3EyP/+GlhoaEGoWOZUmFmoITP7zOJyHIMm+DYRd8o3PvHA==", + "version": "7.27.1", + "resolved": "https://registry.npmjs.org/@babel/helper-string-parser/-/helper-string-parser-7.27.1.tgz", + "integrity": 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"version": "9.0.0", - "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-9.0.0.tgz", - "integrity": "sha512-G8ura3S+3Z2G+mkgNRq8dqaFZAuxfsxpBB8OCTGRTCtp+l/v9nbFNmCUP1BZMts3G1142MsZfn6eeUKrr4PD1Q==", + "version": "9.0.2", + "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-9.0.2.tgz", + "integrity": "sha512-42AtmgqjV+X1VpdOfyTGOYRi0/zsoLqtXQckTmqTeybT+BDIbM/Guxo7x3pE2vtpr1ok6xRqM9OpBe+Jyoqyww==", + "license": "MIT", "peer": true, "dependencies": { "ansi-styles": "^6.2.1", @@ -5943,9 +7577,10 @@ } }, "node_modules/wrap-ansi/node_modules/ansi-regex": { - "version": "6.1.0", - "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.1.0.tgz", - "integrity": "sha512-7HSX4QQb4CspciLpVFwyRe79O3xsIZDDLER21kERQ71oaPodF8jL725AgJMFAYbooIqolJoRLuM81SpeUkpkvA==", + "version": "6.2.2", + "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.2.2.tgz", + "integrity": "sha512-Bq3SmSpyFHaWjPk8If9yc6svM8c56dB5BAtW4Qbw5jHTwwXXcTLoRMkpDJp6VL0XzlWaCHTXrkFURMYmD0sLqg==", + "license": "MIT", "peer": true, "engines": { "node": ">=12" @@ -5954,10 +7589,24 @@ "url": "https://github.com/chalk/ansi-regex?sponsor=1" } }, + "node_modules/wrap-ansi/node_modules/ansi-styles": { + "version": "6.2.3", + "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-6.2.3.tgz", + "integrity": "sha512-4Dj6M28JB+oAH8kFkTLUo+a2jwOFkuqb3yucU0CANcRRUbxS0cP0nZYCGjcc3BNXwRIsUVmDGgzawme7zvJHvg==", + "license": "MIT", + "peer": true, + "engines": { + "node": ">=12" + }, + "funding": { + "url": "https://github.com/chalk/ansi-styles?sponsor=1" + } + }, "node_modules/wrap-ansi/node_modules/strip-ansi": { - "version": "7.1.0", - "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.0.tgz", - "integrity": "sha512-iq6eVVI64nQQTRYq2KtEg2d2uU7LElhTJwsH4YzIHZshxlgZms/wIc4VoDQTlG/IvVIrBKG06CrZnp0qv7hkcQ==", + "version": "7.1.2", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.2.tgz", + "integrity": "sha512-gmBGslpoQJtgnMAvOVqGZpEz9dyoKTCzy2nfz/n8aIFhN/jCE/rCmcxabB6jOOHV+0WNnylOxaxBQPSvcWklhA==", + "license": "MIT", "peer": true, "dependencies": { "ansi-regex": "^6.0.1" @@ -5973,12 +7622,14 @@ "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", - "dev": true + "dev": true, + "license": "ISC" }, "node_modules/y18n": { "version": "5.0.8", "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==", + "license": "ISC", "peer": true, "engines": { "node": ">=10" @@ -5995,6 +7646,7 @@ "version": "18.0.0", "resolved": "https://registry.npmjs.org/yargs/-/yargs-18.0.0.tgz", "integrity": "sha512-4UEqdc2RYGHZc7Doyqkrqiln3p9X2DZVxaGbwhn2pi7MrRagKaOcIKe8L3OxYcbhXLgLFUS3zAYuQjKBQgmuNg==", + "license": "MIT", "peer": true, "dependencies": { "cliui": "^9.0.1", @@ -6012,6 +7664,7 @@ "version": "22.0.0", "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-22.0.0.tgz", "integrity": "sha512-rwu/ClNdSMpkSrUb+d6BRsSkLUq1fmfsY6TOpYzTwvwkg1/NRG85KBy3kq++A8LKQwX6lsu+aWad+2khvuXrqw==", + "license": "ISC", "peer": true, "engines": { "node": "^20.19.0 || ^22.12.0 || >=23" @@ -6022,6 +7675,7 @@ "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", "dev": true, + "license": "MIT", "engines": { "node": ">=10" }, @@ -6033,6 +7687,7 @@ "version": "2.0.4", "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz", "integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==", + "license": "MIT", "funding": { "type": "github", "url": "https://github.com/sponsors/wooorm" diff --git a/ui/package.json b/ui/package.json index 7ccc253f..78ba8c5f 100644 --- a/ui/package.json +++ b/ui/package.json @@ -12,6 +12,7 @@ "generate-types-local": "npx openapi-typescript http://localhost:8000/openapi.json -o bedbase-types.d.ts" }, "dependencies": { + "@databio/gtars": "file:../../gtars/gtars-wasm/pkg", "@tanstack/react-query": "^5.28.0", "@tanstack/react-query-devtools": "^5.28.0", "@tanstack/react-table": "^8.15.3", @@ -23,7 +24,6 @@ "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", "framer-motion": "^11.0.20", - "gtars-js": "file:../../gtars/gtars-wasm/pkg", "js-yaml": "^4.1.0", "pako": "^2.1.0", "react": "^18.2.0", @@ -38,7 +38,9 @@ "react-router-dom": "^7.5.2", "rehype-highlight": "^7.0.0", "three": "^0.177.0", - "vega-embed": "^7.0.2" + "vega-embed": "^7.0.2", + "vite-plugin-top-level-await": "^1.6.0", + "vite-plugin-wasm": "^3.5.0" }, "devDependencies": { "@types/js-yaml": "^4.0.9", diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index c9e661eb..83100862 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -1,6 +1,6 @@ import { useState, useRef } from 'react'; import { Layout } from '../components/layout.tsx'; -import { RegionSet } from 'gtars-js'; +import { RegionSet } from '@databio/gtars'; import { handleBedFileInput, type BedEntry } from '../utils.ts'; export const BEDAnalytics = () => { diff --git a/ui/vite.config.ts b/ui/vite.config.ts index 5a33944a..443bb22f 100644 --- a/ui/vite.config.ts +++ b/ui/vite.config.ts @@ -1,7 +1,17 @@ import { defineConfig } from 'vite' import react from '@vitejs/plugin-react' +import topLevelAwait from 'vite-plugin-top-level-await'; +import wasm from 'vite-plugin-wasm'; // https://vitejs.dev/config/ export default defineConfig({ - plugins: [react()], + plugins: [wasm(), topLevelAwait(), react()], + build: { + target: 'esnext', // Ensure ESNext target for WASM support + }, + server: { + fs: { + allow: ['..'], // Allow serving files from one level up to the project root + }, + }, }) From 9b31bac1e7b4e0b88cac831def86b39d1b01ec9a Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Thu, 16 Oct 2025 16:56:01 -0400 Subject: [PATCH 03/42] add loading sign --- ui/src/pages/bed-analytics.tsx | 79 ++++++++++++++++++++++++---------- 1 file changed, 56 insertions(+), 23 deletions(-) diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index 83100862..79169efe 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -8,15 +8,27 @@ export const BEDAnalytics = () => { const [Rs, setRs] = useState(null); const [loadingRS, setLoadingRS] = useState(false); const regionsetFileInputRef = useRef(null); + const [processingTime, setProcessingTime] = useState(null); - const initializeRegionSet = (regionsetRegions) => { + const initializeRegionSet = async (regionsetRegions: BedEntry[] | null) => { if (regionsetRegions) { console.log('initializing regionset'); console.log(regionsetRegions); setLoadingRS(true); - const rs = new RegionSet(regionsetRegions); - setRs(rs); - setLoadingRS(false); + setProcessingTime(null); + + // Use setTimeout to allow the UI to update before processing + setTimeout(() => { + const startTime = performance.now(); + const rs = new RegionSet(regionsetRegions); + const endTime = performance.now(); + const processingTimeMs = endTime - startTime; + + console.log(rs.digest()); + setRs(rs); + setProcessingTime(processingTimeMs); + setLoadingRS(false); + }, 10); } else { setLoadingRS(false); } @@ -24,16 +36,17 @@ export const BEDAnalytics = () => { return ( -
+

BED analyzer

+
- + { @@ -49,26 +62,21 @@ export const BEDAnalytics = () => { /> {regionsetRegions && (

- {regionsetRegions.length} regions in universe + {regionsetRegions.length} regions in provided BED file

)}
-
- {Rs &&

RegionSet initialized with {Rs.get_phi} regions

} -
- -
+
-
+ {loadingRS && (
- - RegionSet ready - -
+ className="d-inline-flex align-items-center gap-2 px-3 py-2 bg-success bg-opacity-10 border border-success border-opacity-25 rounded-pill"> +
+ Loading... +
+ + Analyzing RegionSet... + +
+ )} + + {Rs && !loadingRS && ( +
+
+ + Results ready + +
+ )} +
{Rs && (

Mean region width: {Rs.mean_region_width}

Total number of regions: {Rs.number_of_regions}

Total number of nucleotides: {Rs.total_nucleotides}

+

Identifier: {Rs.digest()}

+ {processingTime !== null && ( +

Processing time: {(processingTime / 1000).toFixed(3)} seconds

+ )}
)}
From b82c8a92eccfbbe1cf863ec9693ef124416fbf90 Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Thu, 16 Oct 2025 17:25:30 -0400 Subject: [PATCH 04/42] more ui bedqc improvements --- ui/src/pages/bed-analytics.tsx | 117 +++++++++++++++++++++------------ 1 file changed, 74 insertions(+), 43 deletions(-) diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index 79169efe..a6dfbb0c 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -7,30 +7,43 @@ export const BEDAnalytics = () => { const [regionsetRegions, setregionsetRegions] = useState(null); const [Rs, setRs] = useState(null); const [loadingRS, setLoadingRS] = useState(false); - const regionsetFileInputRef = useRef(null); - const [processingTime, setProcessingTime] = useState(null); + const regionsetFileInputRef = useRef(null); + const [totalProcessingTime, setTotalProcessingTime] = useState(null); + const [selectedFile, setSelectedFile] = useState(null); - const initializeRegionSet = async (regionsetRegions: BedEntry[] | null) => { - if (regionsetRegions) { - console.log('initializing regionset'); - console.log(regionsetRegions); + const initializeRegionSet = async () => { + if (selectedFile) { setLoadingRS(true); - setProcessingTime(null); + setTotalProcessingTime(null); - // Use setTimeout to allow the UI to update before processing - setTimeout(() => { + try { + // Start timing from the beginning of file loading const startTime = performance.now(); - const rs = new RegionSet(regionsetRegions); - const endTime = performance.now(); - const processingTimeMs = endTime - startTime; - console.log(rs.digest()); - setRs(rs); - setProcessingTime(processingTimeMs); + // Create a synthetic event for handleBedFileInput + const syntheticEvent = { + target: { files: [selectedFile] }, + } as unknown as Event; + + await handleBedFileInput(syntheticEvent, (entries) => { + setregionsetRegions(entries); + + // Process the RegionSet immediately after loading + setTimeout(() => { + const rs = new RegionSet(entries); + const endTime = performance.now(); + const totalTimeMs = endTime - startTime; + + console.log(rs.digest()); + setRs(rs); + setTotalProcessingTime(totalTimeMs); + setLoadingRS(false); + }, 10); + }); + } catch (error) { setLoadingRS(false); - }, 10); - } else { - setLoadingRS(false); + console.error('Error loading file:', error); + } } }; @@ -50,42 +63,41 @@ export const BEDAnalytics = () => { }} type="file" onChange={(e) => { - const input = e.target as HTMLInputElement; - const file = input.files?.[0]; + const file = e.target.files?.[0]; if (file) { - // @ts-expect-error its fine :) - handleBedFileInput(e, (entries) => { - setregionsetRegions(entries); - }); + setSelectedFile(file); } }} /> + {selectedFile && ( +

+ Selected file: {selectedFile.name} +

+ )} {regionsetRegions && (

- {regionsetRegions.length} regions in provided BED file + {regionsetRegions.length} regions loaded from BED file

)}
- Analyzing RegionSet... - + Loading and analyzing... +
)} @@ -120,21 +132,40 @@ export const BEDAnalytics = () => { style={{ width: '8px', height: '8px' }} /> - Results ready - + Results ready +
)}
{Rs && (
-

Mean region width: {Rs.mean_region_width}

-

Total number of regions: {Rs.number_of_regions}

-

Total number of nucleotides: {Rs.total_nucleotides}

-

Identifier: {Rs.digest()}

- {processingTime !== null && ( -

Processing time: {(processingTime / 1000).toFixed(3)} seconds

- )} + + + + + + + + + + + + + + + + + + + {totalProcessingTime !== null && ( + + + + + )} + +
Mean region width{Rs.mean_region_width}
Total number of regions{Rs.number_of_regions}
Total number of nucleotides{Rs.total_nucleotides}
Identifier{Rs.digest()}
Total processing time{(totalProcessingTime / 1000).toFixed(3)} seconds
)}
From cf727212848eb672e11b2036a7825a28d83e326b Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Sun, 19 Oct 2025 23:38:19 -0400 Subject: [PATCH 05/42] added more statistics --- .../chromosome-stats-panel.tsx | 148 ++++++++++++++++++ ui/src/pages/bed-analytics.tsx | 82 ++++++---- 2 files changed, 196 insertions(+), 34 deletions(-) create mode 100644 ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx new file mode 100644 index 00000000..28f5d981 --- /dev/null +++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx @@ -0,0 +1,148 @@ +import React from 'react'; +import { ChromosomeStats, RegionSet } from '@databio/gtars'; + +interface Props { + Rs: RegionSet; + selectedFile: File | null; +} + +const ChromosomeStatsPanel: React.FC = ({ Rs, selectedFile }) => { + const calc = Rs.calculate_statistics?.(); + if (!calc) return null; + + const statsEntries = Array.from(calc.entries()) + .map(([chrom, stats]: [unknown, ChromosomeStats]) => { + const cs = stats as ChromosomeStats; + const row = { + chromosome: String(chrom), + count: cs.count, + minimum: cs.minimum, + maximum: cs.maximum, + mean: cs.mean.toFixed(2), + median: cs.median.toFixed(2), + start: cs.start, + end: cs.end, + }; + try { + (cs as unknown as { free?: () => void }).free?.(); + } catch (e) { + /* ignore */ + } + return row; + }) + .sort((a, b) => + a.chromosome.localeCompare(b.chromosome, undefined, { + numeric: true, + sensitivity: 'base', + }), + ); + + return ( +
+
+
Number of regions per chromosome:
+
+ + {(() => { + const barWidth = 36; + const gap = 24; + const maxCount = Math.max(...statsEntries.map(s => s.count), 1); + const chartHeight = 100; + return statsEntries.map((s, i) => { + const x = i * (barWidth + gap) + 16; + const barH = Math.round((s.count / maxCount) * chartHeight); + const y = 20 + (chartHeight - barH); + return ( + + + + {s.count} + + + {s.chromosome} + + + ); + }); + })()} + + +
+
+ +
+
+
+
Chromosome regions statatistics
+
+ +
+
+ + + + + + + + + + + + + + + + {statsEntries.map((s) => ( + + + + + + + + + + + ))} + +
ChromosomeCountStartEndMinMaxMeanMedian
{s.chromosome}{s.count}{s.start}{s.end}{s.minimum}{s.maximum}{s.mean}{s.median}
+
+
+
+ ); +}; + +export default ChromosomeStatsPanel; \ No newline at end of file diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index a6dfbb0c..57429e61 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -1,7 +1,8 @@ import { useState, useRef } from 'react'; import { Layout } from '../components/layout.tsx'; -import { RegionSet } from '@databio/gtars'; +import { RegionSet, ChromosomeStats } from '@databio/gtars'; import { handleBedFileInput, type BedEntry } from '../utils.ts'; +import ChromosomeStatsPanel from '../components/bed-analytics-components/chromosome-stats-panel.tsx'; export const BEDAnalytics = () => { const [regionsetRegions, setregionsetRegions] = useState(null); @@ -11,6 +12,15 @@ export const BEDAnalytics = () => { const [totalProcessingTime, setTotalProcessingTime] = useState(null); const [selectedFile, setSelectedFile] = useState(null); + + const formatFileSize = (bytes: number): string => { + if (bytes === 0) return '0 B'; + const k = 1024; + const sizes = ['B', 'KB', 'MB', 'GB']; + const i = Math.floor(Math.log(bytes) / Math.log(k)); + return parseFloat((bytes / Math.pow(k, i)).toFixed(2)) + ' ' + sizes[i]; + }; + const initializeRegionSet = async () => { if (selectedFile) { setLoadingRS(true); @@ -34,7 +44,7 @@ export const BEDAnalytics = () => { const endTime = performance.now(); const totalTimeMs = endTime - startTime; - console.log(rs.digest()); + console.log(rs.digest); setRs(rs); setTotalProcessingTime(totalTimeMs); setLoadingRS(false); @@ -65,19 +75,22 @@ export const BEDAnalytics = () => { onChange={(e) => { const file = e.target.files?.[0]; if (file) { + // unload any previous results when a new file is selected + setRs(null); + setregionsetRegions(null); + setTotalProcessingTime(null); setSelectedFile(file); } }} /> {selectedFile && ( -

- Selected file: {selectedFile.name} -

- )} - {regionsetRegions && ( -

- {regionsetRegions.length} regions loaded from BED file -

+
+
Selected file: {selectedFile.name}
+
File size: {formatFileSize(selectedFile.size)}
+ {Rs && totalProcessingTime !== null && ( +
Total processing time: {(totalProcessingTime / 1000).toFixed(3)}s
+ )} +
)}
@@ -140,32 +153,33 @@ export const BEDAnalytics = () => {
{Rs && (
- - - - - - - - - - - - - - - - - - - {totalProcessingTime !== null && ( +
+
Mean region width{Rs.mean_region_width}
Total number of regions{Rs.number_of_regions}
Total number of nucleotides{Rs.total_nucleotides}
Identifier{Rs.digest()}
+ + + + + + + + + - - + + - )} - -
Identifier{Rs.digest}
Mean region width{Rs.mean_region_width}
Total processing time{(totalProcessingTime / 1000).toFixed(3)} secondsTotal number of regions{Rs.number_of_regions}
+ + Total number of nucleotides + {Rs.total_nucleotides} + + + +
+
+

Interval chromosome length statistics

+ + {Rs.calculate_statistics && } +
)} From ceece9d3f40a64959d26c7b98325b260d64d60c7 Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Mon, 20 Oct 2025 00:02:52 -0400 Subject: [PATCH 06/42] Added url as input option --- ui/src/pages/bed-analytics.tsx | 189 ++++++++++++++++++++++----------- 1 file changed, 129 insertions(+), 60 deletions(-) diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index 57429e61..02614b3b 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -11,7 +11,8 @@ export const BEDAnalytics = () => { const regionsetFileInputRef = useRef(null); const [totalProcessingTime, setTotalProcessingTime] = useState(null); const [selectedFile, setSelectedFile] = useState(null); - + const [inputMode, setInputMode] = useState<'file' | 'url'>('file'); + const [bedUrl, setBedUrl] = useState(''); const formatFileSize = (bytes: number): string => { if (bytes === 0) return '0 B'; @@ -21,24 +22,44 @@ export const BEDAnalytics = () => { return parseFloat((bytes / Math.pow(k, i)).toFixed(2)) + ' ' + sizes[i]; }; + const fetchBedFromUrl = async (url: string): Promise => { + const response = await fetch(url); + if (!response.ok) { + throw new Error(`Failed to fetch BED file: ${response.statusText}`); + } + const blob = await response.blob(); + const fileName = url.split('/').pop() || 'remote-bed-file.bed'; + return new File([blob], fileName, { type: 'text/plain' }); + }; + const initializeRegionSet = async () => { - if (selectedFile) { + let fileToProcess: File | null = null; + + if (inputMode === 'file' && selectedFile) { + fileToProcess = selectedFile; + } else if (inputMode === 'url' && bedUrl.trim()) { + try { + fileToProcess = await fetchBedFromUrl(bedUrl.trim()); + } catch (error) { + console.error('Error fetching URL:', error); + return; + } + } + + if (fileToProcess) { setLoadingRS(true); setTotalProcessingTime(null); try { - // Start timing from the beginning of file loading const startTime = performance.now(); - // Create a synthetic event for handleBedFileInput const syntheticEvent = { - target: { files: [selectedFile] }, + target: { files: [fileToProcess] }, } as unknown as Event; await handleBedFileInput(syntheticEvent, (entries) => { setregionsetRegions(entries); - // Process the RegionSet immediately after loading setTimeout(() => { const rs = new RegionSet(entries); const endTime = performance.now(); @@ -57,64 +78,118 @@ export const BEDAnalytics = () => { } }; + const clearAll = () => { + setRs(null); + setregionsetRegions(null); + setTotalProcessingTime(null); + setSelectedFile(null); + setBedUrl(''); + if (regionsetFileInputRef.current) { + regionsetFileInputRef.current.value = ''; + } + }; + return (

BED analyzer

-
- - { - const file = e.target.files?.[0]; - if (file) { - // unload any previous results when a new file is selected - setRs(null); - setregionsetRegions(null); - setTotalProcessingTime(null); - setSelectedFile(file); - } - }} - /> - {selectedFile && ( -
-
Selected file: {selectedFile.name}
-
File size: {formatFileSize(selectedFile.size)}
- {Rs && totalProcessingTime !== null && ( -
Total processing time: {(totalProcessingTime / 1000).toFixed(3)}s
+
+
+
+ setInputMode('file')} + /> + +
+
+ setInputMode('url')} + /> + +
+
+ + {inputMode === 'file' ? ( +
+ + { + const file = e.target.files?.[0]; + if (file) { + clearAll(); + setSelectedFile(file); + } + }} + /> + {selectedFile && ( +
+
Selected file: {selectedFile.name}
+
File size: {formatFileSize(selectedFile.size)}
+
+ )} +
+ ) : ( +
+ + { + setBedUrl(e.target.value); + if (Rs) clearAll(); + }} + /> + {bedUrl && ( +
+ URL: {bedUrl} +
)}
)} + + {Rs && totalProcessingTime !== null && ( +
+ Total processing time: {(totalProcessingTime / 1000).toFixed(3)}s +
+ )}
-
+
@@ -124,11 +199,7 @@ export const BEDAnalytics = () => { {loadingRS && (
-
+
Loading...
@@ -140,10 +211,7 @@ export const BEDAnalytics = () => { {Rs && !loadingRS && (
-
+
Results ready @@ -166,7 +234,7 @@ export const BEDAnalytics = () => { Total number of regions - {Rs.number_of_regions} + {Rs.total_nucleotides} Total number of nucleotides @@ -177,8 +245,9 @@ export const BEDAnalytics = () => {

Interval chromosome length statistics

- - {Rs.calculate_statistics && } + {Rs.calculate_statistics && ( + + )}
)} From 4f248ffddca7a34a77da18db72dcccd20a5c2e33 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 21 Oct 2025 04:53:11 +0000 Subject: [PATCH 07/42] Bump vite from 6.3.6 to 6.4.1 in /ui Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 6.3.6 to 6.4.1. - [Release notes](https://github.com/vitejs/vite/releases) - [Changelog](https://github.com/vitejs/vite/blob/main/packages/vite/CHANGELOG.md) - [Commits](https://github.com/vitejs/vite/commits/create-vite@6.4.1/packages/vite) --- updated-dependencies: - dependency-name: vite dependency-version: 6.4.1 dependency-type: direct:development ... Signed-off-by: dependabot[bot] --- ui/package-lock.json | 9 +++++---- ui/package.json | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/ui/package-lock.json b/ui/package-lock.json index 463ba7ef..2d032b5c 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -47,7 +47,7 @@ "eslint-plugin-react-refresh": "^0.4.5", "sass": "^1.72.0", "typescript": "^5.2.2", - "vite": "^6.3.6" + "vite": "^6.4.1" } }, "node_modules/@aashutoshrathi/word-wrap": { @@ -5963,10 +5963,11 @@ } }, "node_modules/vite": { - "version": "6.3.6", - "resolved": "https://registry.npmjs.org/vite/-/vite-6.3.6.tgz", - "integrity": "sha512-0msEVHJEScQbhkbVTb/4iHZdJ6SXp/AvxL2sjwYQFfBqleHtnCqv1J3sa9zbWz/6kW1m9Tfzn92vW+kZ1WV6QA==", + "version": "6.4.1", + "resolved": "https://registry.npmjs.org/vite/-/vite-6.4.1.tgz", + "integrity": "sha512-+Oxm7q9hDoLMyJOYfUYBuHQo+dkAloi33apOPP56pzj+vsdJDzr+j1NISE5pyaAuKL4A3UD34qd0lx5+kfKp2g==", "dev": true, + "license": "MIT", "dependencies": { "esbuild": "^0.25.0", "fdir": "^6.4.4", diff --git a/ui/package.json b/ui/package.json index 8cd690a3..a33e10af 100644 --- a/ui/package.json +++ b/ui/package.json @@ -51,6 +51,6 @@ "eslint-plugin-react-refresh": "^0.4.5", "sass": "^1.72.0", "typescript": "^5.2.2", - "vite": "^6.3.6" + "vite": "^6.4.1" } } From fe981301485530b5a757683b2d0f6a39b60c3a47 Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Fri, 24 Oct 2025 16:56:13 -0400 Subject: [PATCH 08/42] Adding region distribution plot --- ui/package-lock.json | 2 +- .../bed-analytics-components/bed-plots.tsx | 123 ++++++++++++++++++ .../chromosome-stats-panel.tsx | 4 +- ui/src/main.tsx | 2 +- ui/src/pages/bed-analytics.tsx | 71 +++++----- 5 files changed, 168 insertions(+), 34 deletions(-) create mode 100644 ui/src/components/bed-analytics-components/bed-plots.tsx diff --git a/ui/package-lock.json b/ui/package-lock.json index 55c99c46..b80b72b1 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -56,7 +56,7 @@ }, "../../gtars/gtars-wasm/pkg": { "name": "@databio/gtars", - "version": "0.5.0" + "version": "0.5.1" }, "node_modules/@babel/code-frame": { "version": "7.27.1", diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx new file mode 100644 index 00000000..accb67ee --- /dev/null +++ b/ui/src/components/bed-analytics-components/bed-plots.tsx @@ -0,0 +1,123 @@ +import { useEffect, useRef } from 'react'; +import embed from 'vega-embed'; + + +interface Props { + xlab?: string; + ylab?: string; + height?: number; + color?: number; + angle?: boolean; + maxLength?: number; +} + +const distributionSpec = (data: any, props: Props = {}) => { + const { xlab = 'Label', ylab = 'Value', height = 300, color = 0, angle = false, maxLength = 15 } = props; + + // Transform data to match the new schema requirements + const transformedData = data.map((item: any, index: number) => ({ + chr: item.chr, + withinGroupID: item.rid, + N: item.n, + start: item.start, + end: item.end, + })); + + return { + $schema: 'https://vega-github.io/schema/vega-lite/v6.json', + config: { + axis: { + grid: false, + }, + facet: { + spacing: -1, + }, + view: { + continuousHeight: 300, + continuousWidth: 300, + strokeWidth: 0, + cursor: 'inherit', + }, + }, + data: { + values: transformedData, + }, + encoding: { + row: { + field: 'chr', + header: { + labelAlign: 'right', + labelAngle: 0, + labelOrient: 'right', + labelPadding: 5, + }, + sort: [ + 'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', + 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', + 'chr21', 'chr22', 'chrX', 'chrY', 'chrM', + ], + title: 'Number of Regions', + type: 'ordinal', + }, + x: { + axis: { + // labelExpr: 'datum.value == 0 ? \'start\' : datum.value == 183 ? \'end\' : \'\'', + values: [0, 300.0], + }, + field: 'withinGroupID', + scale: { + domain: [0, 300.0], + }, + title: 'Genome', + type: 'quantitative', + }, + y: { + axis: { + values: [10.0, 20.0, 30.0], + }, + field: 'N', + title: '', + type: 'quantitative', + }, + }, + height: 25, + mark: { + cornerRadiusEnd: 0.5, + type: 'bar', + width: 2.5, + }, + width: 750, + }; +}; + +export const ChromosomeBarPlot = (props: Props) => { + const { data, xlab, ylab, height, color, action } = props; + + const plotRef = useRef(null); + const spec = distributionSpec(data, { xlab, ylab, height, color }); + + useEffect(() => { + if (plotRef.current && spec) { + try { + embed(plotRef.current as HTMLDivElement, spec as any, { 'actions': action }) + .catch(error => { + console.error('Embed error after parsing:', error); + }); + } catch (error) { + console.error(error); + } + } + + return () => { + if (plotRef.current) { + plotRef.current.innerHTML = ''; + } + }; + }, [spec, action]); + + return ( +
+ ); +}; + +export default ChromosomeBarPlot; diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx index 28f5d981..50c3be5f 100644 --- a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx +++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx @@ -6,8 +6,8 @@ interface Props { selectedFile: File | null; } -const ChromosomeStatsPanel: React.FC = ({ Rs, selectedFile }) => { - const calc = Rs.calculate_statistics?.(); +const ChromosomeStatsPanel: React.FC = ({ rs, selectedFile }) => { + const calc = rs.calculate_statistics?.(); if (!calc) return null; const statsEntries = Array.from(calc.entries()) diff --git a/ui/src/main.tsx b/ui/src/main.tsx index 929d43c3..243d0b11 100644 --- a/ui/src/main.tsx +++ b/ui/src/main.tsx @@ -81,7 +81,7 @@ const router = createBrowserRouter([ element: , }, { - path: '/qc', + path: '/analyze', element: , }, ]); diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index 02614b3b..bf1b06ad 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -1,26 +1,22 @@ import { useState, useRef } from 'react'; import { Layout } from '../components/layout.tsx'; -import { RegionSet, ChromosomeStats } from '@databio/gtars'; -import { handleBedFileInput, type BedEntry } from '../utils.ts'; +import { RegionSet } from '@databio/gtars'; +import { handleBedFileInput } from '../utils.ts'; +import { bytesToSize } from '../utils.ts'; import ChromosomeStatsPanel from '../components/bed-analytics-components/chromosome-stats-panel.tsx'; +import ChromosomeBarPlot from '../components/bed-analytics-components/bed-plots.tsx'; export const BEDAnalytics = () => { - const [regionsetRegions, setregionsetRegions] = useState(null); - const [Rs, setRs] = useState(null); + + const [rs, setRs] = useState(null); const [loadingRS, setLoadingRS] = useState(false); - const regionsetFileInputRef = useRef(null); const [totalProcessingTime, setTotalProcessingTime] = useState(null); const [selectedFile, setSelectedFile] = useState(null); const [inputMode, setInputMode] = useState<'file' | 'url'>('file'); const [bedUrl, setBedUrl] = useState(''); - const formatFileSize = (bytes: number): string => { - if (bytes === 0) return '0 B'; - const k = 1024; - const sizes = ['B', 'KB', 'MB', 'GB']; - const i = Math.floor(Math.log(bytes) / Math.log(k)); - return parseFloat((bytes / Math.pow(k, i)).toFixed(2)) + ' ' + sizes[i]; - }; + const regionsetFileInputRef = useRef(null); + const fetchBedFromUrl = async (url: string): Promise => { const response = await fetch(url); @@ -58,7 +54,6 @@ export const BEDAnalytics = () => { } as unknown as Event; await handleBedFileInput(syntheticEvent, (entries) => { - setregionsetRegions(entries); setTimeout(() => { const rs = new RegionSet(entries); @@ -78,9 +73,8 @@ export const BEDAnalytics = () => { } }; - const clearAll = () => { + const unloadFile = () => { setRs(null); - setregionsetRegions(null); setTotalProcessingTime(null); setSelectedFile(null); setBedUrl(''); @@ -133,7 +127,7 @@ export const BEDAnalytics = () => { onChange={(e) => { const file = e.target.files?.[0]; if (file) { - clearAll(); + unloadFile(); setSelectedFile(file); } }} @@ -141,7 +135,7 @@ export const BEDAnalytics = () => { {selectedFile && (
Selected file: {selectedFile.name}
-
File size: {formatFileSize(selectedFile.size)}
+
File size: {bytesToSize(selectedFile.size)}
)}
@@ -155,7 +149,7 @@ export const BEDAnalytics = () => { value={bedUrl} onChange={(e) => { setBedUrl(e.target.value); - if (Rs) clearAll(); + if (rs) unloadFile(); }} /> {bedUrl && ( @@ -166,7 +160,7 @@ export const BEDAnalytics = () => {
)} - {Rs && totalProcessingTime !== null && ( + {rs && totalProcessingTime !== null && (
Total processing time: {(totalProcessingTime / 1000).toFixed(3)}s
@@ -178,7 +172,7 @@ export const BEDAnalytics = () => { disabled={ (inputMode === 'file' && !selectedFile) || (inputMode === 'url' && !bedUrl.trim()) || - Rs !== null || + rs !== null || loadingRS } className="btn btn-primary" @@ -187,9 +181,9 @@ export const BEDAnalytics = () => { Analyze RegionSet @@ -208,7 +202,7 @@ export const BEDAnalytics = () => {
)} - {Rs && !loadingRS && ( + {rs && !loadingRS && (
@@ -219,36 +213,53 @@ export const BEDAnalytics = () => { )}
- {Rs && ( + {rs && (
- + - + - + - +
Identifier{Rs.digest}{rs.digest}
Mean region width{Rs.mean_region_width}{rs.mean_region_width}
Total number of regions{Rs.total_nucleotides}{rs.total_nucleotides}
Total number of nucleotides{Rs.total_nucleotides}{rs.total_nucleotides}

Interval chromosome length statistics

- {Rs.calculate_statistics && ( - + {rs && ( + )}
+
+

Region Distribution Plot (DATA)

+ {rs && ( +
+ { + console.log('Chromosome bar clicked:', d); + }} + /> +
+ )} +
)}
From 5bdec960dd968e4af9db6dc3df51b23b42cf164a Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Fri, 24 Oct 2025 18:18:38 -0400 Subject: [PATCH 09/42] added region distribution plot --- .../bed-analytics-components/bed-plots.tsx | 25 +++++++++++-------- ui/src/pages/bed-analytics.tsx | 17 +++++++++---- 2 files changed, 26 insertions(+), 16 deletions(-) diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx index accb67ee..41f87426 100644 --- a/ui/src/components/bed-analytics-components/bed-plots.tsx +++ b/ui/src/components/bed-analytics-components/bed-plots.tsx @@ -38,6 +38,9 @@ const distributionSpec = (data: any, props: Props = {}) => { strokeWidth: 0, cursor: 'inherit', }, + bar: { + continuousBandSize: 2.5, // This controls the bar width without spacing + }, }, data: { values: transformedData, @@ -51,17 +54,17 @@ const distributionSpec = (data: any, props: Props = {}) => { labelOrient: 'right', labelPadding: 5, }, - sort: [ - 'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', - 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', - 'chr21', 'chr22', 'chrX', 'chrY', 'chrM', - ], + // sort: [ + // 'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', + // 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', + // 'chr21', 'chr22', 'chrX', 'chrY', 'chrM', + // ], title: 'Number of Regions', type: 'ordinal', }, x: { axis: { - // labelExpr: 'datum.value == 0 ? \'start\' : datum.value == 183 ? \'end\' : \'\'', + labelExpr: 'datum.value == 0 ? \'start\' : datum.value == 183 ? \'end\' : \'\'', values: [0, 300.0], }, field: 'withinGroupID', @@ -73,7 +76,7 @@ const distributionSpec = (data: any, props: Props = {}) => { }, y: { axis: { - values: [10.0, 20.0, 30.0], + values: [10.0], }, field: 'N', title: '', @@ -82,15 +85,15 @@ const distributionSpec = (data: any, props: Props = {}) => { }, height: 25, mark: { - cornerRadiusEnd: 0.5, + cornerRadiusEnd: -0.5, type: 'bar', width: 2.5, }, - width: 750, + width: 'container', }; }; -export const ChromosomeBarPlot = (props: Props) => { +export const RegionDistributionPlot = (props: Props) => { const { data, xlab, ylab, height, color, action } = props; const plotRef = useRef(null); @@ -120,4 +123,4 @@ export const ChromosomeBarPlot = (props: Props) => { ); }; -export default ChromosomeBarPlot; +export default RegionDistributionPlot; diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index bf1b06ad..8838f8b7 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -4,7 +4,7 @@ import { RegionSet } from '@databio/gtars'; import { handleBedFileInput } from '../utils.ts'; import { bytesToSize } from '../utils.ts'; import ChromosomeStatsPanel from '../components/bed-analytics-components/chromosome-stats-panel.tsx'; -import ChromosomeBarPlot from '../components/bed-analytics-components/bed-plots.tsx'; +import RegionDistributionPlot from '../components/bed-analytics-components/bed-plots.tsx'; export const BEDAnalytics = () => { @@ -244,11 +244,18 @@ export const BEDAnalytics = () => { )}
-

Region Distribution Plot (DATA)

- {rs && ( + {/*

Region Distribution Plot (DATA)

*/} + {/*{rs && (*/} + {/*
*/} + {/* 
*/}
+                  {/*      {JSON.stringify(rs.calculate_region_distribution(), null, 2)}*/}
+                  {/*
*/} + {/*
*/} + {/*)}*/} + {rs && (
- Date: Fri, 24 Oct 2025 19:03:16 -0400 Subject: [PATCH 10/42] small adjustment for region distribution plot --- .../bed-analytics-components/bed-plots.tsx | 23 +++++++++++++++---- ui/src/pages/bed-analytics.tsx | 1 - 2 files changed, 18 insertions(+), 6 deletions(-) diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx index 41f87426..44981474 100644 --- a/ui/src/components/bed-analytics-components/bed-plots.tsx +++ b/ui/src/components/bed-analytics-components/bed-plots.tsx @@ -25,12 +25,25 @@ const distributionSpec = (data: any, props: Props = {}) => { return { $schema: 'https://vega-github.io/schema/vega-lite/v6.json', + title: { + text: 'Region Distribution Plot', + fontSize: 24, + fontWeight: 'bold', + anchor: 'middle', + offset: 10, + }, config: { axis: { grid: false, }, facet: { spacing: -1, + labelFontSize: 12, + titleFontSize: 12, + }, + header: { + labelFontSize: 12, + titleFontSize: 16, }, view: { continuousHeight: 300, @@ -54,11 +67,11 @@ const distributionSpec = (data: any, props: Props = {}) => { labelOrient: 'right', labelPadding: 5, }, - // sort: [ - // 'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', - // 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', - // 'chr21', 'chr22', 'chrX', 'chrY', 'chrM', - // ], + sort: [ + 'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', + 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', + 'chr21', 'chr22', 'chrX', 'chrY', 'chrM', + ], title: 'Number of Regions', type: 'ordinal', }, diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index 8838f8b7..d3e18c43 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -244,7 +244,6 @@ export const BEDAnalytics = () => { )}
- {/*

Region Distribution Plot (DATA)

*/} {/*{rs && (*/} {/*
*/} {/* 
*/}

From 83001a0ada497bad9a2e68577bb57de6b21915fa Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Mon, 27 Oct 2025 13:08:42 -0400
Subject: [PATCH 11/42] small corrections for wasm plots

---
 .../bed-analytics-components/bed-plots.tsx    |  47 ++++----
 .../chromosome-stats-panel.tsx                | 105 +++++++++++++-----
 ui/src/pages/bed-analytics.tsx                |   2 +-
 3 files changed, 108 insertions(+), 46 deletions(-)

diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx
index 44981474..c2ce644e 100644
--- a/ui/src/components/bed-analytics-components/bed-plots.tsx
+++ b/ui/src/components/bed-analytics-components/bed-plots.tsx
@@ -1,18 +1,18 @@
 import { useEffect, useRef } from 'react';
 import embed from 'vega-embed';
 
-
 interface Props {
+  data?: any;
   xlab?: string;
   ylab?: string;
   height?: number;
-  color?: number;
-  angle?: boolean;
-  maxLength?: number;
+  color?: any;
+  maxLength?: any;
+  action?: boolean;
 }
 
 const distributionSpec = (data: any, props: Props = {}) => {
-  const { xlab = 'Label', ylab = 'Value', height = 300, color = 0, angle = false, maxLength = 15 } = props;
+  const { xlab = 'Label', ylab = 'Value', height = 1000, color = 'rgba(0, 128, 128, 0.6)', maxLength = 'container' } = props;
 
   // Transform data to match the new schema requirements
   const transformedData = data.map((item: any, index: number) => ({
@@ -46,13 +46,13 @@ const distributionSpec = (data: any, props: Props = {}) => {
         titleFontSize: 16,
       },
       view: {
-        continuousHeight: 300,
+        continuousHeight: height,
         continuousWidth: 300,
         strokeWidth: 0,
         cursor: 'inherit',
       },
       bar: {
-        continuousBandSize: 2.5, // This controls the bar width without spacing
+        continuousBandSize: 2.5,
       },
     },
     data: {
@@ -62,10 +62,10 @@ const distributionSpec = (data: any, props: Props = {}) => {
       row: {
         field: 'chr',
         header: {
-          labelAlign: 'right',
+          labelAlign: 'left',
           labelAngle: 0,
-          labelOrient: 'right',
-          labelPadding: 5,
+          labelOrient: 'left',
+          labelPadding: 10,
         },
         sort: [
           'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10',
@@ -74,6 +74,9 @@ const distributionSpec = (data: any, props: Props = {}) => {
         ],
         title: 'Number of Regions',
         type: 'ordinal',
+        color: {
+          value: color,
+        },
       },
       x: {
         axis: {
@@ -88,9 +91,7 @@ const distributionSpec = (data: any, props: Props = {}) => {
         type: 'quantitative',
       },
       y: {
-        axis: {
-          values: [10.0],
-        },
+        axis: null,
         field: 'N',
         title: '',
         type: 'quantitative',
@@ -101,21 +102,27 @@ const distributionSpec = (data: any, props: Props = {}) => {
       cornerRadiusEnd: -0.5,
       type: 'bar',
       width: 2.5,
+      color: color,
     },
-    width: 'container',
+    width: maxLength,
+    autosize: {
+      type: 'fit',
+      contains: 'padding'
+    }
   };
 };
 
 export const RegionDistributionPlot = (props: Props) => {
-  const { data, xlab, ylab, height, color, action } = props;
+  const { data, xlab, ylab, height = 1000, color, action } = props;
 
   const plotRef = useRef(null);
   const spec = distributionSpec(data, { xlab, ylab, height, color });
 
   useEffect(() => {
-    if (plotRef.current && spec) {
+    const element = plotRef.current;
+    if (element && spec) {
       try {
-        embed(plotRef.current as HTMLDivElement, spec as any, { 'actions': action })
+        embed(element, spec as any, { 'actions': action })
           .catch(error => {
             console.error('Embed error after parsing:', error);
           });
@@ -125,8 +132,8 @@ export const RegionDistributionPlot = (props: Props) => {
     }
 
     return () => {
-      if (plotRef.current) {
-        plotRef.current.innerHTML = '';
+      if (element) {
+        element.innerHTML = '';
       }
     };
   }, [spec, action]);
@@ -136,4 +143,4 @@ export const RegionDistributionPlot = (props: Props) => {
   );
 };
 
-export default RegionDistributionPlot;
+export default RegionDistributionPlot;
\ No newline at end of file
diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
index 50c3be5f..a8fb28ab 100644
--- a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
+++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
@@ -39,38 +39,93 @@ const ChromosomeStatsPanel: React.FC = ({ rs, selectedFile }) => {
 
   return (
     

-      

+      {/*This section is AI rendered. It provides statistics on number of regions per chromosome.*/}
+      

         
Number of regions per chromosome: 

-        

+        

           
             {(() => {
-              const barWidth = 36;
-              const gap = 24;
+              const barWidth = 40;
+              const gap = 30;
               const maxCount = Math.max(...statsEntries.map(s => s.count), 1);
-              const chartHeight = 100;
-              return statsEntries.map((s, i) => {
-                const x = i * (barWidth + gap) + 16;
-                const barH = Math.round((s.count / maxCount) * chartHeight);
-                const y = 20 + (chartHeight - barH);
-                return (
-                  
-                    
-                    
-                      {s.count}
-                    
-                    
-                      {s.chromosome}
-                    
-                  
-                );
-              });
+              const chartHeight = 120;
+              const chartTop = 30;
+
+              return (
+                
+                  {/* Grid lines */}
+                  {[0, 0.25, 0.5, 0.75, 1].map(ratio => (
+                    
+                      
+                      
+                        {Math.round(maxCount * ratio)}
+                      
+                    
+                  ))}
+
+                  {/* Bars */}
+                  {statsEntries.map((s, i) => {
+                    const x = i * (barWidth + gap) + 40;
+                    const barH = Math.max(2, Math.round((s.count / maxCount) * chartHeight));
+                    const y = chartTop + (chartHeight - barH);
+
+                    return (
+                      
+                        
+                        
+                          {s.count}
+                        
+                        
+                          {s.chromosome}
+                        
+                      
+                    );
+                  })}
+                
+              );
             })()}
-            
           
         

       

diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx
index d3e18c43..2845041f 100644
--- a/ui/src/pages/bed-analytics.tsx
+++ b/ui/src/pages/bed-analytics.tsx
@@ -228,7 +228,7 @@ export const BEDAnalytics = () => {
                     
                     
                       Total number of regions
-                      {rs.total_nucleotides}
+                      {rs.number_of_regions}
                     
                     
                       Total number of nucleotides

From b1fbdd1345446f505a8d7dab8076681708e5692d Mon Sep 17 00:00:00 2001
From: Nathan LeRoy 
Date: Mon, 27 Oct 2025 13:58:29 -0400
Subject: [PATCH 12/42] CSS tweaks to the chromosome distribution plot

---
 .../bed-analytics-components/bed-plots.tsx    | 55 +++++++++++--------
 .../chromosome-stats-panel.tsx                |  2 +-
 ui/src/custom.scss                            |  8 ++-
 ui/src/main.tsx                               |  1 +
 ui/src/pages/bed-analytics.tsx                |  7 ---
 ui/src/pages/metrics.tsx                      |  1 -
 6 files changed, 40 insertions(+), 34 deletions(-)

diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx
index c2ce644e..fce036c2 100644
--- a/ui/src/components/bed-analytics-components/bed-plots.tsx
+++ b/ui/src/components/bed-analytics-components/bed-plots.tsx
@@ -1,21 +1,24 @@
 import { useEffect, useRef } from 'react';
 import embed from 'vega-embed';
 
-interface Props {
-  data?: any;
-  xlab?: string;
-  ylab?: string;
-  height?: number;
-  color?: any;
-  maxLength?: any;
-  action?: boolean;
+const COLOR = 'rgba(0, 128, 128, 0.6)';
+
+type DistributionSpecDataPoint = {
+  chr: string;
+  start: number;
+  end: number;
+  n: number;
+  rid: number;
+}
+
+interface BedPlotsProps {
+  data: DistributionSpecDataPoint[];
 }
 
-const distributionSpec = (data: any, props: Props = {}) => {
-  const { xlab = 'Label', ylab = 'Value', height = 1000, color = 'rgba(0, 128, 128, 0.6)', maxLength = 'container' } = props;
+const distributionSpec = (data: DistributionSpecDataPoint[]) => {
 
   // Transform data to match the new schema requirements
-  const transformedData = data.map((item: any, index: number) => ({
+  const transformedData = data.map((item: DistributionSpecDataPoint) => ({
     chr: item.chr,
     withinGroupID: item.rid,
     N: item.n,
@@ -46,8 +49,6 @@ const distributionSpec = (data: any, props: Props = {}) => {
         titleFontSize: 16,
       },
       view: {
-        continuousHeight: height,
-        continuousWidth: 300,
         strokeWidth: 0,
         cursor: 'inherit',
       },
@@ -60,6 +61,7 @@ const distributionSpec = (data: any, props: Props = {}) => {
     },
     encoding: {
       row: {
+        title: null,
         field: 'chr',
         header: {
           labelAlign: 'left',
@@ -72,10 +74,9 @@ const distributionSpec = (data: any, props: Props = {}) => {
           'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20',
           'chr21', 'chr22', 'chrX', 'chrY', 'chrM',
         ],
-        title: 'Number of Regions',
         type: 'ordinal',
         color: {
-          value: color,
+          value: COLOR,
         },
       },
       x: {
@@ -93,7 +94,7 @@ const distributionSpec = (data: any, props: Props = {}) => {
       y: {
         axis: null,
         field: 'N',
-        title: '',
+        title: 'Chromosome',
         type: 'quantitative',
       },
     },
@@ -102,9 +103,9 @@ const distributionSpec = (data: any, props: Props = {}) => {
       cornerRadiusEnd: -0.5,
       type: 'bar',
       width: 2.5,
-      color: color,
+      color: COLOR,
     },
-    width: maxLength,
+    width: 'container',
     autosize: {
       type: 'fit',
       contains: 'padding'
@@ -112,17 +113,21 @@ const distributionSpec = (data: any, props: Props = {}) => {
   };
 };
 
-export const RegionDistributionPlot = (props: Props) => {
-  const { data, xlab, ylab, height = 1000, color, action } = props;
+export const RegionDistributionPlot = (props: BedPlotsProps) => {
+  const { data } = props;
 
   const plotRef = useRef(null);
-  const spec = distributionSpec(data, { xlab, ylab, height, color });
+  const spec = distributionSpec(data);
 
   useEffect(() => {
     const element = plotRef.current;
     if (element && spec) {
       try {
-        embed(element, spec as any, { 'actions': action })
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        embed(element, spec as any, {
+          actions: false,
+          renderer: 'svg',
+        })
           .catch(error => {
             console.error('Embed error after parsing:', error);
           });
@@ -136,10 +141,12 @@ export const RegionDistributionPlot = (props: Props) => {
         element.innerHTML = '';
       }
     };
-  }, [spec, action]);
+  }, [spec]);
 
   return (
-    

+    

+      

+    

   );
 };
 
diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
index a8fb28ab..9543fd40 100644
--- a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
+++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
@@ -2,7 +2,7 @@ import React from 'react';
 import { ChromosomeStats, RegionSet } from '@databio/gtars';
 
 interface Props {
-  Rs: RegionSet;
+  rs: RegionSet;
   selectedFile: File | null;
 }
 
diff --git a/ui/src/custom.scss b/ui/src/custom.scss
index 4c40686a..86711690 100644
--- a/ui/src/custom.scss
+++ b/ui/src/custom.scss
@@ -341,4 +341,10 @@ td {
 
 .metric-plot-height {
   height: 450px;
-}
\ No newline at end of file
+}
+
+.chrom-dist-plot-container {
+  width: 85% !important;
+  transform: translateX(-3rem) !important;
+}
+
diff --git a/ui/src/main.tsx b/ui/src/main.tsx
index 243d0b11..f906399a 100644
--- a/ui/src/main.tsx
+++ b/ui/src/main.tsx
@@ -32,6 +32,7 @@ const queryClient = new QueryClient({
     },
   },
   queryCache: new QueryCache({
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     onError: (error: any) => {
       if (error.response && error.response.status === 413) {
         toast.error(`${error.response.data.detail}`);
diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx
index 2845041f..c3783ab6 100644
--- a/ui/src/pages/bed-analytics.tsx
+++ b/ui/src/pages/bed-analytics.tsx
@@ -255,13 +255,6 @@ export const BEDAnalytics = () => {
                       

                          {
-                            console.log('Chromosome bar clicked:', d);
-                          }}
                         />
                       

                     )}
diff --git a/ui/src/pages/metrics.tsx b/ui/src/pages/metrics.tsx
index b3d2757b..fd50acc9 100644
--- a/ui/src/pages/metrics.tsx
+++ b/ui/src/pages/metrics.tsx
@@ -103,7 +103,6 @@ export const Metrics = () => {
       
     );
   }
-  ;
 
   return (
     

From 044e34defe5a4295409f28a08b98e5a67ec2f29b Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Mon, 27 Oct 2025 15:36:37 -0400
Subject: [PATCH 13/42] Updated Region Distribution plot, and wasm return
 values

---
 .../bed-analytics-components/bed-plots.tsx         |  8 ++++----
 .../chromosome-stats-panel.tsx                     | 14 +++++++-------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx
index fce036c2..58931bcb 100644
--- a/ui/src/components/bed-analytics-components/bed-plots.tsx
+++ b/ui/src/components/bed-analytics-components/bed-plots.tsx
@@ -108,8 +108,8 @@ const distributionSpec = (data: DistributionSpecDataPoint[]) => {
     width: 'container',
     autosize: {
       type: 'fit',
-      contains: 'padding'
-    }
+      contains: 'padding',
+    },
   };
 };
 
@@ -125,7 +125,7 @@ export const RegionDistributionPlot = (props: BedPlotsProps) => {
       try {
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
         embed(element, spec as any, {
-          actions: false,
+          actions: { export: true, source: false, compiled: false },
           renderer: 'svg',
         })
           .catch(error => {
@@ -144,7 +144,7 @@ export const RegionDistributionPlot = (props: BedPlotsProps) => {
   }, [spec]);
 
   return (
-    

+    

       

     

   );
diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
index 9543fd40..54e20e00 100644
--- a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
+++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
@@ -15,13 +15,13 @@ const ChromosomeStatsPanel: React.FC = ({ rs, selectedFile }) => {
       const cs = stats as ChromosomeStats;
       const row = {
         chromosome: String(chrom),
-        count: cs.count,
-        minimum: cs.minimum,
-        maximum: cs.maximum,
-        mean: cs.mean.toFixed(2),
-        median: cs.median.toFixed(2),
-        start: cs.start,
-        end: cs.end,
+        count: cs.number_of_regions,
+        minimum: cs.minimum_region_length,
+        maximum: cs.maximum_region_length,
+        mean: cs.mean_region_length.toFixed(2),
+        median: cs.median_region_length.toFixed(2),
+        start: cs.start_nucleotide_position,
+        end: cs.end_nucleotide_position,
       };
       try {
         (cs as unknown as { free?: () => void }).free?.();

From 8af4f882c39fca654175989042a1abbd41d6ca7a Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Mon, 27 Oct 2025 16:19:57 -0400
Subject: [PATCH 14/42] More improvements in bed analyzer

---
 .../bed-analytics-components/bed-plots.tsx    | 14 ++--
 .../chromosome-stats-panel.tsx                | 18 ++---
 ui/src/pages/bed-analytics.tsx                | 69 ++++++++++++++-----
 3 files changed, 67 insertions(+), 34 deletions(-)

diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx
index 58931bcb..782bf799 100644
--- a/ui/src/components/bed-analytics-components/bed-plots.tsx
+++ b/ui/src/components/bed-analytics-components/bed-plots.tsx
@@ -1,7 +1,7 @@
 import { useEffect, useRef } from 'react';
 import embed from 'vega-embed';
 
-const COLOR = 'rgba(0, 128, 128, 0.6)';
+const COLOR = 'rgba(0, 128, 128, 1)';
 
 type DistributionSpecDataPoint = {
   chr: string;
@@ -37,7 +37,7 @@ const distributionSpec = (data: DistributionSpecDataPoint[]) => {
     },
     config: {
       axis: {
-        grid: false,
+        grid: true,
       },
       facet: {
         spacing: -1,
@@ -61,12 +61,12 @@ const distributionSpec = (data: DistributionSpecDataPoint[]) => {
     },
     encoding: {
       row: {
-        title: null,
+        title: "Chromosome",
         field: 'chr',
         header: {
-          labelAlign: 'left',
+          labelAlign: 'right',
           labelAngle: 0,
-          labelOrient: 'left',
+          labelOrient: 'right',
           labelPadding: 10,
         },
         sort: [
@@ -144,8 +144,8 @@ export const RegionDistributionPlot = (props: BedPlotsProps) => {
   }, [spec]);
 
   return (
-    

-      

+    

+      

     

   );
 };
diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
index 54e20e00..9b5b4e18 100644
--- a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
+++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
@@ -138,7 +138,7 @@ const ChromosomeStatsPanel: React.FC = ({ rs, selectedFile }) => {
               

                 

                   {rs && (
+                    // 

+                    //   
Region Distribution Data

+                    //   
+                    //     {JSON.stringify(rs.calculateRegionDistribution(300), null, 2)}
+                    //   

+                    // 

                     

                       
                     

                   )}

From 2c19557c91389181d97abcc73521dd6e8340b9ab Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 4 Nov 2025 14:37:33 -0500
Subject: [PATCH 19/42] updated ui dependencies

---
 ui/package-lock.json | 4 ++--
 ui/package.json      | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/ui/package-lock.json b/ui/package-lock.json
index b80b72b1..0ce60290 100644
--- a/ui/package-lock.json
+++ b/ui/package-lock.json
@@ -8,7 +8,7 @@
       "name": "bedhost-ui-2",
       "version": "0.0.0",
       "dependencies": {
-        "@databio/gtars": "file:../../gtars/gtars-wasm/pkg",
+        "@databio/gtars": "^0.5.2",
         "@tanstack/react-query": "^5.28.0",
         "@tanstack/react-query-devtools": "^5.28.0",
         "@tanstack/react-table": "^8.15.3",
@@ -56,7 +56,7 @@
     },
     "../../gtars/gtars-wasm/pkg": {
       "name": "@databio/gtars",
-      "version": "0.5.1"
+      "version": "0.5.2"
     },
     "node_modules/@babel/code-frame": {
       "version": "7.27.1",
diff --git a/ui/package.json b/ui/package.json
index 78ba8c5f..0d73b9d5 100644
--- a/ui/package.json
+++ b/ui/package.json
@@ -12,7 +12,7 @@
     "generate-types-local": "npx openapi-typescript http://localhost:8000/openapi.json -o bedbase-types.d.ts"
   },
   "dependencies": {
-    "@databio/gtars": "file:../../gtars/gtars-wasm/pkg",
+    "@databio/gtars": "^0.5.2",
     "@tanstack/react-query": "^5.28.0",
     "@tanstack/react-query-devtools": "^5.28.0",
     "@tanstack/react-table": "^8.15.3",

From 343eef0b26b7e773adc97f3ec09a903b9aef272f Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 4 Nov 2025 14:42:03 -0500
Subject: [PATCH 20/42] updated ui dependencies and fixed errors

---
 ui/package-lock.json                                |  7 +++++++
 ui/package.json                                     |  1 +
 .../bed-analytics-components/bed-plots.tsx          |  7 +++----
 .../chromosome-stats-panel.tsx                      | 13 ++++---------
 4 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/ui/package-lock.json b/ui/package-lock.json
index 0ce60290..634059e1 100644
--- a/ui/package-lock.json
+++ b/ui/package-lock.json
@@ -12,6 +12,7 @@
         "@tanstack/react-query": "^5.28.0",
         "@tanstack/react-query-devtools": "^5.28.0",
         "@tanstack/react-table": "^8.15.3",
+        "@types/pako": "^2.0.4",
         "@uidotdev/usehooks": "^2.4.1",
         "axios": "^1.8.2",
         "bootstrap": "^5.3.3",
@@ -2154,6 +2155,12 @@
         "undici-types": "~6.21.0"
       }
     },
+    "node_modules/@types/pako": {
+      "version": "2.0.4",
+      "resolved": "https://registry.npmjs.org/@types/pako/-/pako-2.0.4.tgz",
+      "integrity": "sha512-VWDCbrLeVXJM9fihYodcLiIv0ku+AlOa/TQ1SvYOaBuyrSKgEcro95LJyIsJ4vSo6BXIxOKxiJAat04CmST9Fw==",
+      "license": "MIT"
+    },
     "node_modules/@types/prop-types": {
       "version": "15.7.15",
       "resolved": "https://registry.npmjs.org/@types/prop-types/-/prop-types-15.7.15.tgz",
diff --git a/ui/package.json b/ui/package.json
index 0d73b9d5..351c60d4 100644
--- a/ui/package.json
+++ b/ui/package.json
@@ -16,6 +16,7 @@
     "@tanstack/react-query": "^5.28.0",
     "@tanstack/react-query-devtools": "^5.28.0",
     "@tanstack/react-table": "^8.15.3",
+    "@types/pako": "^2.0.4",
     "@uidotdev/usehooks": "^2.4.1",
     "axios": "^1.8.2",
     "bootstrap": "^5.3.3",
diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx
index 70a0f3c3..5ca1d135 100644
--- a/ui/src/components/bed-analytics-components/bed-plots.tsx
+++ b/ui/src/components/bed-analytics-components/bed-plots.tsx
@@ -9,7 +9,7 @@ type DistributionSpecDataPoint = {
   end: number;
   n: number;
   rid: number;
-  
+
 }
 
 interface BedPlotsProps {
@@ -19,14 +19,13 @@ interface BedPlotsProps {
 const distributionSpec = (data: DistributionSpecDataPoint[]) => {
 
   // Transform data to match the new schema requirements
-  const transformedData = data.map((item: DistributionSpecDataPoint, i: number) => ({
+  const transformedData = data.map((item: DistributionSpecDataPoint) => ({
     chr: item.chr,
     withinGroupID: item.rid,
     N: item.n,
     start: item.start,
     end: item.end,
   }));
-
   return {
     $schema: 'https://vega-github.io/schema/vega-lite/v6.json',
     title: {
@@ -62,7 +61,7 @@ const distributionSpec = (data: DistributionSpecDataPoint[]) => {
     },
     encoding: {
       row: {
-        title: "Chromosome",
+        title: 'Chromosome',
         field: 'chr',
         header: {
           labelAlign: 'right',
diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
index 72e64cf2..26d22cc0 100644
--- a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
+++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
@@ -11,7 +11,8 @@ const ChromosomeStatsPanel: React.FC = ({ rs, selectedFile }) => {
   if (!calc) return null;
 
   const statsEntries = Array.from(calc.entries())
-    .map(([chrom, stats]: [unknown, ChromosomeStatistics]) => {
+    .map((entry) => {
+      const [chrom, stats] = entry as [unknown, ChromosomeStatistics];
       const cs = stats as ChromosomeStatistics;
       const row = {
         chromosome: String(chrom),
@@ -29,20 +30,14 @@ const ChromosomeStatsPanel: React.FC = ({ rs, selectedFile }) => {
         /* ignore */
       }
       return row;
-    })
-    .sort((a, b) =>
-      a.chromosome.localeCompare(b.chromosome, undefined, {
-        numeric: true,
-        sensitivity: 'base',
-      }),
-    );
+    });
 
   return (
     

       {/*This section is AI rendered. It provides statistics on number of regions per chromosome.*/}
       

         
Number of regions per chromosome: 

-        

+        

           
Date: Tue, 4 Nov 2025 15:11:53 -0500
Subject: [PATCH 21/42] Updated ui lock

---
 ui/package-lock.json | 7704 ------------------------------------------
 1 file changed, 7704 deletions(-)
 delete mode 100644 ui/package-lock.json

diff --git a/ui/package-lock.json b/ui/package-lock.json
deleted file mode 100644
index 634059e1..00000000
--- a/ui/package-lock.json
+++ /dev/null
@@ -1,7704 +0,0 @@
-{
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-  "version": "0.0.0",
-  "lockfileVersion": 3,
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From 846320319088d1c7ba5bfb8ff93be2f690090c2d Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 4 Nov 2025 16:06:42 -0500
Subject: [PATCH 22/42] added gtars init

---
 ui/src/main.tsx | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/ui/src/main.tsx b/ui/src/main.tsx
index f906399a..7f8dfe27 100644
--- a/ui/src/main.tsx
+++ b/ui/src/main.tsx
@@ -10,6 +10,7 @@ import { Home } from './pages/home.tsx';
 import { Metrics } from './pages/metrics.tsx';
 import { UMAPGraph } from './pages/visualization.tsx';
 import { BEDAnalytics } from './pages/bed-analytics.tsx';
+import { init } from '@databio/gtars'
 import { HelmetProvider } from 'react-helmet-async';
 
 // css stuff
@@ -87,6 +88,9 @@ const router = createBrowserRouter([
   },
 ]);
 
+// initialize gtars:
+init();
+
 // entry point
 ReactDOM.createRoot(document.getElementById('root')!).render(
   

From a66aa7b6966eeabc68c6598f67790669ac68f487 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 4 Nov 2025 17:26:19 -0500
Subject: [PATCH 23/42] fixing wasm

---
 ui/src/main.tsx | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/ui/src/main.tsx b/ui/src/main.tsx
index 7f8dfe27..7b56ddc5 100644
--- a/ui/src/main.tsx
+++ b/ui/src/main.tsx
@@ -10,7 +10,7 @@ import { Home } from './pages/home.tsx';
 import { Metrics } from './pages/metrics.tsx';
 import { UMAPGraph } from './pages/visualization.tsx';
 import { BEDAnalytics } from './pages/bed-analytics.tsx';
-import { init } from '@databio/gtars'
+import init from '@databio/gtars';
 import { HelmetProvider } from 'react-helmet-async';
 
 // css stuff
@@ -37,14 +37,16 @@ const queryClient = new QueryClient({
     onError: (error: any) => {
       if (error.response && error.response.status === 413) {
         toast.error(`${error.response.data.detail}`);
-      return;}
+        return;
+      }
       if (error.response && error.response.status === 415) {
         toast.error(`${error.response.data.detail}`);
-      return;}
+        return;
+      }
       //
       // console.error(error);
       // toast.error(`Something went wrong: ${error.message}`);
-    }
+    },
   }),
 });
 

From 3730ad5ab22a028b56e47bcad9365b57394fa47b Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 11 Nov 2025 11:30:41 -0500
Subject: [PATCH 24/42] Added umap endpoint

---
 bedhost/routers/bed_api.py                 | 25 ++++++++++++++++++++++
 deployment/config/api-dev.bedbase.org.yaml |  1 +
 requirements/requirements-all.txt          |  4 ++--
 3 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/bedhost/routers/bed_api.py b/bedhost/routers/bed_api.py
index ce885a2d..96a889b3 100644
--- a/bedhost/routers/bed_api.py
+++ b/bedhost/routers/bed_api.py
@@ -261,6 +261,31 @@ async def embed_bed_file(
             embedding = bbagent.bed._embed_file(region_set)
     return embedding.tolist()[0]
 
+@router.post(
+    "/umap",
+    summary="Get embeddings for a bed file.",
+    response_model=List[float],
+)
+async def embed_bed_file(
+    file: UploadFile = File(None),
+):
+    """
+    Create embedding for bed file
+    """
+    _LOGGER.info("Embedding file..")
+
+    if file is not None:
+        with tempfile.TemporaryDirectory() as dirpath:
+            file_path = os.path.join(dirpath, file.filename)
+
+            with open(file_path, "wb") as bed_file:
+                shutil.copyfileobj(file.file, bed_file)
+
+            region_set = RegionSet(file_path)
+
+            embedding = bbagent.bed._get_umap_file(region_set)
+    return embedding.tolist()[0]
+
 
 @router.get(
     "/missing_plots",
diff --git a/deployment/config/api-dev.bedbase.org.yaml b/deployment/config/api-dev.bedbase.org.yaml
index f3bba70e..ab3ab944 100644
--- a/deployment/config/api-dev.bedbase.org.yaml
+++ b/deployment/config/api-dev.bedbase.org.yaml
@@ -4,6 +4,7 @@ path:
   # region2vec: databio/r2v-pretrained-for-search
   region2vec: databio/r2v-encode-hg38
   vec2vec: 'databio/v2v-sentencetransformers-encode'
+  umap_model: "https://github.com/databio/bedbase-loader/raw/refs/heads/master/umap/hg38_umap_umap_model.joblib"
 database:
   host: $POSTGRES_HOST
   port: 5432
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index 580bd04f..cba08d95 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -1,5 +1,5 @@
-# bbconf @ git+https://github.com/databio/bbconf.git@comp_search#egg=bbconf
-bbconf>=0.12.0
+bbconf @ git+https://github.com/databio/bbconf.git@umap#egg=bbconf
+# bbconf>=0.12.0
 fastapi>=0.103.0
 logmuse>=0.2.7
 markdown

From 3d9367af5c12a8e0d73813955528edd666348632 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 11 Nov 2025 11:32:21 -0500
Subject: [PATCH 25/42] linting

---
 bedhost/routers/bed_api.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bedhost/routers/bed_api.py b/bedhost/routers/bed_api.py
index 96a889b3..5cbd9b5a 100644
--- a/bedhost/routers/bed_api.py
+++ b/bedhost/routers/bed_api.py
@@ -261,6 +261,7 @@ async def embed_bed_file(
             embedding = bbagent.bed._embed_file(region_set)
     return embedding.tolist()[0]
 
+
 @router.post(
     "/umap",
     summary="Get embeddings for a bed file.",

From 23e00a41d4854f7f8ed60b5a15fd9b6638a6fba1 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 11 Nov 2025 16:10:22 -0500
Subject: [PATCH 26/42] fixed test query parameter for multiple endpoints

---
 bedhost/helpers.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/bedhost/helpers.py b/bedhost/helpers.py
index eaf9b015..7d8e44d2 100644
--- a/bedhost/helpers.py
+++ b/bedhost/helpers.py
@@ -81,12 +81,10 @@ def drs_response(status_code, msg):
     return JSONResponse(status_code=status_code, content=content)
 
 
-test_query_parameter = (
-    Query(
-        False,
-        description="Internal parameter for testing purposes. If true, the request will not be counted.",
-        include_in_schema=False,
-    ),
+test_query_parameter = Query(
+    False,
+    description="Internal parameter for testing purposes. If true, the request will not be counted.",
+    include_in_schema=False,
 )
 
 

From 4faf3e6524e0f8dfbdca75f692f2b24b92cf71a6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 13 Nov 2025 22:33:37 +0000
Subject: [PATCH 27/42] Bump vega-interpreter from 2.0.0 to 2.2.1 in /ui

Bumps [vega-interpreter](https://github.com/vega/vega) from 2.0.0 to 2.2.1.
- [Release notes](https://github.com/vega/vega/releases)
- [Commits](https://github.com/vega/vega/compare/v2.0.0...v2.2.1)

---
updated-dependencies:
- dependency-name: vega-interpreter
  dependency-version: 2.2.1
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] 
---
 ui/package-lock.json | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/ui/package-lock.json b/ui/package-lock.json
index 463ba7ef..e671fd54 100644
--- a/ui/package-lock.json
+++ b/ui/package-lock.json
@@ -5660,13 +5660,20 @@
       }
     },
     "node_modules/vega-interpreter": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/vega-interpreter/-/vega-interpreter-2.0.0.tgz",
-      "integrity": "sha512-ZjA7AC+xjfi4k9vgA49N5F/bS4fzf9E1KC0ljey4uMgHbmtKR53BWyOOzxHk+btfS9bEJ5gUvuoZzfqG3wIWEg==",
+      "version": "2.2.1",
+      "resolved": "https://registry.npmjs.org/vega-interpreter/-/vega-interpreter-2.2.1.tgz",
+      "integrity": "sha512-o+4ZEme2mdFLewlpF76dwPWW2VkZ3TAF3DMcq75/NzA5KPvnN4wnlCM8At2FVawbaHRyGdVkJSS5ROF5KwpHPQ==",
+      "license": "BSD-3-Clause",
       "dependencies": {
-        "vega-util": "^2.0.0"
+        "vega-util": "^2.1.0"
       }
     },
+    "node_modules/vega-interpreter/node_modules/vega-util": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/vega-util/-/vega-util-2.1.0.tgz",
+      "integrity": "sha512-PGfp0m0QCufDmcxKJCWQy4Ov23FoF8DSXmoJwSezi3itQaa2hbxK0+xwsTMP2vy4PR16Pu25HMzgMwXVW1+33w==",
+      "license": "BSD-3-Clause"
+    },
     "node_modules/vega-label": {
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/vega-label/-/vega-label-2.0.0.tgz",

From fa15ea282f9a1779d7ccb1fb47c4a67db9ca737b Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 13 Nov 2025 22:33:50 +0000
Subject: [PATCH 28/42] Bump vega-expression, vega and vega-lite in /ui

Bumps [vega-expression](https://github.com/vega/vega), [vega](https://github.com/vega/vega) and [vega-lite](https://github.com/vega/vega-lite). These dependencies needed to be updated together.

Updates `vega-expression` from 6.0.0 to 6.1.0
- [Release notes](https://github.com/vega/vega/releases)
- [Commits](https://github.com/vega/vega/compare/v6.0.0...v6.1.0)

Updates `vega` from 6.1.2 to 6.2.0
- [Release notes](https://github.com/vega/vega/releases)
- [Commits](https://github.com/vega/vega/compare/v6.1.2...v6.2.0)

Updates `vega-lite` from 6.2.0 to 6.4.1
- [Release notes](https://github.com/vega/vega-lite/releases)
- [Changelog](https://github.com/vega/vega-lite/blob/main/CHANGELOG.md)
- [Commits](https://github.com/vega/vega-lite/compare/v6.2.0...v6.4.1)

---
updated-dependencies:
- dependency-name: vega-expression
  dependency-version: 6.1.0
  dependency-type: indirect
- dependency-name: vega
  dependency-version: 6.2.0
  dependency-type: indirect
- dependency-name: vega-lite
  dependency-version: 6.4.1
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] 
---
 ui/package-lock.json | 502 ++++++++++++++++++++-----------------------
 1 file changed, 232 insertions(+), 270 deletions(-)

diff --git a/ui/package-lock.json b/ui/package-lock.json
index 463ba7ef..d29c4db9 100644
--- a/ui/package-lock.json
+++ b/ui/package-lock.json
@@ -885,6 +885,7 @@
       "version": "7946.0.16",
       "resolved": "https://registry.npmjs.org/@types/geojson/-/geojson-7946.0.16.tgz",
       "integrity": "sha512-6C8nqWur3j98U6+lXDfTUWIfgvZU+EumvpHKcYjujKH7woYyLj2sUmff0tRhrqM7BohUw7Pz3ZB1jj2gW9Fvmg==",
+      "license": "MIT",
       "peer": true
     },
     "node_modules/@types/hast": {
@@ -1676,6 +1677,7 @@
       "version": "7.2.0",
       "resolved": "https://registry.npmjs.org/commander/-/commander-7.2.0.tgz",
       "integrity": "sha512-QrWXB+ZQSVPmIWIhtEO9H+gwHaMGYiF5ChvoJ+K9ZGHG/sVsa6yiesAD1GC/x46sET00Xlwo1u49RVVVzvcSkw==",
+      "license": "MIT",
       "peer": true,
       "engines": {
         "node": ">= 10"
@@ -1750,6 +1752,7 @@
       "version": "6.0.4",
       "resolved": "https://registry.npmjs.org/d3-delaunay/-/d3-delaunay-6.0.4.tgz",
       "integrity": "sha512-mdjtIZ1XLAM8bm/hx3WwjfHt6Sggek7qH043O8KEjDXN40xi3vx/6pYSVTwLjEgiXQTbvaouWKynLBiUZ6SK6A==",
+      "license": "ISC",
       "peer": true,
       "dependencies": {
         "delaunator": "5"
@@ -1770,6 +1773,7 @@
       "version": "3.0.1",
       "resolved": "https://registry.npmjs.org/d3-dsv/-/d3-dsv-3.0.1.tgz",
       "integrity": "sha512-UG6OvdI5afDIFP9w4G0mNq50dSOsXHJaRE8arAS5o9ApWnIElp8GZw1Dun8vP8OyHOZ/QJUKUJwxiiCCnUwm+Q==",
+      "license": "ISC",
       "peer": true,
       "dependencies": {
         "commander": "7",
@@ -1795,6 +1799,7 @@
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/d3-force/-/d3-force-3.0.0.tgz",
       "integrity": "sha512-zxV/SsA+U4yte8051P4ECydjD/S+qeYtnaIyAs9tgHCqfguma/aAQDjo85A9Z6EKhBirHRJHXIgJUlffT4wdLg==",
+      "license": "ISC",
       "peer": true,
       "dependencies": {
         "d3-dispatch": "1 - 3",
@@ -1832,6 +1837,7 @@
       "version": "3.1.1",
       "resolved": "https://registry.npmjs.org/d3-geo/-/d3-geo-3.1.1.tgz",
       "integrity": "sha512-637ln3gXKXOwhalDzinUgY83KzNWZRKbYubaG+fGVuc/dxO64RRljtCTnf5ecMyE1RIdtqpkVcq0IbtU2S8j2Q==",
+      "license": "ISC",
       "peer": true,
       "dependencies": {
         "d3-array": "2.5.0 - 3"
@@ -1844,6 +1850,7 @@
       "version": "4.0.0",
       "resolved": "https://registry.npmjs.org/d3-geo-projection/-/d3-geo-projection-4.0.0.tgz",
       "integrity": "sha512-p0bK60CEzph1iqmnxut7d/1kyTmm3UWtPlwdkM31AU+LW+BXazd5zJdoCn7VFxNCHXRngPHRnsNn5uGjLRGndg==",
+      "license": "ISC",
       "peer": true,
       "dependencies": {
         "commander": "7",
@@ -1865,6 +1872,7 @@
       "version": "3.1.2",
       "resolved": "https://registry.npmjs.org/d3-hierarchy/-/d3-hierarchy-3.1.2.tgz",
       "integrity": "sha512-FX/9frcub54beBdugHjDCdikxThEqjnR93Qt7PvQTOHxyiNCAlvMrHhclk3cD5VeAaq9fxmfRp+CnWw9rEMBuA==",
+      "license": "ISC",
       "peer": true,
       "engines": {
         "node": ">=12"
@@ -1890,6 +1898,7 @@
       "version": "3.1.0",
       "resolved": "https://registry.npmjs.org/d3-path/-/d3-path-3.1.0.tgz",
       "integrity": "sha512-p3KP5HCf/bvjBSSKuXid6Zqijx7wIfNW+J/maPs+iwR35at5JCbLUT0LzF1cnjbCHWhqzQTIN2Jpe8pRebIEFQ==",
+      "license": "ISC",
       "peer": true,
       "engines": {
         "node": ">=12"
@@ -1942,6 +1951,7 @@
       "version": "3.2.0",
       "resolved": "https://registry.npmjs.org/d3-shape/-/d3-shape-3.2.0.tgz",
       "integrity": "sha512-SaLBuwGm3MOViRq2ABk3eLoxwZELpH6zhl3FbAoJ7Vm1gofKx6El1Ib5z23NUEhF9AsGl7y+dzLe5Cw2AArGTA==",
+      "license": "ISC",
       "peer": true,
       "dependencies": {
         "d3-path": "^3.1.0"
@@ -1991,15 +2001,6 @@
         "node": ">=12"
       }
     },
-    "node_modules/data-uri-to-buffer": {
-      "version": "4.0.1",
-      "resolved": "https://registry.npmjs.org/data-uri-to-buffer/-/data-uri-to-buffer-4.0.1.tgz",
-      "integrity": "sha512-0R9ikRb668HB7QDxT1vkpuUBtqc53YyAwMwGeUFKRojY/NWKvdZ+9UYtRfGmhqNbRkTSVpMbmyhXipFFv2cb/A==",
-      "peer": true,
-      "engines": {
-        "node": ">= 12"
-      }
-    },
     "node_modules/debug": {
       "version": "4.3.4",
       "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.4.tgz",
@@ -2038,6 +2039,7 @@
       "version": "5.0.1",
       "resolved": "https://registry.npmjs.org/delaunator/-/delaunator-5.0.1.tgz",
       "integrity": "sha512-8nvh+XBe96aCESrGOqMp/84b13H9cdKbG5P2ejQCh4d4sK9RL4371qou9drQjMhvnPmhWl5hnmqbEE0fXr9Xnw==",
+      "license": "ISC",
       "peer": true,
       "dependencies": {
         "robust-predicates": "^3.0.2"
@@ -2583,29 +2585,6 @@
         "reusify": "^1.0.4"
       }
     },
-    "node_modules/fetch-blob": {
-      "version": "3.2.0",
-      "resolved": "https://registry.npmjs.org/fetch-blob/-/fetch-blob-3.2.0.tgz",
-      "integrity": "sha512-7yAQpD2UMJzLi1Dqv7qFYnPbaPx7ZfFK6PiIxQ4PfkGPyNyl2Ugx+a/umUonmKqjhM4DnfbMvdX6otXq83soQQ==",
-      "funding": [
-        {
-          "type": "github",
-          "url": "https://github.com/sponsors/jimmywarting"
-        },
-        {
-          "type": "paypal",
-          "url": "https://paypal.me/jimmywarting"
-        }
-      ],
-      "peer": true,
-      "dependencies": {
-        "node-domexception": "^1.0.0",
-        "web-streams-polyfill": "^3.0.3"
-      },
-      "engines": {
-        "node": "^12.20 || >= 14.13"
-      }
-    },
     "node_modules/file-entry-cache": {
       "version": "6.0.1",
       "resolved": "https://registry.npmjs.org/file-entry-cache/-/file-entry-cache-6.0.1.tgz",
@@ -2725,18 +2704,6 @@
         "node": ">= 6"
       }
     },
-    "node_modules/formdata-polyfill": {
-      "version": "4.0.10",
-      "resolved": "https://registry.npmjs.org/formdata-polyfill/-/formdata-polyfill-4.0.10.tgz",
-      "integrity": "sha512-buewHzMvYL29jdeQTVILecSaZKnt/RJWjoZCF5OW60Z67/GmSLBkOFM7qh1PI3zFNtJbaZL5eQu1vLfazOwj4g==",
-      "peer": true,
-      "dependencies": {
-        "fetch-blob": "^3.1.2"
-      },
-      "engines": {
-        "node": ">=12.20.0"
-      }
-    },
     "node_modules/framer-motion": {
       "version": "11.0.20",
       "resolved": "https://registry.npmjs.org/framer-motion/-/framer-motion-11.0.20.tgz",
@@ -3093,6 +3060,7 @@
       "version": "0.6.3",
       "resolved": "https://registry.npmjs.org/iconv-lite/-/iconv-lite-0.6.3.tgz",
       "integrity": "sha512-4fCk79wshMdzMp2rH06qWrJE4iolqLhCUH+OiuIgU++RB0+94NlDL81atO7GX55uUKueo0txHNtvEyI6D7WdMw==",
+      "license": "MIT",
       "peer": true,
       "dependencies": {
         "safer-buffer": ">= 2.1.2 < 3.0.0"
@@ -4158,44 +4126,6 @@
       "resolved": "https://registry.npmjs.org/ngraph.random/-/ngraph.random-1.2.0.tgz",
       "integrity": "sha512-4EUeAGbB2HWX9njd6bP6tciN6ByJfoaAvmVL9QTaZSeXrW46eNGA9GajiXiPBbvFqxUWFkEbyo6x5qsACUuVfA=="
     },
-    "node_modules/node-domexception": {
-      "version": "1.0.0",
-      "resolved": "https://registry.npmjs.org/node-domexception/-/node-domexception-1.0.0.tgz",
-      "integrity": "sha512-/jKZoMpw0F8GRwl4/eLROPA3cfcXtLApP0QzLmUT/HuPCZWyB7IY9ZrMeKw2O/nFIqPQB3PVM9aYm0F312AXDQ==",
-      "deprecated": "Use your platform's native DOMException instead",
-      "funding": [
-        {
-          "type": "github",
-          "url": "https://github.com/sponsors/jimmywarting"
-        },
-        {
-          "type": "github",
-          "url": "https://paypal.me/jimmywarting"
-        }
-      ],
-      "peer": true,
-      "engines": {
-        "node": ">=10.5.0"
-      }
-    },
-    "node_modules/node-fetch": {
-      "version": "3.3.2",
-      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-3.3.2.tgz",
-      "integrity": "sha512-dRB78srN/l6gqWulah9SrxeYnxeddIG30+GOqK/9OlLVyLg3HPnr6SqOWTWOXKRwC2eGYCkZ59NNuSgvSrpgOA==",
-      "peer": true,
-      "dependencies": {
-        "data-uri-to-buffer": "^4.0.0",
-        "fetch-blob": "^3.1.4",
-        "formdata-polyfill": "^4.0.10"
-      },
-      "engines": {
-        "node": "^12.20.0 || ^14.13.1 || >=16.0.0"
-      },
-      "funding": {
-        "type": "opencollective",
-        "url": "https://opencollective.com/node-fetch"
-      }
-    },
     "node_modules/node-releases": {
       "version": "2.0.19",
       "resolved": "https://registry.npmjs.org/node-releases/-/node-releases-2.0.19.tgz",
@@ -4832,6 +4762,7 @@
       "version": "3.0.2",
       "resolved": "https://registry.npmjs.org/robust-predicates/-/robust-predicates-3.0.2.tgz",
       "integrity": "sha512-IXgzBWvWQwE6PrDI05OvmXUIruQTcoMDzRsOd5CDvHCVLcLHMTSYvOK5Cm46kWqlV3yAbuSpBZdJ5oP5OUoStg==",
+      "license": "Unlicense",
       "peer": true
     },
     "node_modules/rollup": {
@@ -4901,12 +4832,14 @@
       "version": "1.3.3",
       "resolved": "https://registry.npmjs.org/rw/-/rw-1.3.3.tgz",
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+      "version": "6.1.0",
+      "resolved": "https://registry.npmjs.org/vega-selections/-/vega-selections-6.1.0.tgz",
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+      "license": "BSD-3-Clause",
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       "dependencies": {
         "d3-array": "3.2.4",
-        "vega-expression": "^6.0.0",
-        "vega-util": "^2.0.0"
+        "vega-expression": "^6.1.0",
+        "vega-util": "^2.1.0"
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     },
     "node_modules/vega-statistics": {
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@@ -5833,14 +5796,15 @@
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+      "version": "3.1.0",
+      "resolved": "https://registry.npmjs.org/vega-time/-/vega-time-3.1.0.tgz",
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-        "vega-util": "^2.0.0"
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     "node_modules/vega-tooltip": {
@@ -5855,84 +5819,91 @@
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+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/vega-transforms/-/vega-transforms-5.1.0.tgz",
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+      "license": "BSD-3-Clause",
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         "d3-array": "^3.2.4",
-        "vega-dataflow": "^6.0.0",
+        "vega-dataflow": "^6.1.0",
         "vega-statistics": "^2.0.0",
-        "vega-time": "^3.0.0",
-        "vega-util": "^2.0.0"
+        "vega-time": "^3.1.0",
+        "vega-util": "^2.1.0"
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     "node_modules/vega-typings": {
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-        "vega-scenegraph": "^5.0.0",
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-        "vega-dataflow": "^6.0.0",
-        "vega-scenegraph": "^5.0.0",
-        "vega-util": "^2.0.0"
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+        "vega-scenegraph": "^5.1.0",
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     "node_modules/vega-voronoi": {
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-      "resolved": "https://registry.npmjs.org/vega-voronoi/-/vega-voronoi-5.0.0.tgz",
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+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/vega-voronoi/-/vega-voronoi-5.1.0.tgz",
+      "integrity": "sha512-uKdsoR9x60mz7eYtVG+NhlkdQXeVdMr6jHNAHxs+W+i6kawkUp5S9jp1xf1FmW/uZvtO1eqinHQNwATcDRsiUg==",
+      "license": "BSD-3-Clause",
       "peer": true,
       "dependencies": {
         "d3-delaunay": "^6.0.4",
-        "vega-dataflow": "^6.0.0",
-        "vega-util": "^2.0.0"
+        "vega-dataflow": "^6.1.0",
+        "vega-util": "^2.1.0"
       }
     },
     "node_modules/vega-wordcloud": {
-      "version": "5.0.0",
-      "resolved": "https://registry.npmjs.org/vega-wordcloud/-/vega-wordcloud-5.0.0.tgz",
-      "integrity": "sha512-Rm46D1ginGdunWLtsiymllU5RvJTEtpKRaWcc/pABpFiz7QHGGrZ9FhOczxW1o3n89h07gzc9n8xlWYco06Fdw==",
+      "version": "5.1.0",
+      "resolved": "https://registry.npmjs.org/vega-wordcloud/-/vega-wordcloud-5.1.0.tgz",
+      "integrity": "sha512-sSdNmT8y2D7xXhM2h76dKyaYn3PA4eV49WUUkfYfqHz/vpcu10GSAoFxLhQQTkbZXR+q5ZB63tFUow9W2IFo6g==",
+      "license": "BSD-3-Clause",
       "peer": true,
       "dependencies": {
         "vega-canvas": "^2.0.0",
-        "vega-dataflow": "^6.0.0",
-        "vega-scale": "^8.0.0",
+        "vega-dataflow": "^6.1.0",
+        "vega-scale": "^8.1.0",
         "vega-statistics": "^2.0.0",
-        "vega-util": "^2.0.0"
+        "vega-util": "^2.1.0"
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     },
     "node_modules/vfile": {
@@ -6072,15 +6043,6 @@
         "loose-envify": "^1.0.0"
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-    "node_modules/web-streams-polyfill": {
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-      "resolved": "https://registry.npmjs.org/web-streams-polyfill/-/web-streams-polyfill-3.3.3.tgz",
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-      "peer": true,
-      "engines": {
-        "node": ">= 8"
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-    },
     "node_modules/which": {
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       "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",

From 3b1c57e92bed1e8db38ea68af7774f7547c7b68f Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Fri, 14 Nov 2025 14:27:28 -0500
Subject: [PATCH 29/42] fixed test query parameter for multiple endpoints

---
 ui/package-lock.json | 5684 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 5684 insertions(+)
 create mode 100644 ui/package-lock.json

diff --git a/ui/package-lock.json b/ui/package-lock.json
new file mode 100644
index 00000000..5c7725fa
--- /dev/null
+++ b/ui/package-lock.json
@@ -0,0 +1,5684 @@
+{
+  "name": "bedhost-ui-2",
+  "version": "0.0.0",
+  "lockfileVersion": 3,
+  "requires": true,
+  "packages": {
+    "": {
+      "name": "bedhost-ui-2",
+      "version": "0.0.0",
+      "dependencies": {
+        "@databio/gtars": "^0.5.2",
+        "@tanstack/react-query": "^5.28.0",
+        "@tanstack/react-query-devtools": "^5.28.0",
+        "@tanstack/react-table": "^8.15.3",
+        "@types/pako": "^2.0.4",
+        "@uidotdev/usehooks": "^2.4.1",
+        "axios": "^1.12.0",
+        "bootstrap": "^5.3.3",
+        "bootstrap-icons": "^1.11.3",
+        "chart.js": "^4.4.2",
+        "chartjs-chart-error-bars": "^4.4.0",
+        "chartjs-plugin-datalabels": "^2.2.0",
+        "framer-motion": "^11.0.20",
+        "js-yaml": "^4.1.0",
+        "pako": "^2.1.0",
+        "react": "^18.2.0",
+        "react-bootstrap": "^2.10.1",
+        "react-chartjs-2": "^5.2.0",
+        "react-dom": "^18.2.0",
+        "react-dropzone": "^14.2.3",
+        "react-force-graph-3d": "^1.27.0",
+        "react-helmet-async": "^2.0.4",
+        "react-hot-toast": "^2.4.1",
+        "react-markdown": "^9.0.1",
+        "react-router-dom": "^7.5.2",
+        "rehype-highlight": "^7.0.0",
+        "three": "^0.177.0",
+        "vega-embed": "^7.0.2",
+        "vite-plugin-top-level-await": "^1.6.0",
+        "vite-plugin-wasm": "^3.5.0"
+      },
+      "devDependencies": {
+        "@types/js-yaml": "^4.0.9",
+        "@types/node": "^20.11.27",
+        "@types/react": "^18.2.64",
+        "@types/react-dom": "^18.2.21",
+        "@typescript-eslint/eslint-plugin": "^7.1.1",
+        "@typescript-eslint/parser": "^7.1.1",
+        "@vitejs/plugin-react": "^4.4.1",
+        "eslint": "^8.57.0",
+        "eslint-plugin-react-hooks": "^4.6.0",
+        "eslint-plugin-react-refresh": "^0.4.5",
+        "sass": "^1.72.0",
+        "typescript": "^5.2.2",
+        "vite": "^6.4.1"
+      }
+    },
+    "../../gtars/gtars-wasm/pkg": {
+      "name": "@databio/gtars",
+      "version": "0.5.2"
+    },
+    "node_modules/@babel/code-frame": {
+      "version": "7.27.1",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@babel/helper-validator-identifier": "^7.27.1",
+        "js-tokens": "^4.0.0",
+        "picocolors": "^1.1.1"
+      },
+      "engines": {
+        "node": ">=6.9.0"
+      }
+    },
+    "node_modules/@babel/compat-data": {
+      "version": "7.28.4",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=6.9.0"
+      }
+    },
+    "node_modules/@babel/core": {
+      "version": "7.28.4",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@babel/code-frame": "^7.27.1",
+        "@babel/generator": "^7.28.3",
+        "@babel/helper-compilation-targets": "^7.27.2",
+        "@babel/helper-module-transforms": "^7.28.3",
+        "@babel/helpers": "^7.28.4",
+        "@babel/parser": "^7.28.4",
+        "@babel/template": "^7.27.2",
+        "@babel/traverse": "^7.28.4",
+        "@babel/types": "^7.28.4",
+        "@jridgewell/remapping": "^2.3.5",
+        "convert-source-map": "^2.0.0",
+        "debug": "^4.1.0",
+        "gensync": "^1.0.0-beta.2",
+        "json5": "^2.2.3",
+        "semver": "^6.3.1"
+      },
+      "engines": {
+        "node": ">=6.9.0"
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+      "version": "2.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-array": "^3.2.4",
+        "d3-format": "^3.1.0",
+        "d3-time-format": "^4.1.0",
+        "vega-time": "^3.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-functions": {
+      "version": "6.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-array": "^3.2.4",
+        "d3-color": "^3.1.0",
+        "d3-geo": "^3.1.1",
+        "vega-dataflow": "^6.1.0",
+        "vega-expression": "^6.1.0",
+        "vega-scale": "^8.1.0",
+        "vega-scenegraph": "^5.1.0",
+        "vega-selections": "^6.1.0",
+        "vega-statistics": "^2.0.0",
+        "vega-time": "^3.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-geo": {
+      "version": "5.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-array": "^3.2.4",
+        "d3-color": "^3.1.0",
+        "d3-geo": "^3.1.1",
+        "vega-canvas": "^2.0.0",
+        "vega-dataflow": "^6.1.0",
+        "vega-projection": "^2.1.0",
+        "vega-statistics": "^2.0.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-hierarchy": {
+      "version": "5.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-hierarchy": "^3.1.2",
+        "vega-dataflow": "^6.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-interpreter": {
+      "version": "2.2.1",
+      "license": "BSD-3-Clause",
+      "dependencies": {
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-label": {
+      "version": "2.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "vega-canvas": "^2.0.0",
+        "vega-dataflow": "^6.1.0",
+        "vega-scenegraph": "^5.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-lite": {
+      "version": "6.4.1",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "json-stringify-pretty-compact": "~4.0.0",
+        "tslib": "~2.8.1",
+        "vega-event-selector": "~4.0.0",
+        "vega-expression": "~6.1.0",
+        "vega-util": "~2.1.0",
+        "yargs": "~18.0.0"
+      },
+      "bin": {
+        "vl2pdf": "bin/vl2pdf",
+        "vl2png": "bin/vl2png",
+        "vl2svg": "bin/vl2svg",
+        "vl2vg": "bin/vl2vg"
+      },
+      "engines": {
+        "node": ">=18"
+      },
+      "funding": {
+        "url": "https://app.hubspot.com/payments/GyPC972GD9Rt"
+      },
+      "peerDependencies": {
+        "vega": "^6.0.0"
+      }
+    },
+    "node_modules/vega-loader": {
+      "version": "5.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-dsv": "^3.0.1",
+        "topojson-client": "^3.1.0",
+        "vega-format": "^2.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-parser": {
+      "version": "7.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "vega-dataflow": "^6.1.0",
+        "vega-event-selector": "^4.0.0",
+        "vega-functions": "^6.1.0",
+        "vega-scale": "^8.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-projection": {
+      "version": "2.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-geo": "^3.1.1",
+        "d3-geo-projection": "^4.0.0",
+        "vega-scale": "^8.1.0"
+      }
+    },
+    "node_modules/vega-regression": {
+      "version": "2.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-array": "^3.2.4",
+        "vega-dataflow": "^6.1.0",
+        "vega-statistics": "^2.0.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-runtime": {
+      "version": "7.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "vega-dataflow": "^6.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-scale": {
+      "version": "8.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-array": "^3.2.4",
+        "d3-interpolate": "^3.0.1",
+        "d3-scale": "^4.0.2",
+        "d3-scale-chromatic": "^3.1.0",
+        "vega-time": "^3.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-scenegraph": {
+      "version": "5.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-path": "^3.1.0",
+        "d3-shape": "^3.2.0",
+        "vega-canvas": "^2.0.0",
+        "vega-loader": "^5.1.0",
+        "vega-scale": "^8.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-schema-url-parser": {
+      "version": "3.0.2",
+      "license": "BSD-3-Clause"
+    },
+    "node_modules/vega-selections": {
+      "version": "6.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-array": "3.2.4",
+        "vega-expression": "^6.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-statistics": {
+      "version": "2.0.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-array": "^3.2.4"
+      }
+    },
+    "node_modules/vega-themes": {
+      "version": "3.0.0",
+      "license": "BSD-3-Clause",
+      "funding": {
+        "url": "https://app.hubspot.com/payments/GyPC972GD9Rt"
+      },
+      "peerDependencies": {
+        "vega": "*",
+        "vega-lite": "*"
+      }
+    },
+    "node_modules/vega-time": {
+      "version": "3.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-array": "^3.2.4",
+        "d3-time": "^3.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-tooltip": {
+      "version": "1.0.0",
+      "license": "BSD-3-Clause",
+      "dependencies": {
+        "vega-util": "^2.0.0"
+      },
+      "funding": {
+        "url": "https://app.hubspot.com/payments/GyPC972GD9Rt"
+      }
+    },
+    "node_modules/vega-transforms": {
+      "version": "5.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-array": "^3.2.4",
+        "vega-dataflow": "^6.1.0",
+        "vega-statistics": "^2.0.0",
+        "vega-time": "^3.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-typings": {
+      "version": "2.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "@types/geojson": "7946.0.16",
+        "vega-event-selector": "^4.0.0",
+        "vega-expression": "^6.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-util": {
+      "version": "2.1.0",
+      "license": "BSD-3-Clause"
+    },
+    "node_modules/vega-view": {
+      "version": "6.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-array": "^3.2.4",
+        "d3-timer": "^3.0.1",
+        "vega-dataflow": "^6.1.0",
+        "vega-format": "^2.1.0",
+        "vega-functions": "^6.1.0",
+        "vega-runtime": "^7.1.0",
+        "vega-scenegraph": "^5.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-view-transforms": {
+      "version": "5.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "vega-dataflow": "^6.1.0",
+        "vega-scenegraph": "^5.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-voronoi": {
+      "version": "5.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "d3-delaunay": "^6.0.4",
+        "vega-dataflow": "^6.1.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vega-wordcloud": {
+      "version": "5.1.0",
+      "license": "BSD-3-Clause",
+      "peer": true,
+      "dependencies": {
+        "vega-canvas": "^2.0.0",
+        "vega-dataflow": "^6.1.0",
+        "vega-scale": "^8.1.0",
+        "vega-statistics": "^2.0.0",
+        "vega-util": "^2.1.0"
+      }
+    },
+    "node_modules/vfile": {
+      "version": "6.0.3",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0",
+        "vfile-message": "^4.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/vfile-message": {
+      "version": "4.0.3",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0",
+        "unist-util-stringify-position": "^4.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/vite": {
+      "version": "6.4.1",
+      "license": "MIT",
+      "dependencies": {
+        "esbuild": "^0.25.0",
+        "fdir": "^6.4.4",
+        "picomatch": "^4.0.2",
+        "postcss": "^8.5.3",
+        "rollup": "^4.34.9",
+        "tinyglobby": "^0.2.13"
+      },
+      "bin": {
+        "vite": "bin/vite.js"
+      },
+      "engines": {
+        "node": "^18.0.0 || ^20.0.0 || >=22.0.0"
+      },
+      "funding": {
+        "url": "https://github.com/vitejs/vite?sponsor=1"
+      },
+      "optionalDependencies": {
+        "fsevents": "~2.3.3"
+      },
+      "peerDependencies": {
+        "@types/node": "^18.0.0 || ^20.0.0 || >=22.0.0",
+        "jiti": ">=1.21.0",
+        "less": "*",
+        "lightningcss": "^1.21.0",
+        "sass": "*",
+        "sass-embedded": "*",
+        "stylus": "*",
+        "sugarss": "*",
+        "terser": "^5.16.0",
+        "tsx": "^4.8.1",
+        "yaml": "^2.4.2"
+      },
+      "peerDependenciesMeta": {
+        "@types/node": {
+          "optional": true
+        },
+        "jiti": {
+          "optional": true
+        },
+        "less": {
+          "optional": true
+        },
+        "lightningcss": {
+          "optional": true
+        },
+        "sass": {
+          "optional": true
+        },
+        "sass-embedded": {
+          "optional": true
+        },
+        "stylus": {
+          "optional": true
+        },
+        "sugarss": {
+          "optional": true
+        },
+        "terser": {
+          "optional": true
+        },
+        "tsx": {
+          "optional": true
+        },
+        "yaml": {
+          "optional": true
+        }
+      }
+    },
+    "node_modules/vite-plugin-top-level-await": {
+      "version": "1.6.0",
+      "license": "MIT",
+      "dependencies": {
+        "@rollup/plugin-virtual": "^3.0.2",
+        "@swc/core": "^1.12.14",
+        "@swc/wasm": "^1.12.14",
+        "uuid": "10.0.0"
+      },
+      "peerDependencies": {
+        "vite": ">=2.8"
+      }
+    },
+    "node_modules/vite-plugin-wasm": {
+      "version": "3.5.0",
+      "license": "MIT",
+      "peerDependencies": {
+        "vite": "^2 || ^3 || ^4 || ^5 || ^6 || ^7"
+      }
+    },
+    "node_modules/vite/node_modules/fdir": {
+      "version": "6.5.0",
+      "license": "MIT",
+      "engines": {
+        "node": ">=12.0.0"
+      },
+      "peerDependencies": {
+        "picomatch": "^3 || ^4"
+      },
+      "peerDependenciesMeta": {
+        "picomatch": {
+          "optional": true
+        }
+      }
+    },
+    "node_modules/vite/node_modules/picomatch": {
+      "version": "4.0.3",
+      "license": "MIT",
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/jonschlinkert"
+      }
+    },
+    "node_modules/warning": {
+      "version": "4.0.3",
+      "license": "MIT",
+      "dependencies": {
+        "loose-envify": "^1.0.0"
+      }
+    },
+    "node_modules/which": {
+      "version": "2.0.2",
+      "dev": true,
+      "license": "ISC",
+      "dependencies": {
+        "isexe": "^2.0.0"
+      },
+      "bin": {
+        "node-which": "bin/node-which"
+      },
+      "engines": {
+        "node": ">= 8"
+      }
+    },
+    "node_modules/word-wrap": {
+      "version": "1.2.5",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
+    "node_modules/wrap-ansi": {
+      "version": "9.0.2",
+      "license": "MIT",
+      "peer": true,
+      "dependencies": {
+        "ansi-styles": "^6.2.1",
+        "string-width": "^7.0.0",
+        "strip-ansi": "^7.1.0"
+      },
+      "engines": {
+        "node": ">=18"
+      },
+      "funding": {
+        "url": "https://github.com/chalk/wrap-ansi?sponsor=1"
+      }
+    },
+    "node_modules/wrap-ansi/node_modules/ansi-regex": {
+      "version": "6.2.2",
+      "license": "MIT",
+      "peer": true,
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/chalk/ansi-regex?sponsor=1"
+      }
+    },
+    "node_modules/wrap-ansi/node_modules/ansi-styles": {
+      "version": "6.2.3",
+      "license": "MIT",
+      "peer": true,
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/chalk/ansi-styles?sponsor=1"
+      }
+    },
+    "node_modules/wrap-ansi/node_modules/strip-ansi": {
+      "version": "7.1.2",
+      "license": "MIT",
+      "peer": true,
+      "dependencies": {
+        "ansi-regex": "^6.0.1"
+      },
+      "engines": {
+        "node": ">=12"
+      },
+      "funding": {
+        "url": "https://github.com/chalk/strip-ansi?sponsor=1"
+      }
+    },
+    "node_modules/wrappy": {
+      "version": "1.0.2",
+      "dev": true,
+      "license": "ISC"
+    },
+    "node_modules/y18n": {
+      "version": "5.0.8",
+      "license": "ISC",
+      "peer": true,
+      "engines": {
+        "node": ">=10"
+      }
+    },
+    "node_modules/yallist": {
+      "version": "3.1.1",
+      "dev": true,
+      "license": "ISC"
+    },
+    "node_modules/yargs": {
+      "version": "18.0.0",
+      "license": "MIT",
+      "peer": true,
+      "dependencies": {
+        "cliui": "^9.0.1",
+        "escalade": "^3.1.1",
+        "get-caller-file": "^2.0.5",
+        "string-width": "^7.2.0",
+        "y18n": "^5.0.5",
+        "yargs-parser": "^22.0.0"
+      },
+      "engines": {
+        "node": "^20.19.0 || ^22.12.0 || >=23"
+      }
+    },
+    "node_modules/yargs-parser": {
+      "version": "22.0.0",
+      "license": "ISC",
+      "peer": true,
+      "engines": {
+        "node": "^20.19.0 || ^22.12.0 || >=23"
+      }
+    },
+    "node_modules/yocto-queue": {
+      "version": "0.1.0",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=10"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
+    "node_modules/zwitch": {
+      "version": "2.0.4",
+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
+    }
+  }
+}

From f8dbe745bdb8b2b99c5ff00ca75b81019a90d719 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 25 Nov 2025 14:27:18 -0500
Subject: [PATCH 30/42] Added umap visualizer

---
 ui/src/components/layout.tsx                  |  39 +-
 ui/src/components/umap/atlas-tooltip.tsx      |  93 +++
 .../components/umap/bed-embedding-atlas.tsx   |  86 +++
 ui/src/components/umap/bed-embedding-plot.tsx | 207 ++++++
 ui/src/components/umap/bed-embedding-view.tsx | 611 ++++++++++++++++++
 ui/src/const.ts                               |   2 +
 .../contexts/mosaic-coordinator-context.tsx   | 167 +++++
 ui/src/custom.scss                            |  70 +-
 ui/src/main.tsx                               |  11 +-
 ui/src/pages/bed-umap.tsx                     |  18 +
 ui/src/queries/useBedUmap.ts                  |  29 +
 ui/src/utils.ts                               |  65 +-
 12 files changed, 1358 insertions(+), 40 deletions(-)
 create mode 100644 ui/src/components/umap/atlas-tooltip.tsx
 create mode 100644 ui/src/components/umap/bed-embedding-atlas.tsx
 create mode 100644 ui/src/components/umap/bed-embedding-plot.tsx
 create mode 100644 ui/src/components/umap/bed-embedding-view.tsx
 create mode 100644 ui/src/contexts/mosaic-coordinator-context.tsx
 create mode 100644 ui/src/pages/bed-umap.tsx
 create mode 100644 ui/src/queries/useBedUmap.ts

diff --git a/ui/src/components/layout.tsx b/ui/src/components/layout.tsx
index f006bcec..a91cfc96 100644
--- a/ui/src/components/layout.tsx
+++ b/ui/src/components/layout.tsx
@@ -12,6 +12,7 @@ type LayoutProps = {
   fullWidth?: boolean;
   footer?: boolean;
   fullHeight?: boolean;
+  flexLayout?: boolean;
 };
 
 const Footer = () => {
@@ -67,16 +68,40 @@ const Footer = () => {
 };
 
 export const Layout = (props: LayoutProps) => {
-  const { children, title, description, image, footer, fullHeight } = props;
-  const mainContainerClass = fullHeight ? 'container min-h-screen' : 'container';
+  const { children, title, description, image, footer, fullHeight, fullWidth, flexLayout } = props;
+
+  if (flexLayout) {
+    return (
+      
+        
+        

+          

+            

+          

+            {children}
+          

+          {!!footer && 
}
+        

+      
+    );
+  }
+
+  const fluidContainer = `${fullWidth ? 'container-fluid' : 'container'}`;
   return (
     
       
-      

-        

-      
{children}

-      {footer === true && 

       {showOptions && (
diff --git a/ui/src/components/search/search-selector.tsx b/ui/src/components/search/search-selector.tsx
index 41cef61c..64cd1bc5 100644
--- a/ui/src/components/search/search-selector.tsx
+++ b/ui/src/components/search/search-selector.tsx
@@ -13,39 +13,39 @@ export const SearchSelector = (props: Props) => {
   const [params, setParams] = useSearchParams();
   return (
     

-      

+      

         
+   {
+      params.set('view', 't2b');
+      params.delete('q');
+      setParams(params);
+      setView('t2b');
+    }}
+  >
+    Text-to-BED
+  
+   {
+      params.set('view', 'b2b');
+      params.delete('q');
+      setParams(params);
+      setView('b2b');
+    }}
+  >
+    BED-to-BED
+  
+   {
+      params.set('view', 't2bs');
+      params.delete('q');
+      setParams(params);
+      setView('t2bs');
+    }}
+  >
+    Text-to-BEDset
+  
+
       

     

   );
diff --git a/ui/src/components/search/text2bedset.tsx b/ui/src/components/search/text2bedset.tsx
index a0213bce..0fedb944 100644
--- a/ui/src/components/search/text2bedset.tsx
+++ b/ui/src/components/search/text2bedset.tsx
@@ -75,7 +75,8 @@ export const Text2BedSet = () => {
               

             ) : (
               

-                Try searching for some BEDsets! e.g. K562 or excluderanges
+                Find collections of BED files by entering a text query above.

+                For example, try searching for "excluderanges" or "a562".
               

             )}
           

diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx
index de80c4b6..b59438ed 100644
--- a/ui/src/pages/home.tsx
+++ b/ui/src/pages/home.tsx
@@ -8,6 +8,7 @@ import rehypeHighlight from 'rehype-highlight';
 import { CODE_SNIPPETS } from '../const';
 import { BBCONF_SNIPPETS } from '../const';
 // import { useExampleBed } from '../queries/useExampleBed';
+import toast from 'react-hot-toast';
 import { useExampleBedSet } from '../queries/useExampleBedSet';
 import { useStats } from '../queries/useStats.ts';
 
@@ -24,9 +25,19 @@ export const Home = () => {
   const [searchTerm, setSearchTerm] = useState('');
   const [searchTermSmall, setSearchTermSmall] = useState('Kidney cancer in humans');
   const [copied, setCopied] = useState(false);
+  const [searchType, setSearchType] = useState('t2b');
 
   const navigate = useNavigate();
 
+  const handleSearch = () => {
+    if (!searchTerm) {
+      toast.error('Please enter a search term.');
+      return;
+    }
+    navigate(`/search?q=${searchTerm}&view=${searchType}`);
+  };
+
+
   // const { data: exampleBedMetadata } = useExampleBed(); # if example will be dynamic again
   const { data: exampleBedSetMetadata } = useExampleBedSet();
   const { data: bedbaseStats } = useStats();
@@ -49,46 +60,62 @@ export const Home = () => {
         {/*    */}
         {/*  */}
         {/*
*/}
-        
Welcome to BEDbase

-        

+        
BEDbase

+        
Find, analyze, and understand genomic region data - all in one
+          place

+
+        

         

-          

-            BEDbase is a unified platform for aggregating, analyzing, and serving genomic region data. BEDbase redefines
-            the way to manage genomic region data and allows users to search for BED files of interest and create
-            collections tailored to research needs. BEDbase is composed of a web server and an API. Users can explore
+          

+            BEDbase is a unified platform for searching, analyzing, visualizing and serving genomic region data.
+            BEDbase redefines the way to manage genomic region data and allows users to search for BED files of
+            interest, visualize them, and create
+            collections tailored to research needs. Users can explore
             comprehensive descriptions of specific BED files via a user-oriented web interface and programmatically
             interact with the data via an OpenAPI-compatible API.
           

         

-        

-           setSearchTerm(e.target.value)}
-            onKeyDown={(e) => {
-              if (e.key === 'Enter') {
-                if (searchTerm.length === 0) {
-                  return;
-                }
-                navigate(`/search?q=${searchTerm}`);
-              }
-            }}
-          />
-          
         

         

@@ -229,18 +256,21 @@ export const Home = () => {
               

             
           
-          
+          
             
               
BED Embedding Visualization

               

-                BEDbase supports visualization of UMAP of hg38 BED embeddings. It allows users to explore the
+                BEDbase provides visualization of UMAP of hg38 BED embeddings. It allows users to explore the
                 similarity of genomic regions based on their embeddings, and
                 providing insights into the relationships between different BED files.
                 The visualization is available on the UMAP visualization.
               

             
             
-              UMAP visualization
+              
+                UMAP visualization
+              
             
           
           
@@ -306,7 +336,7 @@ export const Home = () => {
               

             
 
-            
+            
               

                 
@@ -348,6 +378,22 @@ export const Home = () => {
               

             
           
+          
+            
+              
BED Analyzer

+              

+                BEDbase includes an interactive BED Analyzer that lets you quickly explore any BED file.
+                You can upload your own file or provide a URL, and the analyzer will generate key
+                statistics, summary tables, and visualizations. It gives you an instant overview of
+                region counts, lengths, genome coverage, and other useful properties. Analyze your file:  Analyzer
+              

+            
+            
+              BED analyzer
+            
+          
           
             
               
Data Availability Summary


From 53ab00bb529f6d5e31c9e14b064e1d1f1362f2fc Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 25 Nov 2025 17:33:58 -0500
Subject: [PATCH 32/42] Improvements of home page

---
 ui/public/analyzer_icon.svg                   | 572 +++++++++++++++
 ui/public/api_icon.svg                        | 674 ++++++++++++++++++
 ui/public/search.svg                          | 542 ++++++++++++++
 ui/public/stats_icon.svg                      | 542 ++++++++++++++
 .../bed2bed/b2b-search-results-table.tsx      |  34 +-
 .../text2bed/t2b-search-results-table.tsx     |  20 +-
 ui/src/motions/landing-animations.tsx         |  60 +-
 ui/src/pages/home.tsx                         |  89 +--
 8 files changed, 2402 insertions(+), 131 deletions(-)
 create mode 100644 ui/public/analyzer_icon.svg
 create mode 100644 ui/public/api_icon.svg
 create mode 100644 ui/public/search.svg
 create mode 100644 ui/public/stats_icon.svg

diff --git a/ui/public/analyzer_icon.svg b/ui/public/analyzer_icon.svg
new file mode 100644
index 00000000..082ab25b
--- /dev/null
+++ b/ui/public/analyzer_icon.svg
@@ -0,0 +1,572 @@
+
+
+
+
diff --git a/ui/public/api_icon.svg b/ui/public/api_icon.svg
new file mode 100644
index 00000000..da662f02
--- /dev/null
+++ b/ui/public/api_icon.svg
@@ -0,0 +1,674 @@
+
+
+
+
diff --git a/ui/public/search.svg b/ui/public/search.svg
new file mode 100644
index 00000000..fdcd246c
--- /dev/null
+++ b/ui/public/search.svg
@@ -0,0 +1,542 @@
+
+
+
+
diff --git a/ui/public/stats_icon.svg b/ui/public/stats_icon.svg
new file mode 100644
index 00000000..aa74e9e0
--- /dev/null
+++ b/ui/public/stats_icon.svg
@@ -0,0 +1,542 @@
+
+
+
+
diff --git a/ui/src/components/search/bed2bed/b2b-search-results-table.tsx b/ui/src/components/search/bed2bed/b2b-search-results-table.tsx
index 59915d72..4c6ddb93 100644
--- a/ui/src/components/search/bed2bed/b2b-search-results-table.tsx
+++ b/ui/src/components/search/bed2bed/b2b-search-results-table.tsx
@@ -126,16 +126,22 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
       id: 'info',
     }),
     columnHelper.accessor('score', {
-      cell: (info) => (
-        
-          
-        
-      ),
+      cell: (info) => {
+        const scoreValue = (info.getValue() ?? 0) * 100;
+        const getScoreColor = (score: number) => {
+          // if (score >= 80) return 'text-success';
+          // if (score >= 60) return 'text-warning';
+          // if (score >= 40) return 'text-info';
+          // return 'text-danger';
+          return 'text-success';
+        };
+
+        return (
+          
+        {roundToTwoDecimals(scoreValue)}%
+      
+        );
+      },
       footer: (info) => info.column.id,
       header: () => scoreTooltip,
       id: 'score',
@@ -144,7 +150,7 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
       cell: (info) => {
         const bedId = info.getValue();
         const rowData = info.row.original; // Get the full row data
-        
+
         return (
           

             {cart[bedId || ''] ? (
@@ -167,12 +173,12 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
                 onClick={(e) => {
                   e.preventDefault();
                   e.stopPropagation();
-                  
+
                   if (bedId === undefined) {
                     toast.error('No bed ID found', { position: 'top-center' });
                     return;
                   }
-                  
+
                   const bedItem = {
                     id: bedId,
                     name: rowData.metadata?.name || 'No name',
@@ -183,7 +189,7 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
                     description: rowData.metadata?.description || '',
                     assay: rowData.metadata?.annotation?.assay || 'N/A',
                   };
-                  
+
                   addBedToCart(bedItem);
                 }}
               >
diff --git a/ui/src/components/search/text2bed/t2b-search-results-table.tsx b/ui/src/components/search/text2bed/t2b-search-results-table.tsx
index 4bdbfcbc..e85fc2cd 100644
--- a/ui/src/components/search/text2bed/t2b-search-results-table.tsx
+++ b/ui/src/components/search/text2bed/t2b-search-results-table.tsx
@@ -117,12 +117,16 @@ export const Text2BedSearchResultsTable = (props: Props) => {
               
             
             
-              
+               {
+                const scoreValue = (result.score ?? 0) * 100;
+                // if (scoreValue >= 80) return 'text-success';
+                // if (scoreValue >= 60) return 'text-warning';
+                // if (scoreValue >= 40) return 'text-info';
+                // return 'text-danger';
+                return 'text-success';
+              })()}`}>
+                {roundToTwoDecimals((result.score ?? 0) * 100)}%
+              
             
             
               {cart[result?.metadata?.id || ''] ? (
@@ -149,7 +153,7 @@ export const Text2BedSearchResultsTable = (props: Props) => {
                       toast.error('No bed ID found', { position: 'top-center' });
                       return;
                     }
-                    
+
                     // Create the simplified bed item object
                     const bedItem = {
                       id: result.metadata.id,
@@ -161,7 +165,7 @@ export const Text2BedSearchResultsTable = (props: Props) => {
                       description: result.metadata.description || '',
                       assay: result.metadata.annotation?.assay || 'N/A',
                     };
-                    
+
                     addBedToCart(bedItem);
                   }}
                 >
diff --git a/ui/src/motions/landing-animations.tsx b/ui/src/motions/landing-animations.tsx
index b714e2f7..98e2e49e 100644
--- a/ui/src/motions/landing-animations.tsx
+++ b/ui/src/motions/landing-animations.tsx
@@ -8,7 +8,7 @@ export const InPaths = () => {
   return (
      {
       
-       {
         y2="50%"
         strokeWidth={STROKE_WIDTH}
         animate={{
-          strokeDashoffset: [100, 90, 80, 70, 60, 50, 40, 30, 20, 10, 0, -10, -20],
-        }}
-        strokeDasharray="6,6"
-        transition={{
-          duration: STROKE_SPEAD,
-          repeat: Infinity,
-          repeatType: 'loop',
-          ease: 'linear',
-        }}
-        stroke="#000"
-      />
-       {
           repeatType: 'loop',
           ease: 'linear',
         }}
+        stroke={PRIMARY_COLOR}
       />
        {
        {
        {
             
           
         

-        

-          {/*Or, explore an example BED file*/}
+        

           Or, explore an example BED file
           or an{' '} example BEDset
         

 
-        

-          

-            
-              
-                Bed files
-              
-              BED file icon
-            
-            
-              
-                {' '}
-                BigBed files
-              
-              BigBed file icon
-            
-            
-              
-                Wig files
-              
-              Wiggle file icon
-            
-            
-              
-                BigWig files
-              
-              BigWig file icon
-            
-            
-              
-                BedGraph files
-              
-              BDG file icon
-            
+        

+          

+            

+              
Search

+              

+                Search icon
+              

+            

+            

+              
Analyzer

+              

+                Analyzer icon
+              

+            

+            

+              
API and Clients

+              

+                API icon
+              

+            

           

           
           

             

-              BEDbase logo
+              BEDbase logo
             

           

           
           

             

               
Statistics

-              

-                Statistics icon
+              

+                Statistics icon
               

             

             

               
BED sets

-              

-                Statistics icon
+              

+                Statistics icon
               

             

             

               
Embeddings

-              

-                Statistics icon
+              

+                Statistics icon
               

             

           


From 99baebeeb1cbdd1e4e78778f759b257e8feb8607 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 25 Nov 2025 17:41:51 -0500
Subject: [PATCH 33/42] Added motion for better visualization

---
 ui/src/pages/home.tsx | 65 +++++++++++++++++++++++++++++++++----------
 1 file changed, 51 insertions(+), 14 deletions(-)

diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx
index d0c3437a..1e3e0eff 100644
--- a/ui/src/pages/home.tsx
+++ b/ui/src/pages/home.tsx
@@ -11,6 +11,7 @@ import { BBCONF_SNIPPETS } from '../const';
 import toast from 'react-hot-toast';
 import { useExampleBedSet } from '../queries/useExampleBedSet';
 import { useStats } from '../queries/useStats.ts';
+import { motion } from 'framer-motion';
 
 type FileBadgeProps = {
   children?: React.ReactNode;
@@ -126,51 +127,87 @@ export const Home = () => {
         

           

-            

+            {/*Added everywhere motion div for better visualization */}
+            
               
Search

               

                 Search icon
               

-            

-            

+            
+            
               
Analyzer

               

                 Analyzer icon
               

-            

-            

+            
+            
               
API and Clients

               

                 API icon
               

-            

+            
           

           
-          

+          
             

               BEDbase logo
             

-          

+          
           
           

-            

+            
               
Statistics

               

                 Statistics icon
               

-            

-            

+            
+            
               
BED sets

               

                 Statistics icon
               

-            

-            

+            
+            
               
Embeddings

               

                 Statistics icon
               

-            

+            
           

         

         


From 1e7ddf50b2583fa4e0fa68f079768e5480832671 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 25 Nov 2025 17:55:01 -0500
Subject: [PATCH 34/42] Added links to the home page icons

---
 ui/src/pages/home.tsx | 74 +++++++++++++++++++++++++------------------
 1 file changed, 43 insertions(+), 31 deletions(-)

diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx
index 1e3e0eff..2f083403 100644
--- a/ui/src/pages/home.tsx
+++ b/ui/src/pages/home.tsx
@@ -13,14 +13,14 @@ import { useExampleBedSet } from '../queries/useExampleBedSet';
 import { useStats } from '../queries/useStats.ts';
 import { motion } from 'framer-motion';
 
-type FileBadgeProps = {
-  children?: React.ReactNode;
-};
+// type FileBadgeProps = {
+//   children?: React.ReactNode;
+// };
 
-const FileBadge = (props: FileBadgeProps) => {
-  const { children } = props;
-  return 
{children}
;
-};
+// const FileBadge = (props: FileBadgeProps) => {
+//   const { children } = props;
+//   return 
{children}
;
+// };
 
 export const Home = () => {
   const [searchTerm, setSearchTerm] = useState('');
@@ -134,10 +134,12 @@ export const Home = () => {
               animate={{ opacity: 1, x: 0 }}
               transition={{ duration: 0.5, delay: 0.2 }}
             >
-              
Search

-              

-                Search icon
-              

+              
+                
Search

+                

+                  Search icon
+                

+              
             
              {
               animate={{ opacity: 1, x: 0 }}
               transition={{ duration: 0.5, delay: 0.4 }}
             >
-              
Analyzer

-              

-                Analyzer icon
-              

+              
+                
Analyzer

+                

+                  Analyzer icon
+                

+              
             
              {
               animate={{ opacity: 1, x: 0 }}
               transition={{ duration: 0.5, delay: 0.6 }}
             >
-              
API and Clients

-              

-                API icon
-              

+              
+                
API and Clients

+                

+                  API icon
+                

+              
             
           

           
@@ -181,10 +187,12 @@ export const Home = () => {
               animate={{ opacity: 1, x: 0 }}
               transition={{ duration: 0.5, delay: 0.2 }}
             >
-              
Statistics

-              

-                Statistics icon
-              

+              
+                
Statistics

+                

+                  Statistics icon
+                

+              
             
              {
               animate={{ opacity: 1, x: 0 }}
               transition={{ duration: 0.5, delay: 0.4 }}
             >
-              
BED sets

-              

-                Statistics icon
-              

+              
+                
BED sets

+                

+                  Statistics icon
+                

+              
             
              {
               animate={{ opacity: 1, x: 0 }}
               transition={{ duration: 0.5, delay: 0.6 }}
             >
-              
Embeddings

-              

-                Statistics icon
-              

+              
+                
Embeddings

+                

+                  Statistics icon
+                

+              
             
           

         


From fc5f6ba71314e437a7018279a942417b6c6f4711 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 25 Nov 2025 17:59:53 -0500
Subject: [PATCH 35/42] fixed search errors

---
 ui/src/components/search/bed2bed/b2b-search-results-table.tsx | 4 ++--
 .../components/search/text2bed/t2b-search-results-table.tsx   | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/ui/src/components/search/bed2bed/b2b-search-results-table.tsx b/ui/src/components/search/bed2bed/b2b-search-results-table.tsx
index 4c6ddb93..4a354b56 100644
--- a/ui/src/components/search/bed2bed/b2b-search-results-table.tsx
+++ b/ui/src/components/search/bed2bed/b2b-search-results-table.tsx
@@ -14,7 +14,7 @@ import {
 } from '@tanstack/react-table';
 import { useState } from 'react';
 import { components } from '../../../../bedbase-types';
-import { OverlayTrigger, ProgressBar, Tooltip } from 'react-bootstrap';
+import { OverlayTrigger, Tooltip } from 'react-bootstrap';
 import { roundToTwoDecimals } from '../../../utils';
 import YAML from 'js-yaml';
 import { useBedCart } from '../../../contexts/bedcart-context';
@@ -129,7 +129,7 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
       cell: (info) => {
         const scoreValue = (info.getValue() ?? 0) * 100;
         const getScoreColor = (score: number) => {
-          // if (score >= 80) return 'text-success';
+          if (score >= 80) return 'text-success';
           // if (score >= 60) return 'text-warning';
           // if (score >= 40) return 'text-info';
           // return 'text-danger';
diff --git a/ui/src/components/search/text2bed/t2b-search-results-table.tsx b/ui/src/components/search/text2bed/t2b-search-results-table.tsx
index e85fc2cd..7da0fac5 100644
--- a/ui/src/components/search/text2bed/t2b-search-results-table.tsx
+++ b/ui/src/components/search/text2bed/t2b-search-results-table.tsx
@@ -1,4 +1,4 @@
-import { ProgressBar } from 'react-bootstrap';
+// import { ProgressBar } from 'react-bootstrap';
 import { components } from '../../../../bedbase-types';
 import { roundToTwoDecimals } from '../../../utils';
 import { useBedCart } from '../../../contexts/bedcart-context';
@@ -118,7 +118,7 @@ export const Text2BedSearchResultsTable = (props: Props) => {
             
             
                {
-                const scoreValue = (result.score ?? 0) * 100;
+                // const scoreValue = (result.score ?? 0) * 100;
                 // if (scoreValue >= 80) return 'text-success';
                 // if (scoreValue >= 60) return 'text-warning';
                 // if (scoreValue >= 40) return 'text-info';

From d56d03fece4fbc08f4a7eeecb5bc693553500b11 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Tue, 25 Nov 2025 18:20:59 -0500
Subject: [PATCH 36/42] Updated analyze page

---
 .../bed-analytics-components/bed-plots.tsx    | 127 +++++---
 ui/src/pages/bed-analytics.tsx                | 298 ++++++++++--------
 2 files changed, 248 insertions(+), 177 deletions(-)

diff --git a/ui/src/components/bed-analytics-components/bed-plots.tsx b/ui/src/components/bed-analytics-components/bed-plots.tsx
index 5ca1d135..b2da7887 100644
--- a/ui/src/components/bed-analytics-components/bed-plots.tsx
+++ b/ui/src/components/bed-analytics-components/bed-plots.tsx
@@ -1,4 +1,4 @@
-import { useEffect, useRef } from 'react';
+import { useEffect, useRef, useState } from 'react';
 import embed from 'vega-embed';
 
 const COLOR = 'rgba(0, 128, 128, 1)';
@@ -9,16 +9,13 @@ type DistributionSpecDataPoint = {
   end: number;
   n: number;
   rid: number;
-
-}
+};
 
 interface BedPlotsProps {
   data: DistributionSpecDataPoint[];
 }
 
 const distributionSpec = (data: DistributionSpecDataPoint[]) => {
-
-  // Transform data to match the new schema requirements
   const transformedData = data.map((item: DistributionSpecDataPoint) => ({
     chr: item.chr,
     withinGroupID: item.rid,
@@ -28,33 +25,27 @@ const distributionSpec = (data: DistributionSpecDataPoint[]) => {
   }));
   return {
     $schema: 'https://vega-github.io/schema/vega-lite/v6.json',
-    title: {
-      text: 'Region Distribution Plot',
-      fontSize: 24,
-      fontWeight: 'bold',
-      anchor: 'middle',
-      offset: 10,
-    },
+    // title: {
+    //   text: 'Region Distribution Plot',
+    //   fontSize: 24,
+    //   fontWeight: 'bold',
+    //   anchor: 'middle',
+    //   offset: 10,
+    // },
     config: {
       axis: {
-        grid: true,
+        grid: false,
       },
       facet: {
         spacing: -1,
-        labelFontSize: 12,
-        titleFontSize: 12,
-      },
-      header: {
-        labelFontSize: 12,
-        titleFontSize: 16,
       },
       view: {
         strokeWidth: 0,
         cursor: 'inherit',
       },
-      bar: {
-        continuousBandSize: 2.5,
-      },
+      // bar: {
+      //   continuousBandSize: 2.5,
+      // },
     },
     data: {
       values: transformedData,
@@ -64,15 +55,39 @@ const distributionSpec = (data: DistributionSpecDataPoint[]) => {
         title: 'Chromosome',
         field: 'chr',
         header: {
-          labelAlign: 'right',
+          labelAlign: 'left',
           labelAngle: 0,
-          labelOrient: 'right',
-          labelPadding: 10,
+          labelOrient: 'left',
+          labelPadding: 5,
+          labelBaseline: 'top',
+          labelFontSize: 9,
         },
         sort: [
-          'chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10',
-          'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20',
-          'chr21', 'chr22', 'chrX', 'chrY', 'chrM',
+          'chr1',
+          'chr2',
+          'chr3',
+          'chr4',
+          'chr5',
+          'chr6',
+          'chr7',
+          'chr8',
+          'chr9',
+          'chr10',
+          'chr11',
+          'chr12',
+          'chr13',
+          'chr14',
+          'chr15',
+          'chr16',
+          'chr17',
+          'chr18',
+          'chr19',
+          'chr20',
+          'chr21',
+          'chr22',
+          'chrX',
+          'chrY',
+          'chrM',
         ],
         type: 'ordinal',
         color: {
@@ -81,7 +96,7 @@ const distributionSpec = (data: DistributionSpecDataPoint[]) => {
       },
       x: {
         axis: {
-          labelExpr: 'datum.value == 0 ? \'start\' : datum.value == 183 ? \'end\' : \'\'',
+          labelExpr: 'datum.value == 0 ? \'start\' : datum.value == 300 ? \'end\' : \'\'',
           values: [0, 300.0],
         },
         field: 'withinGroupID',
@@ -92,24 +107,22 @@ const distributionSpec = (data: DistributionSpecDataPoint[]) => {
         type: 'quantitative',
       },
       y: {
-        axis: null,
+        axis: {
+          labels: false,
+          ticks: false,
+        },
         field: 'N',
-        title: 'Chromosome',
+        title: '',
         type: 'quantitative',
       },
     },
     height: 25,
     mark: {
-      cornerRadiusEnd: -0.5,
+      cornerRadiusEnd: 0.5,
       type: 'bar',
       width: 2.5,
       color: COLOR,
     },
-    width: 'container',
-    autosize: {
-      type: 'fit',
-      contains: 'padding',
-    },
   };
 };
 
@@ -117,20 +130,37 @@ export const RegionDistributionPlot = (props: BedPlotsProps) => {
   const { data } = props;
 
   const plotRef = useRef(null);
-  const spec = distributionSpec(data);
+  const [containerWidth, setContainerWidth] = useState(0);
+
+  useEffect(() => {
+    const updateWidth = () => {
+      if (plotRef.current) {
+        const width = plotRef.current.offsetWidth * 0.8;
+        setContainerWidth(width);
+      }
+    };
+
+    updateWidth();
+    window.addEventListener('resize', updateWidth);
+    return () => window.removeEventListener('resize', updateWidth);
+  }, []);
 
   useEffect(() => {
     const element = plotRef.current;
-    if (element && spec) {
+    if (element && containerWidth > 0) {
+      const spec = {
+        ...distributionSpec(data),
+        width: containerWidth,
+      };
+
       try {
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
         embed(element, spec as any, {
           actions: { export: true, source: false, compiled: false },
           renderer: 'svg',
-        })
-          .catch(error => {
-            console.error('Embed error after parsing:', error);
-          });
+        }).catch((error) => {
+          console.error('Embed error after parsing:', error);
+        });
       } catch (error) {
         console.error(error);
       }
@@ -141,13 +171,16 @@ export const RegionDistributionPlot = (props: BedPlotsProps) => {
         element.innerHTML = '';
       }
     };
-  }, [spec]);
+  }, [containerWidth, data]);
 
   return (
-    

-      

+    

+      

     

   );
 };
 
-export default RegionDistributionPlot;
\ No newline at end of file
+export default RegionDistributionPlot;
diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx
index ed053d70..3839d9b8 100644
--- a/ui/src/pages/bed-analytics.tsx
+++ b/ui/src/pages/bed-analytics.tsx
@@ -14,9 +14,12 @@ export const BEDAnalytics = () => {
   const [selectedFile, setSelectedFile] = useState(null);
   const [inputMode, setInputMode] = useState<'file' | 'url'>('file');
   const [bedUrl, setBedUrl] = useState('');
+  const [triggerSearch, setTriggerSearch] = useState(0);
   const [searchParams] = useSearchParams();
   const navigate = useNavigate();
 
+  const fileInputRef = useRef(null);
+
   useEffect(() => {
     const urlParam = searchParams.get('bedUrl');
     if (urlParam) {
@@ -25,14 +28,17 @@ export const BEDAnalytics = () => {
     }
   }, [searchParams]);
 
-  const regionsetFileInputRef = useRef(null);
+  useEffect(() => {
+    initializeRegionSet();
+  }, [triggerSearch]);
 
   const fetchBedFromUrl = async (url: string): Promise => {
-    console.log(`${url[0]}, ${url[1]}, ${url}`);
-    const fetchUrl = url.length === 32 && !url.startsWith('http')
-      ? `https://api.bedbase.org/v1/files/files/${url[0]}/${url[1]}/${url}.bed.gz`
-      : url;
-    console.log(`${fetchUrl}`);
+    // console.log(`${url[0]}, ${url[1]}, ${url}`);
+    const fetchUrl =
+      url.length === 32 && !url.startsWith('http')
+        ? `https://api.bedbase.org/v1/files/files/${url[0]}/${url[1]}/${url}.bed.gz`
+        : url;
+    // console.log(`${fetchUrl}`);
     const response = await fetch(fetchUrl);
     if (!response.ok) {
       throw new Error(`Failed to fetch BED file: ${response.statusText}`);
@@ -90,8 +96,19 @@ export const BEDAnalytics = () => {
     setTotalProcessingTime(null);
     setSelectedFile(null);
     setBedUrl('');
-    if (regionsetFileInputRef.current) {
-      regionsetFileInputRef.current.value = '';
+    if (fileInputRef.current) {
+      fileInputRef.current.value = '';
+    }
+  };
+
+  const handleOnKeyDown = (e: React.KeyboardEvent): void => {
+    if (e.key === 'Enter') {
+      if (inputMode === 'url') {
+        const params = new URLSearchParams(searchParams);
+        params.set('bedUrl', bedUrl);
+        navigate(`?${params.toString()}`);
+      }
+      setTriggerSearch(triggerSearch + 1);
     }
   };
 
@@ -99,140 +116,161 @@ export const BEDAnalytics = () => {
     
       
BED analyzer

       

-        

-          

-            

-               setInputMode('file')}
-              />
-              
-            

-            

-               setInputMode('url')}
-              />
-              
-            

-          

-
-          {inputMode === 'file' ? (
-            

-              
-               {
-                  const file = e.target.files?.[0];
-                  if (file) {
+        

+          

+            

+              {inputMode === 'file' ? (
+                <>
+                  {!!selectedFile ? (
+                    <>
+                       fileInputRef.current?.click()}
+                        readOnly
+                      />
+                       {
+                          const file = e.target.files?.[0];
+                          if (file) {
+                            unloadFile();
+                            setSelectedFile(file);
+                            setTriggerSearch(triggerSearch + 1);
+                          }
+                        }}
+                      />
+                    
+                  ) : (
+                     {
+                        const file = e.target.files?.[0];
+                        if (file) {
+                          unloadFile();
+                          setSelectedFile(file);
+                          setTriggerSearch(triggerSearch + 1);
+                        }
+                      }}
+                    />
+                  )}
+                
+              ) : (
+                 {
+                    const newUrl = e.target.value;
+                    setBedUrl(newUrl);
+                    if (rs) unloadFile();
+                  }}
+                  onKeyDown={handleOnKeyDown}
+                />
+              )}
+              {(!!rs || !!selectedFile || !!bedUrl.trim()) && (
+                
               )}
-            

-          ) : (
-            

-              
-               {
-                  const newUrl = e.target.value;
-                  setBedUrl(newUrl);
-                  if (rs) unloadFile();
-
-                  // Update the URL query parameter
-                  const params = new URLSearchParams(searchParams);
-                  if (newUrl.trim()) {
-                    params.set('bedUrl', newUrl);
-                  } else {
-                    params.delete('bedUrl');
-                  }
-                  navigate(`?${params.toString()}`);
+                  unloadFile();
+                  setInputMode(e.target.value as 'file' | 'url');
                 }}
-              />
-              {bedUrl && (
-                

-                  URL: {bedUrl}
-                

-              )}
+              >
+                
+                
+              
             

-          )}
-          {inputMode === 'file' && !selectedFile && (
-            
-          )}
+                }
+                setTriggerSearch(triggerSearch + 1);
+              }}
+              disabled={
+                (inputMode === 'file' && !selectedFile) ||
+                (inputMode === 'url' && !bedUrl.trim()) ||
+                rs !== null ||
+                loadingRS
+              }
+            >
+              Analyze!
+            
+          

+        

 
+        

+          

+            {inputMode === 'file' ? (
+              

+                {selectedFile && (
+                  <>
+                    
Selected file: {selectedFile.name}

+                    
File size: {bytesToSize(selectedFile.size)}

+                  
+                )}
+              

+            ) : (
+              
{!!rs && bedUrl && 
Source: {bedUrl}
}

+            )}
+            {!(!!rs || !!selectedFile || !!bedUrl.trim()) && (
+              

+                No input provided. Try this{' '}
+                 {
+                    e.preventDefault();
+                    const exampleUrl =
+                      'https://api.bedbase.org/v1/files/files/d/c/dcc005e8761ad5599545cc538f6a2a4d.bed.gz';
+                    setInputMode('url');
+                    setBedUrl(exampleUrl);
 
-          {rs && totalProcessingTime !== null && (
-            

-          )}
-        

+                    const params = new URLSearchParams(searchParams);
+                    params.set('bedUrl', exampleUrl);
+                    navigate(`?${params.toString()}`);
+                    setTriggerSearch(triggerSearch + 1);
+                  }}
+                >
+                  example file
+                
+                .
+              

+            )}
 
-        

-          
-          
+            {rs && !!totalProcessingTime && (
+              
Total processing time: {(totalProcessingTime / 1000).toFixed(3)}s

+            )}
+          

         

 
+
         

           {loadingRS && (
             

Date: Tue, 25 Nov 2025 18:53:11 -0500
Subject: [PATCH 37/42] few font improvements

---
 .../chromosome-stats-panel.tsx                  |  2 +-
 ui/src/const.ts                                 | 17 +++++++++++++++++
 ui/src/pages/home.tsx                           |  4 +++-
 3 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
index 26d22cc0..7b25fc9e 100644
--- a/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
+++ b/ui/src/components/bed-analytics-components/chromosome-stats-panel.tsx
@@ -91,7 +91,7 @@ const ChromosomeStatsPanel: React.FC = ({ rs, selectedFile }) => {
                           width={barWidth}
                           height={barH}
                           rx={3}
-                          fill="#0d6efd"
+                          fill="#008000ff"
                           stroke="#0856d1"
                           strokeWidth="0.5"
                         />
diff --git a/ui/src/const.ts b/ui/src/const.ts
index 8a65a4e2..418a036b 100644
--- a/ui/src/const.ts
+++ b/ui/src/const.ts
@@ -129,6 +129,18 @@ print(bed_granges)
 \`\`\`
 `;
 
+export const CLIENT_RUST_CODE_RAW = `
+\`\`\`python
+use gtars::bbclient::BBClient;
+
+let mut bbc = BBClient::new(Some(cache_folder.clone()), None).expect("Failed to create BBClient");
+
+let bed_id: String = bbc
+            .add_local_bed_to_cache(PathBuf::from(_path/to.bed.gz), None)
+            .unwrap();
+\`\`\`
+`;
+
 
 export const BBCONF_SNIPPETS = [
   {
@@ -141,4 +153,9 @@ export const BBCONF_SNIPPETS = [
     code: CLIENT_R_CODE_RAW,
     raw: CLIENT_R_CODE_RAW,
   },
+  {
+    language: 'Rust',
+    code: CLIENT_RUST_CODE_RAW,
+    raw: CLIENT_RUST_CODE_RAW,
+  },
 ];
\ No newline at end of file
diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx
index 2f083403..1f5b6675 100644
--- a/ui/src/pages/home.tsx
+++ b/ui/src/pages/home.tsx
@@ -404,12 +404,14 @@ export const Home = () => {
                 You can upload your own file or provide a URL, and the analyzer will generate key
                 statistics, summary tables, and visualizations. It gives you an instant overview of
                 region counts, lengths, genome coverage, and other useful properties. Analyze your file:  Analyzer
+                href="/analyze"> Analyzer.
               

             
             
+              
               BED analyzer
+              
             
           
           

From 46f4f9d95a7368f41c5b57ff979247acbad05134 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Wed, 26 Nov 2025 15:56:36 -0500
Subject: [PATCH 38/42] polished animation

---
 ui/src/motions/landing-animations.tsx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ui/src/motions/landing-animations.tsx b/ui/src/motions/landing-animations.tsx
index 98e2e49e..6397e4fa 100644
--- a/ui/src/motions/landing-animations.tsx
+++ b/ui/src/motions/landing-animations.tsx
@@ -1,7 +1,7 @@
 import { motion } from 'framer-motion';
 import { PRIMARY_COLOR } from '../const';
 
-const STROKE_WIDTH = 2;
+const STROKE_WIDTH = 2.5;
 const STROKE_SPEAD = 0;
 
 export const InPaths = () => {

From bc425a129e6877e7e44a777203304d649e7ed55f Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Mon, 1 Dec 2025 17:07:32 -0500
Subject: [PATCH 39/42] updated version and configs

---
 bedhost/_version.py                        | 2 +-
 deployment/config/api-dev.bedbase.org.yaml | 2 +-
 deployment/config/api.bedbase.org.yaml     | 1 +
 requirements/requirements-all.txt          | 4 ++--
 ui/package.json                            | 2 +-
 5 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/bedhost/_version.py b/bedhost/_version.py
index daecfa51..ea370a8e 100644
--- a/bedhost/_version.py
+++ b/bedhost/_version.py
@@ -1 +1 @@
-__version__ = "0.10.6"
+__version__ = "0.12.0"
diff --git a/deployment/config/api-dev.bedbase.org.yaml b/deployment/config/api-dev.bedbase.org.yaml
index ab3ab944..79da07a2 100644
--- a/deployment/config/api-dev.bedbase.org.yaml
+++ b/deployment/config/api-dev.bedbase.org.yaml
@@ -4,7 +4,7 @@ path:
   # region2vec: databio/r2v-pretrained-for-search
   region2vec: databio/r2v-encode-hg38
   vec2vec: 'databio/v2v-sentencetransformers-encode'
-  umap_model: "https://github.com/databio/bedbase-loader/raw/refs/heads/master/umap/hg38_umap_umap_model.joblib"
+  umap_model: "https://huggingface.co/databio/bedbase-umap/resolve/main/hg38_umap_umap_model.joblib"
 database:
   host: $POSTGRES_HOST
   port: 5432
diff --git a/deployment/config/api.bedbase.org.yaml b/deployment/config/api.bedbase.org.yaml
index fabac7ec..9c483233 100644
--- a/deployment/config/api.bedbase.org.yaml
+++ b/deployment/config/api.bedbase.org.yaml
@@ -4,6 +4,7 @@ path:
   # region2vec: databio/r2v-pretrained-for-search
   region2vec: databio/r2v-encode-hg38
   vec2vec: "databio/v2v-sentencetransformers-encode"
+  umap_model: "https://huggingface.co/databio/bedbase-umap/resolve/main/hg38_umap_umap_model.joblib"
 database:
   host: $POSTGRES_HOST
   port: 5432
diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
index cba08d95..35b1911d 100644
--- a/requirements/requirements-all.txt
+++ b/requirements/requirements-all.txt
@@ -1,5 +1,5 @@
-bbconf @ git+https://github.com/databio/bbconf.git@umap#egg=bbconf
-# bbconf>=0.12.0
+# bbconf @ git+https://github.com/databio/bbconf.git@umap#egg=bbconf
+bbconf>=0.13.0
 fastapi>=0.103.0
 logmuse>=0.2.7
 markdown
diff --git a/ui/package.json b/ui/package.json
index 4e7421b9..a85962b1 100644
--- a/ui/package.json
+++ b/ui/package.json
@@ -1,7 +1,7 @@
 {
   "name": "bedhost-ui-2",
   "private": true,
-  "version": "0.0.0",
+  "version": "0.12.0",
   "type": "module",
   "scripts": {
     "dev": "vite",

From 310c0dcb302aa06444d957f792fbde834f523abc Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Mon, 1 Dec 2025 17:10:41 -0500
Subject: [PATCH 40/42] updated yaml

---
 ui/package-lock.json | 5684 ------------------------------------------
 ui/package.json      |    2 +-
 2 files changed, 1 insertion(+), 5685 deletions(-)
 delete mode 100644 ui/package-lock.json

diff --git a/ui/package-lock.json b/ui/package-lock.json
deleted file mode 100644
index 5c7725fa..00000000
--- a/ui/package-lock.json
+++ /dev/null
@@ -1,5684 +0,0 @@
-{
-  "name": "bedhost-ui-2",
-  "version": "0.0.0",
-  "lockfileVersion": 3,
-  "requires": true,
-  "packages": {
-    "": {
-      "name": "bedhost-ui-2",
-      "version": "0.0.0",
-      "dependencies": {
-        "@databio/gtars": "^0.5.2",
-        "@tanstack/react-query": "^5.28.0",
-        "@tanstack/react-query-devtools": "^5.28.0",
-        "@tanstack/react-table": "^8.15.3",
-        "@types/pako": "^2.0.4",
-        "@uidotdev/usehooks": "^2.4.1",
-        "axios": "^1.12.0",
-        "bootstrap": "^5.3.3",
-        "bootstrap-icons": "^1.11.3",
-        "chart.js": "^4.4.2",
-        "chartjs-chart-error-bars": "^4.4.0",
-        "chartjs-plugin-datalabels": "^2.2.0",
-        "framer-motion": "^11.0.20",
-        "js-yaml": "^4.1.0",
-        "pako": "^2.1.0",
-        "react": "^18.2.0",
-        "react-bootstrap": "^2.10.1",
-        "react-chartjs-2": "^5.2.0",
-        "react-dom": "^18.2.0",
-        "react-dropzone": "^14.2.3",
-        "react-force-graph-3d": "^1.27.0",
-        "react-helmet-async": "^2.0.4",
-        "react-hot-toast": "^2.4.1",
-        "react-markdown": "^9.0.1",
-        "react-router-dom": "^7.5.2",
-        "rehype-highlight": "^7.0.0",
-        "three": "^0.177.0",
-        "vega-embed": "^7.0.2",
-        "vite-plugin-top-level-await": "^1.6.0",
-        "vite-plugin-wasm": "^3.5.0"
-      },
-      "devDependencies": {
-        "@types/js-yaml": "^4.0.9",
-        "@types/node": "^20.11.27",
-        "@types/react": "^18.2.64",
-        "@types/react-dom": "^18.2.21",
-        "@typescript-eslint/eslint-plugin": "^7.1.1",
-        "@typescript-eslint/parser": "^7.1.1",
-        "@vitejs/plugin-react": "^4.4.1",
-        "eslint": "^8.57.0",
-        "eslint-plugin-react-hooks": "^4.6.0",
-        "eslint-plugin-react-refresh": "^0.4.5",
-        "sass": "^1.72.0",
-        "typescript": "^5.2.2",
-        "vite": "^6.4.1"
-      }
-    },
-    "../../gtars/gtars-wasm/pkg": {
-      "name": "@databio/gtars",
-      "version": "0.5.2"
-    },
-    "node_modules/@babel/code-frame": {
-      "version": "7.27.1",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "@babel/helper-validator-identifier": "^7.27.1",
-        "js-tokens": "^4.0.0",
-        "picocolors": "^1.1.1"
-      },
-      "engines": {
-        "node": ">=6.9.0"
-      }
-    },
-    "node_modules/@babel/compat-data": {
-      "version": "7.28.4",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=6.9.0"
-      }
-    },
-    "node_modules/@babel/core": {
-      "version": "7.28.4",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "@babel/code-frame": "^7.27.1",
-        "@babel/generator": "^7.28.3",
-        "@babel/helper-compilation-targets": "^7.27.2",
-        "@babel/helper-module-transforms": "^7.28.3",
-        "@babel/helpers": "^7.28.4",
-        "@babel/parser": "^7.28.4",
-        "@babel/template": "^7.27.2",
-        "@babel/traverse": "^7.28.4",
-        "@babel/types": "^7.28.4",
-        "@jridgewell/remapping": "^2.3.5",
-        "convert-source-map": "^2.0.0",
-        "debug": "^4.1.0",
-        "gensync": "^1.0.0-beta.2",
-        "json5": "^2.2.3",
-        "semver": "^6.3.1"
-      },
-      "engines": {
-        "node": ">=6.9.0"
-      },
-      "funding": {
-        "type": "opencollective",
-        "url": "https://opencollective.com/babel"
-      }
-    },
-    "node_modules/@babel/core/node_modules/semver": {
-      "version": "6.3.1",
-      "dev": true,
-      "license": "ISC",
-      "bin": {
-        "semver": "bin/semver.js"
-      }
-    },
-    "node_modules/@babel/generator": {
-      "version": "7.28.3",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "@babel/parser": "^7.28.3",
-        "@babel/types": "^7.28.2",
-        "@jridgewell/gen-mapping": "^0.3.12",
-        "@jridgewell/trace-mapping": "^0.3.28",
-        "jsesc": "^3.0.2"
-      },
-      "engines": {
-        "node": ">=6.9.0"
-      }
-    },
-    "node_modules/@babel/helper-compilation-targets": {
-      "version": "7.27.2",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "@babel/compat-data": "^7.27.2",
-        "@babel/helper-validator-option": "^7.27.1",
-        "browserslist": "^4.24.0",
-        "lru-cache": "^5.1.1",
-        "semver": "^6.3.1"
-      },
-      "engines": {
-        "node": ">=6.9.0"
-      }
-    },
-    "node_modules/@babel/helper-compilation-targets/node_modules/semver": {
-      "version": "6.3.1",
-      "dev": true,
-      "license": "ISC",
-      "bin": {
-        "semver": "bin/semver.js"
-      }
-    },
-    "node_modules/@babel/helper-globals": {
-      "version": "7.28.0",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=6.9.0"
-      }
-    },
-    "node_modules/@babel/helper-module-imports": {
-      "version": "7.27.1",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "@babel/traverse": "^7.27.1",
-        "@babel/types": "^7.27.1"
-      },
-      "engines": {
-        "node": ">=6.9.0"
-      }
-    },
-    "node_modules/@babel/helper-module-transforms": {
-      "version": "7.28.3",
-      "dev": true,
-      "license": "MIT",
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-      "funding": {
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-      },
-      "peerDependencies": {
-        "vega": "*",
-        "vega-lite": "*"
-      }
-    },
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-      }
-    },
-    "node_modules/vega-tooltip": {
-      "version": "1.0.0",
-      "license": "BSD-3-Clause",
-      "dependencies": {
-        "vega-util": "^2.0.0"
-      },
-      "funding": {
-        "url": "https://app.hubspot.com/payments/GyPC972GD9Rt"
-      }
-    },
-    "node_modules/vega-transforms": {
-      "version": "5.1.0",
-      "license": "BSD-3-Clause",
-      "peer": true,
-      "dependencies": {
-        "d3-array": "^3.2.4",
-        "vega-dataflow": "^6.1.0",
-        "vega-statistics": "^2.0.0",
-        "vega-time": "^3.1.0",
-        "vega-util": "^2.1.0"
-      }
-    },
-    "node_modules/vega-typings": {
-      "version": "2.1.0",
-      "license": "BSD-3-Clause",
-      "peer": true,
-      "dependencies": {
-        "@types/geojson": "7946.0.16",
-        "vega-event-selector": "^4.0.0",
-        "vega-expression": "^6.1.0",
-        "vega-util": "^2.1.0"
-      }
-    },
-    "node_modules/vega-util": {
-      "version": "2.1.0",
-      "license": "BSD-3-Clause"
-    },
-    "node_modules/vega-view": {
-      "version": "6.1.0",
-      "license": "BSD-3-Clause",
-      "peer": true,
-      "dependencies": {
-        "d3-array": "^3.2.4",
-        "d3-timer": "^3.0.1",
-        "vega-dataflow": "^6.1.0",
-        "vega-format": "^2.1.0",
-        "vega-functions": "^6.1.0",
-        "vega-runtime": "^7.1.0",
-        "vega-scenegraph": "^5.1.0",
-        "vega-util": "^2.1.0"
-      }
-    },
-    "node_modules/vega-view-transforms": {
-      "version": "5.1.0",
-      "license": "BSD-3-Clause",
-      "peer": true,
-      "dependencies": {
-        "vega-dataflow": "^6.1.0",
-        "vega-scenegraph": "^5.1.0",
-        "vega-util": "^2.1.0"
-      }
-    },
-    "node_modules/vega-voronoi": {
-      "version": "5.1.0",
-      "license": "BSD-3-Clause",
-      "peer": true,
-      "dependencies": {
-        "d3-delaunay": "^6.0.4",
-        "vega-dataflow": "^6.1.0",
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-      }
-    },
-    "node_modules/vega-wordcloud": {
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-      "license": "BSD-3-Clause",
-      "peer": true,
-      "dependencies": {
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-      }
-    },
-    "node_modules/vfile": {
-      "version": "6.0.3",
-      "license": "MIT",
-      "dependencies": {
-        "@types/unist": "^3.0.0",
-        "vfile-message": "^4.0.0"
-      },
-      "funding": {
-        "type": "opencollective",
-        "url": "https://opencollective.com/unified"
-      }
-    },
-    "node_modules/vfile-message": {
-      "version": "4.0.3",
-      "license": "MIT",
-      "dependencies": {
-        "@types/unist": "^3.0.0",
-        "unist-util-stringify-position": "^4.0.0"
-      },
-      "funding": {
-        "type": "opencollective",
-        "url": "https://opencollective.com/unified"
-      }
-    },
-    "node_modules/vite": {
-      "version": "6.4.1",
-      "license": "MIT",
-      "dependencies": {
-        "esbuild": "^0.25.0",
-        "fdir": "^6.4.4",
-        "picomatch": "^4.0.2",
-        "postcss": "^8.5.3",
-        "rollup": "^4.34.9",
-        "tinyglobby": "^0.2.13"
-      },
-      "bin": {
-        "vite": "bin/vite.js"
-      },
-      "engines": {
-        "node": "^18.0.0 || ^20.0.0 || >=22.0.0"
-      },
-      "funding": {
-        "url": "https://github.com/vitejs/vite?sponsor=1"
-      },
-      "optionalDependencies": {
-        "fsevents": "~2.3.3"
-      },
-      "peerDependencies": {
-        "@types/node": "^18.0.0 || ^20.0.0 || >=22.0.0",
-        "jiti": ">=1.21.0",
-        "less": "*",
-        "lightningcss": "^1.21.0",
-        "sass": "*",
-        "sass-embedded": "*",
-        "stylus": "*",
-        "sugarss": "*",
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-        },
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-        },
-        "lightningcss": {
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-          "optional": true
-        },
-        "sass-embedded": {
-          "optional": true
-        },
-        "stylus": {
-          "optional": true
-        },
-        "sugarss": {
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-        },
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-        }
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-      "version": "1.6.0",
-      "license": "MIT",
-      "dependencies": {
-        "@rollup/plugin-virtual": "^3.0.2",
-        "@swc/core": "^1.12.14",
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-        "uuid": "10.0.0"
-      },
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-        "vite": ">=2.8"
-      }
-    },
-    "node_modules/vite-plugin-wasm": {
-      "version": "3.5.0",
-      "license": "MIT",
-      "peerDependencies": {
-        "vite": "^2 || ^3 || ^4 || ^5 || ^6 || ^7"
-      }
-    },
-    "node_modules/vite/node_modules/fdir": {
-      "version": "6.5.0",
-      "license": "MIT",
-      "engines": {
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-      },
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-      },
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-        }
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-    },
-    "node_modules/vite/node_modules/picomatch": {
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-      "license": "MIT",
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-      },
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-      "dev": true,
-      "license": "ISC"
-    },
-    "node_modules/y18n": {
-      "version": "5.0.8",
-      "license": "ISC",
-      "peer": true,
-      "engines": {
-        "node": ">=10"
-      }
-    },
-    "node_modules/yallist": {
-      "version": "3.1.1",
-      "dev": true,
-      "license": "ISC"
-    },
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-      "version": "18.0.0",
-      "license": "MIT",
-      "peer": true,
-      "dependencies": {
-        "cliui": "^9.0.1",
-        "escalade": "^3.1.1",
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-        "string-width": "^7.2.0",
-        "y18n": "^5.0.5",
-        "yargs-parser": "^22.0.0"
-      },
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-      }
-    },
-    "node_modules/yargs-parser": {
-      "version": "22.0.0",
-      "license": "ISC",
-      "peer": true,
-      "engines": {
-        "node": "^20.19.0 || ^22.12.0 || >=23"
-      }
-    },
-    "node_modules/yocto-queue": {
-      "version": "0.1.0",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=10"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/sindresorhus"
-      }
-    },
-    "node_modules/zwitch": {
-      "version": "2.0.4",
-      "license": "MIT",
-      "funding": {
-        "type": "github",
-        "url": "https://github.com/sponsors/wooorm"
-      }
-    }
-  }
-}
diff --git a/ui/package.json b/ui/package.json
index a85962b1..37d2ba85 100644
--- a/ui/package.json
+++ b/ui/package.json
@@ -25,7 +25,7 @@
     "chartjs-chart-error-bars": "^4.4.0",
     "chartjs-plugin-datalabels": "^2.2.0",
     "framer-motion": "^11.0.20",
-    "js-yaml": "^4.1.0",
+    "js-yaml": "^4.1.1",
     "pako": "^2.1.0",
     "react": "^18.2.0",
     "react-bootstrap": "^2.10.1",

From d365cfe458dd5f6c90668b99ea846b8438746a6f Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Mon, 1 Dec 2025 17:52:03 -0500
Subject: [PATCH 41/42] updated package libraries

---
 ui/package.json | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/ui/package.json b/ui/package.json
index 37d2ba85..e406eb55 100644
--- a/ui/package.json
+++ b/ui/package.json
@@ -18,12 +18,14 @@
     "@tanstack/react-table": "^8.15.3",
     "@types/pako": "^2.0.4",
     "@uidotdev/usehooks": "^2.4.1",
+    "@uwdata/vgplot": "^0.21.1",
     "axios": "^1.12.0",
     "bootstrap": "^5.3.3",
     "bootstrap-icons": "^1.11.3",
     "chart.js": "^4.4.2",
     "chartjs-chart-error-bars": "^4.4.0",
     "chartjs-plugin-datalabels": "^2.2.0",
+    "embedding-atlas": "^0.13.0",
     "framer-motion": "^11.0.20",
     "js-yaml": "^4.1.1",
     "pako": "^2.1.0",

From 37b786bb6feb98c8ad0fe4c6982b38d8cd30b232 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi 
Date: Mon, 1 Dec 2025 18:07:01 -0500
Subject: [PATCH 42/42] Small search changes

---
 ui/src/pages/home.tsx | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx
index 1f5b6675..6767d614 100644
--- a/ui/src/pages/home.tsx
+++ b/ui/src/pages/home.tsx
@@ -76,12 +76,12 @@ export const Home = () => {
             interact with the data via an OpenAPI-compatible API.
           

         

-        

+        

           

             {searchType === 'b2b' ? (
                {
@@ -94,7 +94,7 @@ export const Home = () => {
             ) : (
                {