From 7e7fecb24de75a96625a79241825340b46295c5a Mon Sep 17 00:00:00 2001 From: Sam Park Date: Fri, 24 Oct 2025 14:48:42 -0400 Subject: [PATCH 01/76] ui cleanup --- .../cards/stat-card-wrapper.tsx | 15 ++++------ .../charts/genomic-feature-bar.tsx | 7 ++++- .../bed-splash-components/header.tsx | 5 ++-- .../bed-splash-components/plots.tsx | 13 ++++---- .../bed-splash-components/refgenome-modal.tsx | 4 +-- .../bedset-splash-components/beds-table.tsx | 2 +- .../cards/gc-content-card.tsx | 8 ++--- .../cards/median-region-width.tsx | 7 ++--- .../cards/median-tss-distance.tsx | 7 ++--- .../cards/stat-card-wrapper.tsx | 15 ++++------ .../charts/genomic-feature-bar.tsx | 10 ++++--- .../bedset-splash-components/header.tsx | 15 +++++----- .../bedset-splash-components/plots.tsx | 10 +++---- ui/src/components/nav/nav-desktop.tsx | 17 +++++------ ui/src/components/nav/nav-logo.tsx | 4 +-- .../text2bed/t2b-search-results-table.tsx | 2 +- ui/src/custom.scss | 6 ++-- ui/src/pages/bed-splash.tsx | 30 +++++++++---------- ui/src/pages/bedset-splash.tsx | 20 ++++++------- ui/src/pages/metrics.tsx | 2 -- ui/src/queries/useText2BedSearch.ts | 1 - ui/src/utils.ts | 8 +++++ 22 files changed, 101 insertions(+), 107 deletions(-) diff --git a/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx b/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx index 7b1b5b46..0fd96d5b 100644 --- a/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx +++ b/ui/src/components/bed-splash-components/cards/stat-card-wrapper.tsx @@ -12,18 +12,15 @@ export const StatCard = (props: Props) => { const renderTooltip = () => {tooltip || 'No tooltip available'}; return ( +
-
-

{title}

-
-

{stat}

-
-
- - - +
+
{title}
+
+

{stat}

+ ); }; diff --git a/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx b/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx index 59342828..c3a65988 100644 --- a/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx +++ b/ui/src/components/bed-splash-components/charts/genomic-feature-bar.tsx @@ -24,6 +24,11 @@ const chartOptions = { display: false, }, }, + layout: { + padding: { + bottom: 25 + } + } }; export const GenomicFeatureBar = (props: Props) => { @@ -98,7 +103,7 @@ export const GenomicFeatureBar = (props: Props) => { } return ( -
+

Genomic Features

diff --git a/ui/src/components/bed-splash-components/header.tsx b/ui/src/components/bed-splash-components/header.tsx index 7a04d4a1..5bf6c884 100644 --- a/ui/src/components/bed-splash-components/header.tsx +++ b/ui/src/components/bed-splash-components/header.tsx @@ -35,7 +35,6 @@ export const BedSplashHeader = (props: Props) => {

- {metadata?.id || 'No ID available'}

-
{metadata.name}
-

{metadata?.description || 'No description available'}

+
{metadata.name}
+

{metadata?.description || 'No description available'}

diff --git a/ui/src/components/bed-splash-components/plots.tsx b/ui/src/components/bed-splash-components/plots.tsx index d04546ee..3680d1db 100644 --- a/ui/src/components/bed-splash-components/plots.tsx +++ b/ui/src/components/bed-splash-components/plots.tsx @@ -30,16 +30,16 @@ const Plot = (props: PlotProps) => { setShow(true); } }} - className="h-100 border rounded p-1 shadow-sm hover-border-primary transition-all" + className="h-100 border rounded p-2 shadow-sm hover-border-primary transition-all" > -
- {title} +
+

{title}

{/* */}
- {alt} + {alt}
{ export const Plots = (props: PlotsProps) => { const { metadata } = props; - const plotNames = metadata.plots ? Object.keys(metadata.plots) : []; + // comment out partitions because we already have it in statistics section + const plotNames = metadata.plots ? Object.keys(metadata.plots).filter((name: string) => name != 'partitions') : []; return ( - + {metadata.plots && chunkArray(plotNames, 3).map((chunk, idx) => ( diff --git a/ui/src/components/bed-splash-components/refgenome-modal.tsx b/ui/src/components/bed-splash-components/refgenome-modal.tsx index e240530f..65cc4cec 100644 --- a/ui/src/components/bed-splash-components/refgenome-modal.tsx +++ b/ui/src/components/bed-splash-components/refgenome-modal.tsx @@ -13,8 +13,6 @@ type Props = { export const RefGenomeModal = (props: Props) => { const { show, onHide, genomeStats } = props; - console.log(genomeStats?.compared_genome) - return ( { ) .map(genome => ( { />
- +
{table.getHeaderGroups().map((headerGroup) => ( diff --git a/ui/src/components/bedset-splash-components/cards/gc-content-card.tsx b/ui/src/components/bedset-splash-components/cards/gc-content-card.tsx index 9983fccd..61b1bbf2 100644 --- a/ui/src/components/bedset-splash-components/cards/gc-content-card.tsx +++ b/ui/src/components/bedset-splash-components/cards/gc-content-card.tsx @@ -13,13 +13,11 @@ export const GCContentCard = (props: Props) => { return (
-

+

{metadata.statistics?.mean?.gc_content ? `${formatNumberWithCommas(Math.round((metadata.statistics?.mean?.gc_content || 0)*100)/100)}` - : 'N/A'} -

- {/* plus minus */} -

± {formatNumberWithCommas(Math.round((metadata.statistics?.sd?.gc_content || 0)*100)/100)}

+ : 'N/A'} {' '} ± {formatNumberWithCommas(Math.round((metadata.statistics?.sd?.gc_content || 0)*100)/100)} +
); diff --git a/ui/src/components/bedset-splash-components/cards/median-region-width.tsx b/ui/src/components/bedset-splash-components/cards/median-region-width.tsx index b198fec2..7337d426 100644 --- a/ui/src/components/bedset-splash-components/cards/median-region-width.tsx +++ b/ui/src/components/bedset-splash-components/cards/median-region-width.tsx @@ -13,11 +13,8 @@ export const MeanRegionWidthCard = (props: Props) => { return (
-

- {formatNumberWithCommas(Math.round(metadata.statistics?.mean?.mean_region_width || 0))} bp -

- {/* plus minus */} -

+

+ {formatNumberWithCommas(Math.round(metadata.statistics?.mean?.mean_region_width || 0))} {' '} ± {formatNumberWithCommas(Math.round(metadata.statistics?.sd?.mean_region_width || 0))} bp

diff --git a/ui/src/components/bedset-splash-components/cards/median-tss-distance.tsx b/ui/src/components/bedset-splash-components/cards/median-tss-distance.tsx index 62cb1347..ac2e61f9 100644 --- a/ui/src/components/bedset-splash-components/cards/median-tss-distance.tsx +++ b/ui/src/components/bedset-splash-components/cards/median-tss-distance.tsx @@ -15,11 +15,8 @@ export const MedianTssDistCard = (props: Props) => { tooltip="The median distance of the regions to the nearest transcription start site." >
-

- {formatNumberWithCommas(Math.round(metadata?.statistics?.mean?.median_tss_dist || 0))} bp -

- {/* plus minus */} -

+

+ {formatNumberWithCommas(Math.round(metadata?.statistics?.mean?.median_tss_dist || 0))} {' '} ± {formatNumberWithCommas(Math.round(metadata?.statistics?.sd?.median_tss_dist || 0))} bp

diff --git a/ui/src/components/bedset-splash-components/cards/stat-card-wrapper.tsx b/ui/src/components/bedset-splash-components/cards/stat-card-wrapper.tsx index 34daf17e..fc51cc25 100644 --- a/ui/src/components/bedset-splash-components/cards/stat-card-wrapper.tsx +++ b/ui/src/components/bedset-splash-components/cards/stat-card-wrapper.tsx @@ -11,16 +11,13 @@ export const StatCard = (props: Props) => { const renderTooltip = () => {tooltip || 'No tooltip available'}; return ( -
-
-

{title}

-
{children}
-
- - - + +
+
+
{title}
+
{children}
-
+ ); }; diff --git a/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx b/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx index fd445c82..c820a99e 100644 --- a/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx +++ b/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx @@ -33,6 +33,11 @@ const chartOptions = { display: false, }, }, + layout: { + padding: { + bottom: 25 + } + } }; export const GenomicFeatureBar = (props: Props) => { @@ -188,7 +193,7 @@ export const GenomicFeatureBar = (props: Props) => { } return ( -
+

Genomic Features

@@ -235,9 +240,6 @@ export const GenomicFeatureBar = (props: Props) => { }} />
-
-

Learn more

-
); diff --git a/ui/src/components/bedset-splash-components/header.tsx b/ui/src/components/bedset-splash-components/header.tsx index c33a1fb8..2896c572 100644 --- a/ui/src/components/bedset-splash-components/header.tsx +++ b/ui/src/components/bedset-splash-components/header.tsx @@ -30,7 +30,6 @@ export const BedsetSplashHeader = (props: Props) => {

- {metadata?.id || 'No name available'}

-

{metadata?.description || 'No description available'}

+

{metadata?.description || 'No description available'}

Author: {metadata?.author || 'None'}

-

Source: {metadata?.source || 'None'}

+

Source: {metadata?.source || 'None'}

-
-
+
+

-

+
{metadata.md5sum}

{metadata.bed_ids && (

-

+
{metadata.bed_ids?.length} BED files
@@ -152,7 +151,7 @@ export const BedsetSplashHeader = (props: Props) => {
+ className="d-flex flex-column flex-md-row justify-content-xl-between align-items-start align-items-xl-end text-sm">

diff --git a/ui/src/components/bedset-splash-components/plots.tsx b/ui/src/components/bedset-splash-components/plots.tsx index 4e2cdce3..86fddb90 100644 --- a/ui/src/components/bedset-splash-components/plots.tsx +++ b/ui/src/components/bedset-splash-components/plots.tsx @@ -31,14 +31,14 @@ const Plot = (props: PlotProps) => { }} className="h-100 border rounded p-1 shadow-sm hover-border-primary transition-all" > -

- {title} +
+ {title} {/* */}
-
- +
+
{ const plotNames = metadata.plots ? Object.keys(metadata.plots) : []; return ( - + {metadata.plots && chunkArray(plotNames, 3).map((chunk, idx) => ( diff --git a/ui/src/components/nav/nav-desktop.tsx b/ui/src/components/nav/nav-desktop.tsx index ab26e083..61b12094 100644 --- a/ui/src/components/nav/nav-desktop.tsx +++ b/ui/src/components/nav/nav-desktop.tsx @@ -6,28 +6,27 @@ export const NavDesktop = () => { const { cart } = useBedCart(); return (
- + diff --git a/ui/src/custom.scss b/ui/src/custom.scss index 4c40686a..eb74476a 100644 --- a/ui/src/custom.scss +++ b/ui/src/custom.scss @@ -98,15 +98,15 @@ a { } .bed-splash-genomic-feature-bar-height { - height: 27rem; + height: 26.375rem; } .bedset-splash-stat-card-height { - min-height: 7rem; + min-height: 9rem; } .bedset-splash-genomic-feature-bar-height { - height: 24rem; + height: 24.875rem; } .min-h-screen { diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx index 75f9521f..0618c31d 100644 --- a/ui/src/pages/bed-splash.tsx +++ b/ui/src/pages/bed-splash.tsx @@ -101,10 +101,10 @@ export const BedSplash = () => { >

Oh no!

-

+

We could not find BED with record identifier:
{bedId} -
+

@@ -141,9 +141,9 @@ export const BedSplash = () => { {metadata !== undefined ? : null} - -

-

Overview

+ + +
Overview
Name Genome Tissue
@@ -199,8 +199,8 @@ export const BedSplash = () => { - -

BEDsets

+ +
BEDsets
@@ -248,31 +248,31 @@ export const BedSplash = () => { - -

Statistics

+ +
Statistics
{metadata && ( - + )} - + - -

Plots

+ +
Plots
 {neighbours && ( - -

Similar BED Files

+ +
Similar BED Files
 diff --git a/ui/src/pages/bedset-splash.tsx b/ui/src/pages/bedset-splash.tsx index d7ffc5af..5b3500e2 100644 --- a/ui/src/pages/bedset-splash.tsx +++ b/ui/src/pages/bedset-splash.tsx @@ -71,10 +71,10 @@ export const BedsetSplash = () => { >

Oh no!

-

+

We could not find BEDset with record identifier:
{bedsetId} -
+

@@ -108,29 +108,29 @@ export const BedsetSplash = () => {

{(metadata !== undefined) && bedfiles ? : null} - -

Statistics

+ +
Statistics
{metadata && ( - + )} - + - + -

Plots

+
Plots
- -

Constituent BED Files

+ +
Constituent BED Files
{isLoadingBedfiles ? (
diff --git a/ui/src/pages/metrics.tsx b/ui/src/pages/metrics.tsx index b3d2757b..c524a755 100644 --- a/ui/src/pages/metrics.tsx +++ b/ui/src/pages/metrics.tsx @@ -73,8 +73,6 @@ export const Metrics = () => { const { data: detailedStats, isLoading: statsIsLoading } = useDetailedStats(); const { data: usageStats, isLoading: usageIsLoading } = useDetailedUsage(); - console.log(detailedStats); - if (statsIsLoading || usageIsLoading) { return ( diff --git a/ui/src/queries/useText2BedSearch.ts b/ui/src/queries/useText2BedSearch.ts index 229eb7e6..f469560c 100644 --- a/ui/src/queries/useText2BedSearch.ts +++ b/ui/src/queries/useText2BedSearch.ts @@ -21,7 +21,6 @@ export const useText2BedSearch = (query: SearchQuery) => { if (autoRun !== undefined && autoRun === true && !!q) { enabled = true; } - console.log(assay) return useQuery({ queryKey: ['search', q, limit, offset, genome, assay], queryFn: async () => { diff --git a/ui/src/utils.ts b/ui/src/utils.ts index 4cc01e5b..8baa86bd 100644 --- a/ui/src/utils.ts +++ b/ui/src/utils.ts @@ -118,6 +118,14 @@ export const snakeToTitleCase = (str: string) => { .join(' '); }; +export const toTitleCase = (str: string): string => { + return str + .toLowerCase() + .split(' ') + .map(word => word.charAt(0).toUpperCase() + word.slice(1)) + .join(' '); +} + export const convertStatusCodeToMessage = (statusCode: number | undefined) => { if (statusCode === undefined) { return 'Unknown Error'; From 836221ba83fb8c7097239e542f4499437a6eac2c Mon Sep 17 00:00:00 2001 From: Sam Park Date: Fri, 24 Oct 2025 20:47:37 -0400 Subject: [PATCH 02/76] try random things --- ui/package-lock.json | 5381 ++++++++++++----- ui/package.json | 5 +- .../bed-splash-components/bed-atlas.tsx | 221 + .../bed-splash-components/header.tsx | 8 +- ui/src/components/nav/nav-desktop.tsx | 8 +- ui/src/components/search/search-bar.tsx | 2 +- ui/src/custom.scss | 25 +- ui/src/pages/bed-splash.tsx | 3 + ui/src/utils.ts | 23 + 9 files changed, 4106 insertions(+), 1570 deletions(-) create mode 100644 ui/src/components/bed-splash-components/bed-atlas.tsx diff --git a/ui/package-lock.json b/ui/package-lock.json index 8e03fbf4..b69667fb 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -18,6 +18,7 @@ "chart.js": "^4.4.2", "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", + "embedding-atlas": "^0.11.0", "framer-motion": "^11.0.20", "js-yaml": "^4.1.0", "react": "^18.2.0", @@ -50,48 +51,25 @@ "vite": "^6.3.6" } }, - "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": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/compat-data/-/compat-data-7.28.5.tgz", + "integrity": "sha512-6uFXyCayocRbqhZOB+6XcuZbkMNimwfVGFji8CTZnCzOHVGvDqzvitu1re2AU5LROliz7eQPhB8CpAMvnx9EjA==", "dev": true, "license": "MIT", "engines": { @@ -99,22 +77,23 @@ } }, "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": "7.28.5", + "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.28.5.tgz", + "integrity": "sha512-e7jT4DxYvIDLk1ZHmU/m/mB19rex9sv0c2ftBtjSBv+kVM/902eh0fINUzD7UwLLNR+jU585GxUJ8/EBfAM5fw==", + "dev": true, + "license": "MIT", + "peer": true, + "dependencies": { + "@babel/code-frame": "^7.27.1", + "@babel/generator": "^7.28.5", + "@babel/helper-compilation-targets": "^7.27.2", + "@babel/helper-module-transforms": "^7.28.3", + "@babel/helpers": "^7.28.4", + "@babel/parser": "^7.28.5", + "@babel/template": "^7.27.2", + "@babel/traverse": "^7.28.5", + "@babel/types": "^7.28.5", + "@jridgewell/remapping": "^2.3.5", "convert-source-map": "^2.0.0", "debug": "^4.1.0", "gensync": "^1.0.0-beta.2", @@ -140,16 +119,16 @@ } }, 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"peer": true, + "license": "ISC", "engines": { "node": ">=10" } @@ -5980,7 +8247,7 @@ "version": "18.0.0", "resolved": "https://registry.npmjs.org/yargs/-/yargs-18.0.0.tgz", "integrity": "sha512-4UEqdc2RYGHZc7Doyqkrqiln3p9X2DZVxaGbwhn2pi7MrRagKaOcIKe8L3OxYcbhXLgLFUS3zAYuQjKBQgmuNg==", - "peer": true, + "license": "MIT", "dependencies": { "cliui": "^9.0.1", "escalade": "^3.1.1", @@ -5997,7 +8264,7 @@ "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==", - "peer": true, + "license": "ISC", "engines": { "node": "^20.19.0 || ^22.12.0 || >=23" } @@ -6007,6 +8274,7 @@ "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" }, @@ -6018,6 +8286,7 @@ "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 081c74b0..a6a7caac 100644 --- a/ui/package.json +++ b/ui/package.json @@ -22,6 +22,7 @@ "chart.js": "^4.4.2", "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", + "embedding-atlas": "^0.11.0", "framer-motion": "^11.0.20", "js-yaml": "^4.1.0", "react": "^18.2.0", @@ -35,8 +36,8 @@ "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/components/bed-splash-components/bed-atlas.tsx b/ui/src/components/bed-splash-components/bed-atlas.tsx new file mode 100644 index 00000000..d7257694 --- /dev/null +++ b/ui/src/components/bed-splash-components/bed-atlas.tsx @@ -0,0 +1,221 @@ +import { EmbeddingAtlas } from 'embedding-atlas/react'; +import { useEffect, useState, useRef, useMemo } from 'react'; +import * as vg from '@uwdata/vgplot' +import { tableau20 } from '../../utils'; + +type Props = { + bedId: string; + neighbors?: any; +} + +export const BEDAtlas = (props: Props) => { + const { } = props; + + const dotPlotRef = useRef(null); + const colorLegendRef = useRef(null); + const containerRef = useRef(null); + + const [containerWidth, setContainerWidth] = useState(900); + const [isReady, setIsReady] = useState(false); + const [colorGrouping, setColorGrouping] = useState('cell_line'); + + const coordinator = useMemo(() => new vg.Coordinator(vg.wasmConnector()), []); + const $legendSelection = vg.Selection.intersect(); + + const initializeData = async (coordinator: any) => { + const url = 'https://raw.githubusercontent.com/databio/bedbase-loader/master/umap/hg38_umap.json'; + await coordinator.exec([ + vg.sql`CREATE OR REPLACE TABLE data AS + SELECT + unnest(nodes, recursive := true) + FROM read_json_auto('${url}')`, + // vg.sql`CREATE OR REPLACE TABLE data AS + // SELECT + // *, + // (DENSE_RANK() OVER (ORDER BY assay) - 1)::INTEGER AS assay_category, + // (DENSE_RANK() OVER (ORDER BY cell_line) - 1)::INTEGER AS cell_line_category + // FROM data` + ]); + } + + const plotData = () => { + let bedQuery = vg.Query.from('data') + .select( + 'x', + 'y', + 'id', + 'name', + 'description', + 'assay', + 'cell_line', + ); + + const dotPlot = vg.plot( + vg.dot(vg.from(bedQuery, {}), { + x: 'x', + y: 'y', + z: colorGrouping, + fill: colorGrouping, + colorRange: tableau20, + opacity: 0.5, + r: 1.5, + channels: { 'Name:': 'name', 'Cell Line:': 'cell_line', 'Assay:': 'assay' }, + tip: { + format: { + 'Name:': true, + 'Cell Line:': true, + 'Assay:': true, + x: false, + y: false, + z: false, + fill: false + }, + }, + }), + vg.highlight({ by: $legendSelection, fill: '#ccc', fillOpacity: 0.2 }), + vg.region({ as: $legendSelection, channels: ['z'] }), + vg.name('dotPlot'), + vg.width(containerWidth), + vg.height(500), + vg.xLabel(null), + vg.yLabel(null), + // vg.gridY(), + // vg.gridX(), + ); + + const colorLegend = vg.colorLegend({ + for: 'dotPlot', + as: $legendSelection, + columns: 1, + }); + + if (dotPlotRef.current) dotPlotRef.current.replaceChildren(dotPlot); + if (colorLegendRef.current) colorLegendRef.current.replaceChildren(colorLegend); + } + + useEffect(() => { + vg.coordinator(coordinator); + + if (containerRef.current) { + setContainerWidth(containerRef.current.offsetWidth); + } + plotData() + }, [isReady, colorGrouping]); + + useEffect(() => { + initializeData(coordinator).then(() => setIsReady(true)); + }, []); + + return ( + <> + {isReady && ( + <> +
+
Embedding Atlas
+
+
+
+ {/* */} +
+
+
+
+
+
+
+ Legend +
+ setColorGrouping(e.target.value)} + /> + + setColorGrouping(e.target.value)} + /> + +
+
+
+
+
+
+ +
+
+ {/* {selectedPoint ? ( +
+

Name: {selectedPoint.name}

+

Cell Line: {selectedPoint.cell_line}

+

Assay: {selectedPoint.assay}

+

Description: {selectedPoint.description}

+
+ ) : ( +

Click a point to view details.

+ )} */} +
+
+
+
+
+
+
+
+
+ +
+
+
+
+
+ + )} + + ); +} \ No newline at end of file diff --git a/ui/src/components/bed-splash-components/header.tsx b/ui/src/components/bed-splash-components/header.tsx index 5bf6c884..3fe26a19 100644 --- a/ui/src/components/bed-splash-components/header.tsx +++ b/ui/src/components/bed-splash-components/header.tsx @@ -152,12 +152,12 @@ export const BedSplashHeader = (props: Props) => { {metadata.files?.bed_file && ( - {(metadata.files?.bed_file?.access_methods || []).map((method) => { + {(metadata.files?.bed_file?.access_methods || []).map((method, index) => { if (method.type === 'local' || method.type === 's3') { return null; } return ( - + {method.access_id ? 'BED file' : 'No download link available'} ( {bytesToSize(metadata.files?.bed_file?.size || 0)}) @@ -167,12 +167,12 @@ export const BedSplashHeader = (props: Props) => { )} {metadata.files?.bigbed_file && ( - {(metadata.files?.bigbed_file?.access_methods || []).map((method) => { + {(metadata.files?.bigbed_file?.access_methods || []).map((method, index) => { if (method.type === 'local' || method.type === 's3') { return null; } return ( - + {method.access_id ? 'BigBED file' : 'No download link available'} ( {bytesToSize(metadata.files?.bigbed_file?.size || 0)}) diff --git a/ui/src/components/nav/nav-desktop.tsx b/ui/src/components/nav/nav-desktop.tsx index 61b12094..1b4cf09a 100644 --- a/ui/src/components/nav/nav-desktop.tsx +++ b/ui/src/components/nav/nav-desktop.tsx @@ -6,22 +6,22 @@ export const NavDesktop = () => { const { cart } = useBedCart(); return (
    -
  • +
  • GitHub
    • -
  • +
  • Docs
    • -
  • +
  • API
    • -
  • +
  • Search diff --git a/ui/src/components/search/search-bar.tsx b/ui/src/components/search/search-bar.tsx index 2538b429..e1437aa1 100644 --- a/ui/src/components/search/search-bar.tsx +++ b/ui/src/components/search/search-bar.tsx @@ -74,7 +74,7 @@ export const SearchBar = (props: Props) => { {searchView === 't2b' && (
Overview
@@ -275,7 +275,7 @@ export const BedSplash = () => { {bedId && ( <> - + {/* */} )} From 361d0c29d42a01decb5f5a0da9c5538be3a19c5b Mon Sep 17 00:00:00 2001 From: Sam Park Date: Wed, 29 Oct 2025 17:46:31 -0400 Subject: [PATCH 05/76] atlas basic functionality --- .../bed-splash-components/bad-atlas.tsx | 317 ++++++++++++++---- ui/src/pages/bed-splash.tsx | 4 +- ui/src/utils.ts | 16 +- 3 files changed, 276 insertions(+), 61 deletions(-) diff --git a/ui/src/components/bed-splash-components/bad-atlas.tsx b/ui/src/components/bed-splash-components/bad-atlas.tsx index 1aba0abc..44df6520 100644 --- a/ui/src/components/bed-splash-components/bad-atlas.tsx +++ b/ui/src/components/bed-splash-components/bad-atlas.tsx @@ -1,8 +1,9 @@ import { EmbeddingViewMosaic } from 'embedding-atlas/react'; import { useEffect, useState, useRef, useMemo } from 'react'; import * as vg from '@uwdata/vgplot' -import { tableau20 } from '../../utils'; -import { eq } from '@uwdata/mosaic-sql'; + +import { isPointInPolygon, tableau20 } from '../../utils'; +import { useBedCart } from '../../contexts/bedcart-context'; type Props = { bedId: string; @@ -11,32 +12,146 @@ type Props = { export const BADAtlas = (props: Props) => { const { bedId } = props; + const { addBedToCart } = useBedCart(); const containerRef = useRef(null); const [containerWidth, setContainerWidth] = useState(900); const [isReady, setIsReady] = useState(false); const [colorGrouping, setColorGrouping] = useState('cell_line_category'); + const [selectedPoints, setSelectedPoints] = useState([]); + const [initialPoint, setInitialPoint] = useState(null); + const [viewportState, setViewportState] = useState(null); + const [legendItems, setLegendItems] = useState([]); + const [filterSelection, setFilterSelection] = useState(null); + const [addedToCart, setAddedToCart] = useState(false); const coordinator = useMemo(() => new vg.Coordinator(vg.wasmConnector()), []); + const filter = useMemo(() => vg.Selection.intersect(), []); + // Create a stable source object for legend filter updates + const legendFilterSource = useMemo(() => ({}), []); - // Point selection (for clicks) - const selection = useMemo(() => { - const sel = vg.Selection.intersect(); - sel.addEventListener('value', (value) => { - console.log('Point selection updated:', value); + const centerOnPoint = (point: any, scale: number = 1) => { + setViewportState({ + x: point.x, + y: point.y, + scale: scale }); - return sel; - }, []); + }; + + const handleLegendClick = (item: any) => { + if (filterSelection?.category === item.category) { + setFilterSelection(null); + // Clear the filter by updating with null predicate using the same source + filter.update({ + source: legendFilterSource, + value: null, + predicate: null + }); + } else { + setFilterSelection(item); + // Update with new filter - will replace previous clause from same source + filter.update({ + source: legendFilterSource, + value: item.category, + predicate: vg.eq(colorGrouping, item.category) + }); + } + }; + + const handlePointSelection = (dataPoints: any[] | null) => { + // console.log('Selection changed via onSelection callback:', dataPoints); + const points = dataPoints || []; + + if (initialPoint) { + const hasInitialPoint = points.some(p => p.identifier === initialPoint.identifier); + if (!hasInitialPoint) { + setSelectedPoints([initialPoint, ...points]); + } else { + setSelectedPoints(points); + } + } else { + setSelectedPoints(points); + } + }; // Range selection (for rectangle/lasso) - const rangeSelection = useMemo(() => { - const sel = vg.Selection.intersect(); - sel.addEventListener('value', (value) => { - console.log('Range selection updated:', value); - }); - return sel; - }, []); + const handleRangeSelection = async (coordinator: any, value: any) => { + // console.log('Range selection updated:', value); + + if (!value) { + return; + } + + let result; + + // Check if rectangle selection (bounding box) + if (typeof value === 'object' && 'xMin' in value) { + result = await coordinator.query( + `SELECT + x, y, + ${colorGrouping} as category, + name as text, + id as identifier, + {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields + FROM data + WHERE x >= ${value.xMin} AND x <= ${value.xMax} AND y >= ${value.yMin} AND y <= ${value.yMax}`, + { type: 'json' } + ) as any[]; + } + // Check if lasso selection (array of points) + else if (Array.isArray(value) && value.length > 0) { + // First get points within bounding box (optimization) + const xCoords = value.map((p: any) => p.x); + const yCoords = value.map((p: any) => p.y); + const xMin = Math.min(...xCoords); + const xMax = Math.max(...xCoords); + const yMin = Math.min(...yCoords); + const yMax = Math.max(...yCoords); + + // Only fetch x, y, identifier for filtering, then get full data for matches + const candidates: any = await coordinator.query( + `SELECT x, y, id as identifier FROM data + WHERE x >= ${xMin} AND x <= ${xMax} AND y >= ${yMin} AND y <= ${yMax}`, + { type: 'json' } + ); + + // Filter to points inside polygon + const filteredIds = candidates + .filter((point: any) => isPointInPolygon(point, value)) + .map((p: any) => `'${p.identifier}'`) + .join(','); + + if (filteredIds) { + result = await coordinator.query( + `SELECT + x, y, + ${colorGrouping} as category, + name as text, + id as identifier, + {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields + FROM data + WHERE id IN (${filteredIds})`, + { type: 'json' } + ) as any[]; + } else { + result = []; + } + } + + if (result && result.length > 0) { + if (initialPoint) { + const hasInitialPoint = result.some((p: any) => p.identifier === initialPoint.identifier); + if (!hasInitialPoint) { + setSelectedPoints([initialPoint, ...result]); + } else { + setSelectedPoints(result); + } + } else { + setSelectedPoints(result); + } + } + }; const initializeData = async (coordinator: any) => { const url = 'https://raw.githubusercontent.com/databio/bedbase-loader/master/umap/hg38_umap.json'; @@ -54,31 +169,71 @@ export const BADAtlas = (props: Props) => { ]); } - useEffect(() => { - if (containerRef.current) { - setContainerWidth(containerRef.current.offsetWidth); - } - }, [isReady]); + const fetchLegendItems = async (coordinator: any) => { + const result = await coordinator.query( + `SELECT DISTINCT + ${colorGrouping.replace('_category', '')} as name, + ${colorGrouping} as category + FROM data + ORDER BY ${colorGrouping}`, + { type: 'json' } + ) as any[]; + + return result + } - useEffect(() => { + useEffect(() => { // initialize data initializeData(coordinator).then(() => { - // Preselect the bedId - selection.update({ - source: {}, - predicate: eq('id', bedId), - value: bedId - }); setIsReady(true); }); }, []); + useEffect(() => { // resize width of view + if (containerRef.current) { + setContainerWidth(containerRef.current.offsetWidth); + } + }, [isReady]); + + useEffect(() => { // set legend items + if (isReady) { + fetchLegendItems(coordinator).then(result => { + setLegendItems(result) + }) + } + }, [isReady, colorGrouping]) + + useEffect(() => { // fetch initial bed id + if (isReady) { + setTimeout(async () => { + const points: any = await coordinator.query( + `SELECT + x, y, + ${colorGrouping} as category, + name as text, + id as identifier, + {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields + FROM data + WHERE id = '${bedId}'`, + { type: 'json' } + ); + + if (points && points.length > 0) { + setInitialPoint(points[0]); + setSelectedPoints([points[0]]); + } + }, 200); + } + }, [isReady, bedId, coordinator, colorGrouping]); + return ( <> {isReady && ( -
-
Bad Embedding Atlas
-
+
+
+
BED Embedding Atlas
+
+
{ config={{ autoLabelEnabled: false, }} - theme={{ - statusBar: true, - }} - tooltip={bedId} - selection={selection} - rangeSelection={rangeSelection} - // onSelection={(dataPoints) => { - // console.log('User clicked:', dataPoints); - // }} - // onRangeSelection={(value) => { - // console.log('User drew rectangle/lasso:', value); - // }} + filter={filter} + viewportState={viewportState} + onViewportState={setViewportState} + selection={selectedPoints} + onSelection={handlePointSelection} + onRangeSelection={(e) => handleRangeSelection(coordinator, e)} />
-
-
+
+
Legend
@@ -151,22 +300,74 @@ export const BADAtlas = (props: Props) => {
-
+
+
+ + {legendItems?.map((item: any) => ( + handleLegendClick(item)} + key={item.category} + > + + + ))} + +
+ + {item.name} +
-
-
- {/* {selectedPoint ? ( -
-

Name: {selectedPoint.name}

-

Cell Line: {selectedPoint.cell_line}

-

Assay: {selectedPoint.assay}

-

Description: {selectedPoint.description}

-
- ) : ( -

Click a point to view details.

- )} */} +
+
+ Selected Points + +
+
+ + + + + + + + + + + {selectedPoints?.map((point: any, index: number) => ( + centerOnPoint(point, 0.3)} key={index}> + + + + + + ))} + +
BED NameAssayCell LineDescription
{point.text}{point.fields.Assay}{point.fields['Cell Line']}{point.fields.Description}
diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx index e2c67436..42ce9fb3 100644 --- a/ui/src/pages/bed-splash.tsx +++ b/ui/src/pages/bed-splash.tsx @@ -17,7 +17,7 @@ import { snakeToTitleCase } from '../utils'; import { Text2BedSearchResultsTable } from '../components/search/text2bed/t2b-search-results-table'; import { useBedNeighbours } from '../queries/useBedNeighbours'; import type { components } from '../../bedbase-types.d.ts'; -import { BEDAtlas } from '../components/bed-splash-components/bed-atlas.tsx'; +// import { BEDAtlas } from '../components/bed-splash-components/bed-atlas.tsx'; import { BADAtlas } from '../components/bed-splash-components/bad-atlas.tsx'; // Use the response type to properly type the metadata @@ -272,7 +272,7 @@ export const BedSplash = () => { - {bedId && ( + {bedId && metadata?.name?.includes('encode') && ( <> {/* */} diff --git a/ui/src/utils.ts b/ui/src/utils.ts index c1721082..dcc06875 100644 --- a/ui/src/utils.ts +++ b/ui/src/utils.ts @@ -165,4 +165,18 @@ export const tableau20 = [ '#dbdb8d', '#17becf', '#9edae5', - ]; \ No newline at end of file + ]; + +// Point-in-polygon test using ray casting algorithm +export const isPointInPolygon = (point: {x: number, y: number}, polygon: {x: number, y: number}[]) => { + let inside = false; + for (let i = 0, j = polygon.length - 1; i < polygon.length; j = i++) { + const xi = polygon[i].x, yi = polygon[i].y; + const xj = polygon[j].x, yj = polygon[j].y; + + const intersect = ((yi > point.y) !== (yj > point.y)) + && (point.x < (xj - xi) * (point.y - yi) / (yj - yi) + xi); + if (intersect) inside = !inside; + } + return inside; +}; \ No newline at end of file From 1d12aa3914942de4e1bd1d30decdb369679e6a0e Mon Sep 17 00:00:00 2001 From: Sam Park Date: Wed, 29 Oct 2025 20:07:20 -0400 Subject: [PATCH 06/76] neighbors in atlas --- .../bed-splash-components/bad-atlas.tsx | 129 ++++++++++++++---- ui/src/pages/bed-splash.tsx | 24 +++- 2 files changed, 121 insertions(+), 32 deletions(-) diff --git a/ui/src/components/bed-splash-components/bad-atlas.tsx b/ui/src/components/bed-splash-components/bad-atlas.tsx index 44df6520..8e0d5446 100644 --- a/ui/src/components/bed-splash-components/bad-atlas.tsx +++ b/ui/src/components/bed-splash-components/bad-atlas.tsx @@ -4,16 +4,20 @@ import * as vg from '@uwdata/vgplot' import { isPointInPolygon, tableau20 } from '../../utils'; import { useBedCart } from '../../contexts/bedcart-context'; +import { components } from '../../../bedbase-types'; + +type SearchResponse = components['schemas']['BedListSearchResult']; type Props = { bedId: string; - neighbors?: any; + neighbors?: SearchResponse; + showNeighbors?: boolean; } export const BADAtlas = (props: Props) => { - const { bedId } = props; + const { bedId, neighbors, showNeighbors } = props; const { addBedToCart } = useBedCart(); - + const containerRef = useRef(null); const [containerWidth, setContainerWidth] = useState(900); @@ -25,13 +29,15 @@ export const BADAtlas = (props: Props) => { const [legendItems, setLegendItems] = useState([]); const [filterSelection, setFilterSelection] = useState(null); const [addedToCart, setAddedToCart] = useState(false); + const [tooltipPoint, setTooltipPoint] = useState(null); const coordinator = useMemo(() => new vg.Coordinator(vg.wasmConnector()), []); const filter = useMemo(() => vg.Selection.intersect(), []); - // Create a stable source object for legend filter updates const legendFilterSource = useMemo(() => ({}), []); + const neighborIDs = useMemo(() => neighbors?.results?.map(result => result.id), [neighbors]); const centerOnPoint = (point: any, scale: number = 1) => { + setTooltipPoint(point); setViewportState({ x: point.x, y: point.y, @@ -39,18 +45,34 @@ export const BADAtlas = (props: Props) => { }); }; + const getSortedSelectedPoints = () => { + if (!selectedPoints || selectedPoints.length === 0) return []; + + const currentBed = selectedPoints.find((p: any) => p.identifier === bedId); + const others = selectedPoints.filter((p: any) => p.identifier !== bedId); + + if (neighbors?.results && neighbors.results.length > 0) { + const scoreMap = new Map(neighbors.results.map(n => [n.id, n.score])); + others.sort((a: any, b: any) => { + const scoreA = scoreMap.get(a.identifier) || 0; + const scoreB = scoreMap.get(b.identifier) || 0; + return scoreB - scoreA; // Descending order + }); + } + + return currentBed ? [currentBed, ...others] : others; + }; + const handleLegendClick = (item: any) => { if (filterSelection?.category === item.category) { setFilterSelection(null); - // Clear the filter by updating with null predicate using the same source filter.update({ - source: legendFilterSource, + source: legendFilterSource, // memoized so that mosaic can keep track of source and clear previous selection value: null, predicate: null }); } else { setFilterSelection(item); - // Update with new filter - will replace previous clause from same source filter.update({ source: legendFilterSource, value: item.category, @@ -62,17 +84,32 @@ export const BADAtlas = (props: Props) => { const handlePointSelection = (dataPoints: any[] | null) => { // console.log('Selection changed via onSelection callback:', dataPoints); const points = dataPoints || []; + const hasInitialPoint = points.some(p => p.identifier === initialPoint?.identifier); + let finalPoints = hasInitialPoint ? points : (initialPoint ? [initialPoint, ...points] : points); - if (initialPoint) { - const hasInitialPoint = points.some(p => p.identifier === initialPoint.identifier); - if (!hasInitialPoint) { - setSelectedPoints([initialPoint, ...points]); - } else { - setSelectedPoints(points); + if (showNeighbors && neighborIDs && neighborIDs.length > 0) { + const selectedIds = new Set(finalPoints.map((p: any) => p.identifier)); + const missingNeighborIds = neighborIDs.filter(id => !selectedIds.has(id)); + + if (missingNeighborIds.length > 0) { + coordinator.query( + `SELECT + x, y, + ${colorGrouping} as category, + name as text, + id as identifier, + {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields + FROM data + WHERE id IN (${missingNeighborIds.map(id => `'${id}'`).join(',')})`, + { type: 'json' } + ).then((neighborPoints: any) => { + setSelectedPoints([...finalPoints, ...neighborPoints]); + }); + return; } - } else { - setSelectedPoints(points); } + + setSelectedPoints(finalPoints); }; // Range selection (for rectangle/lasso) @@ -140,16 +177,31 @@ export const BADAtlas = (props: Props) => { } if (result && result.length > 0) { - if (initialPoint) { - const hasInitialPoint = result.some((p: any) => p.identifier === initialPoint.identifier); - if (!hasInitialPoint) { - setSelectedPoints([initialPoint, ...result]); - } else { - setSelectedPoints(result); + // Always ensure initialPoint is included + const hasInitialPoint = result.some((p: any) => p.identifier === initialPoint?.identifier); + let finalPoints = hasInitialPoint ? result : (initialPoint ? [initialPoint, ...result] : result); + + if (showNeighbors && neighborIDs && neighborIDs.length > 0) { + const selectedIds = new Set(finalPoints.map((p: any) => p.identifier)); + const missingNeighborIds = neighborIDs.filter(id => !selectedIds.has(id)); + + if (missingNeighborIds.length > 0) { // fetch missing neighbor points + const neighborPoints = await coordinator.query( + `SELECT + x, y, + ${colorGrouping} as category, + name as text, + id as identifier, + {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields + FROM data + WHERE id IN (${missingNeighborIds.map(id => `'${id}'`).join(',')})`, + { type: 'json' } + ) as any[]; + finalPoints = [...finalPoints, ...neighborPoints]; } - } else { - setSelectedPoints(result); } + + setSelectedPoints(finalPoints); } }; @@ -202,10 +254,10 @@ export const BADAtlas = (props: Props) => { } }, [isReady, colorGrouping]) - useEffect(() => { // fetch initial bed id + useEffect(() => { // fetch initial bed id and neighbors if (isReady) { setTimeout(async () => { - const points: any = await coordinator.query( + const currentBed: any = await coordinator.query( `SELECT x, y, ${colorGrouping} as category, @@ -216,14 +268,29 @@ export const BADAtlas = (props: Props) => { WHERE id = '${bedId}'`, { type: 'json' } ); + if (!currentBed || currentBed.length === 0) return; + setInitialPoint(currentBed[0]); + setTooltipPoint(currentBed[0]); - if (points && points.length > 0) { - setInitialPoint(points[0]); - setSelectedPoints([points[0]]); + if (showNeighbors && neighborIDs && neighborIDs.length > 0) { + const neighborPoints: any = await coordinator.query( + `SELECT + x, y, + ${colorGrouping} as category, + name as text, + id as identifier, + {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields + FROM data + WHERE id IN (${neighborIDs.map(id => `'${id}'`).join(',')})`, + { type: 'json' } + ); + setSelectedPoints([currentBed[0], ...neighborPoints]); + } else { + setSelectedPoints([currentBed[0]]); } }, 200); } - }, [isReady, bedId, coordinator, colorGrouping]); + }, [isReady, bedId, coordinator, colorGrouping, showNeighbors, neighborIDs]); return ( @@ -237,6 +304,7 @@ export const BADAtlas = (props: Props) => {
{ filter={filter} viewportState={viewportState} onViewportState={setViewportState} + tooltip={tooltipPoint} selection={selectedPoints} onSelection={handlePointSelection} onRangeSelection={(e) => handleRangeSelection(coordinator, e)} @@ -358,7 +427,7 @@ export const BADAtlas = (props: Props) => { - {selectedPoints?.map((point: any, index: number) => ( + {getSortedSelectedPoints().map((point: any, index: number) => ( centerOnPoint(point, 0.3)} key={index}> {point.text} {point.fields.Assay} diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx index 42ce9fb3..8b2857ee 100644 --- a/ui/src/pages/bed-splash.tsx +++ b/ui/src/pages/bed-splash.tsx @@ -19,6 +19,7 @@ import { useBedNeighbours } from '../queries/useBedNeighbours'; import type { components } from '../../bedbase-types.d.ts'; // import { BEDAtlas } from '../components/bed-splash-components/bed-atlas.tsx'; import { BADAtlas } from '../components/bed-splash-components/bad-atlas.tsx'; +import { useState } from 'react'; // Use the response type to properly type the metadata type BedMetadata = components['schemas']['BedMetadataAll']; @@ -27,6 +28,8 @@ export const BedSplash = () => { const params = useParams(); const bedId = params.id; + const [showNeighbors, setShowNeighbors] = useState(true); + const { isLoading, data: metadata, @@ -274,14 +277,31 @@ export const BedSplash = () => { {bedId && metadata?.name?.includes('encode') && ( <> - + {/* */} )} {neighbours && ( -
Similar BED Files
+
+
Similar BED Files
+
+ setShowNeighbors(!showNeighbors)} + /> + +
+
From f28ae299839805998144d97af3e720c749e55bd4 Mon Sep 17 00:00:00 2001 From: Sam Park Date: Thu, 30 Oct 2025 15:43:26 -0400 Subject: [PATCH 07/76] ui updates and mosaic coordinator context --- .../bed-splash-components/atlas-tooltip.tsx | 70 +++++++++++++++++ .../bed-splash-components/bad-atlas.tsx | 75 ++++++++++--------- .../bed-atlas.tsx | 33 ++++---- ui/src/components/search/search-selector.tsx | 12 ++- .../contexts/mosaic-coordinator-context.tsx | 64 ++++++++++++++++ ui/src/main.tsx | 7 +- ui/src/pages/bed-splash.tsx | 2 +- ui/src/pages/search.tsx | 5 +- 8 files changed, 209 insertions(+), 59 deletions(-) create mode 100644 ui/src/components/bed-splash-components/atlas-tooltip.tsx rename ui/src/components/{bed-splash-components => search}/bed-atlas.tsx (53%) create mode 100644 ui/src/contexts/mosaic-coordinator-context.tsx diff --git a/ui/src/components/bed-splash-components/atlas-tooltip.tsx b/ui/src/components/bed-splash-components/atlas-tooltip.tsx new file mode 100644 index 00000000..a9168114 --- /dev/null +++ b/ui/src/components/bed-splash-components/atlas-tooltip.tsx @@ -0,0 +1,70 @@ +import { createRoot, Root } from 'react-dom/client'; + +interface TooltipProps { + tooltip?: { + text: string; + identifier: string; + fields?: { + Assay: string; + 'Cell Line': string; + Description: string; + }; + category?: string; + }; +} + +const TooltipContent = ({ tooltip }: { tooltip: TooltipProps['tooltip'] }) => { + if (!tooltip) return null; + + return ( +
+
{tooltip.text || 'Unnamed BED'}
+ {tooltip.fields && ( + <> +

+ {tooltip.fields.Description || 'No description available'} +

+
+ + cell_line:{' '}{tooltip.fields['Cell Line'] || 'N/A'} + + + assay:{' '}{tooltip.fields.Assay || 'N/A'} + + + id:{' '}{tooltip.identifier || 'N/A'} + +
+ + )} +
+ ); +}; + +export class AtlasTooltip { + private root: Root; + + constructor(target: HTMLElement, props: TooltipProps) { + // Create a React root and render your component + this.root = createRoot(target); + this.update(props); + } + + update(props: TooltipProps) { + // Re-render with new props + this.root.render(); + } + + destroy() { + // Unmount the React component + this.root.unmount(); + } +} \ No newline at end of file diff --git a/ui/src/components/bed-splash-components/bad-atlas.tsx b/ui/src/components/bed-splash-components/bad-atlas.tsx index 8e0d5446..bcbe8676 100644 --- a/ui/src/components/bed-splash-components/bad-atlas.tsx +++ b/ui/src/components/bed-splash-components/bad-atlas.tsx @@ -5,6 +5,8 @@ import * as vg from '@uwdata/vgplot' import { isPointInPolygon, tableau20 } from '../../utils'; import { useBedCart } from '../../contexts/bedcart-context'; import { components } from '../../../bedbase-types'; +import { AtlasTooltip } from './atlas-tooltip'; +import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context'; type SearchResponse = components['schemas']['BedListSearchResult']; @@ -16,6 +18,7 @@ type Props = { export const BADAtlas = (props: Props) => { const { bedId, neighbors, showNeighbors } = props; + const { coordinator, initializeData } = useMosaicCoordinator(); const { addBedToCart } = useBedCart(); const containerRef = useRef(null); @@ -31,7 +34,6 @@ export const BADAtlas = (props: Props) => { const [addedToCart, setAddedToCart] = useState(false); const [tooltipPoint, setTooltipPoint] = useState(null); - const coordinator = useMemo(() => new vg.Coordinator(vg.wasmConnector()), []); const filter = useMemo(() => vg.Selection.intersect(), []); const legendFilterSource = useMemo(() => ({}), []); const neighborIDs = useMemo(() => neighbors?.results?.map(result => result.id), [neighbors]); @@ -109,6 +111,7 @@ export const BADAtlas = (props: Props) => { } } + // setTooltipPoint(finalPoints.slice(-1)[0]) setSelectedPoints(finalPoints); }; @@ -205,22 +208,6 @@ export const BADAtlas = (props: Props) => { } }; - const initializeData = async (coordinator: any) => { - const url = 'https://raw.githubusercontent.com/databio/bedbase-loader/master/umap/hg38_umap.json'; - await coordinator.exec([ - vg.sql`CREATE OR REPLACE TABLE data AS - SELECT - unnest(nodes, recursive := true) - FROM read_json_auto('${url}')`, - vg.sql`CREATE OR REPLACE TABLE data AS - SELECT - *, - (DENSE_RANK() OVER (ORDER BY assay) - 1)::INTEGER AS assay_category, - (DENSE_RANK() OVER (ORDER BY cell_line) - 1)::INTEGER AS cell_line_category - FROM data` - ]); - } - const fetchLegendItems = async (coordinator: any) => { const result = await coordinator.query( `SELECT DISTINCT @@ -235,7 +222,7 @@ export const BADAtlas = (props: Props) => { } useEffect(() => { // initialize data - initializeData(coordinator).then(() => { + initializeData().then(() => { setIsReady(true); }); }, []); @@ -292,19 +279,19 @@ export const BADAtlas = (props: Props) => { } }, [isReady, bedId, coordinator, colorGrouping, showNeighbors, neighborIDs]); - return ( <> - {isReady && ( -
-
-
BED Embedding Atlas
-
-
+
+
+
BED Embedding Atlas
+
+
+ {isReady ? ( +
+
{ viewportState={viewportState} onViewportState={setViewportState} tooltip={tooltipPoint} + customTooltip={{ + class: AtlasTooltip, + props: {} + }} selection={selectedPoints} onSelection={handlePointSelection} onRangeSelection={(e) => handleRangeSelection(coordinator, e)} @@ -330,8 +321,8 @@ export const BADAtlas = (props: Props) => {
-
-
+
+
Legend
@@ -378,9 +369,16 @@ export const BADAtlas = (props: Props) => { onClick={() => handleLegendClick(item)} key={item.category} > - - - {item.name} + + + + {item.name} + + {(filterSelection?.category === item.category) && ( + + )} ))} @@ -389,11 +387,12 @@ export const BADAtlas = (props: Props) => {
-
+
- Selected Points + Selection + {/* */} + {/* */}
@@ -441,6 +442,12 @@ export const BADAtlas = (props: Props) => { + ) : ( +
+
+ Loading... +
+
)} ); diff --git a/ui/src/components/bed-splash-components/bed-atlas.tsx b/ui/src/components/search/bed-atlas.tsx similarity index 53% rename from ui/src/components/bed-splash-components/bed-atlas.tsx rename to ui/src/components/search/bed-atlas.tsx index 0c6ce962..d7799159 100644 --- a/ui/src/components/bed-splash-components/bed-atlas.tsx +++ b/ui/src/components/search/bed-atlas.tsx @@ -1,7 +1,6 @@ import { EmbeddingAtlas } from 'embedding-atlas/react'; -import { useEffect, useState, useMemo } from 'react'; -import * as vg from '@uwdata/vgplot' - +import { useEffect, useState } from 'react'; +import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context'; type Props = { bedId?: string; neighbors?: any; @@ -11,38 +10,26 @@ export const BEDAtlas = (props: Props) => { const {} = props; const [isReady, setIsReady] = useState(false); - - const coordinator = useMemo(() => new vg.Coordinator(vg.wasmConnector()), []); - const initializeData = async (coordinator: any) => { - const url = 'https://raw.githubusercontent.com/databio/bedbase-loader/master/umap/hg38_umap.json'; - await coordinator.exec([ - vg.sql`CREATE OR REPLACE TABLE data AS - SELECT - unnest(nodes, recursive := true) - FROM read_json_auto('${url}')` - ]); - } + const { coordinator, initializeData } = useMosaicCoordinator(); useEffect(() => { - initializeData(coordinator).then(() => setIsReady(true)); + initializeData().then(() => setIsReady(true)); }, []); return ( <> - {isReady && ( + {isReady ? (
-
- Embedding Atlas -
-
+
{
+ ) : ( +
+
+ Loading... +
+
)} ); diff --git a/ui/src/components/search/search-selector.tsx b/ui/src/components/search/search-selector.tsx index 41cef61c..94ffa07f 100644 --- a/ui/src/components/search/search-selector.tsx +++ b/ui/src/components/search/search-selector.tsx @@ -1,7 +1,7 @@ import Nav from 'react-bootstrap/Nav'; import { useSearchParams } from 'react-router-dom'; -type SearchView = 't2b' | 'b2b' | 't2bs'; +type SearchView = 't2b' | 'b2b' | 't2bs' | 'embedding'; type Props = { view: SearchView; @@ -45,6 +45,16 @@ export const SearchSelector = (props: Props) => { > Text-to-BEDset + { + params.set('view', 'embedding'); + params.delete('q'); + setParams(params); + setView('embedding'); + }} + > + Embedding Atlas +
diff --git a/ui/src/contexts/mosaic-coordinator-context.tsx b/ui/src/contexts/mosaic-coordinator-context.tsx new file mode 100644 index 00000000..0da56cc1 --- /dev/null +++ b/ui/src/contexts/mosaic-coordinator-context.tsx @@ -0,0 +1,64 @@ +import { createContext, useContext, useMemo, useRef, ReactNode } from 'react'; +import * as vg from '@uwdata/vgplot'; + +interface MosaicCoordinatorContextType { + getCoordinator: () => vg.Coordinator; + initializeData: () => Promise; +} + +const MosaicCoordinatorContext = createContext(null); + +export const MosaicCoordinatorProvider = ({ children }: { children: ReactNode }) => { + const coordinatorRef = useRef(null); + const dataInitializedRef = useRef(false); + + const getCoordinator = () => { + if (!coordinatorRef.current) { + coordinatorRef.current = new vg.Coordinator(vg.wasmConnector()); + } + return coordinatorRef.current; + }; + + const initializeData = async () => { + if (dataInitializedRef.current) { + return; // Already initialized + } + + const coordinator = getCoordinator(); + const url = 'https://raw.githubusercontent.com/databio/bedbase-loader/master/umap/hg38_umap.json'; + + await coordinator.exec([ + vg.sql`CREATE OR REPLACE TABLE data AS + SELECT + unnest(nodes, recursive := true) + FROM read_json_auto('${url}')`, + vg.sql`CREATE OR REPLACE TABLE data AS + SELECT + *, + (DENSE_RANK() OVER (ORDER BY assay) - 1)::INTEGER AS assay_category, + (DENSE_RANK() OVER (ORDER BY cell_line) - 1)::INTEGER AS cell_line_category + FROM data` as any + ]); + + dataInitializedRef.current = true; + }; + + const value = useMemo(() => ({ getCoordinator, initializeData }), []); + return ( + + {children} + + ); +} + +export const useMosaicCoordinator = () => { + const context = useContext(MosaicCoordinatorContext); + if (!context) { + throw new Error('useMosaicCoordinator must be used within MosaicCoordinatorProvider'); + } + return { + coordinator: context.getCoordinator(), + initializeData: context.initializeData + }; +}; + diff --git a/ui/src/main.tsx b/ui/src/main.tsx index df411949..548e1cb3 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 { HelmetProvider } from 'react-helmet-async'; +import { MosaicCoordinatorProvider } from './contexts/mosaic-coordinator-context.tsx'; // css stuff import 'bootstrap/dist/css/bootstrap.min.css'; @@ -88,8 +89,10 @@ ReactDOM.createRoot(document.getElementById('root')!).render( - - + + + + diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx index 8b2857ee..c3bb980a 100644 --- a/ui/src/pages/bed-splash.tsx +++ b/ui/src/pages/bed-splash.tsx @@ -28,7 +28,7 @@ export const BedSplash = () => { const params = useParams(); const bedId = params.id; - const [showNeighbors, setShowNeighbors] = useState(true); + const [showNeighbors, setShowNeighbors] = useState(false); const { isLoading, diff --git a/ui/src/pages/search.tsx b/ui/src/pages/search.tsx index d2c2f49b..ab1da7ab 100644 --- a/ui/src/pages/search.tsx +++ b/ui/src/pages/search.tsx @@ -7,10 +7,11 @@ import { SearchSelector } from '../components/search/search-selector'; import { Text2Bed } from '../components/search/text2bed/text2bed'; import { Bed2Bed } from '../components/search/bed2bed/bed2bed'; import { Text2BedSet } from '../components/search/text2bedset'; +import { BEDAtlas } from '../components/search/bed-atlas.tsx'; import { SearchViewProvider } from '../contexts/search-view-context.tsx'; -type SearchView = 't2b' | 'b2b' | 't2bs'; +type SearchView = 't2b' | 'b2b' | 't2bs' | 'embedding'; export const SearchPage = () => { const [searchParams] = useSearchParams(); @@ -31,6 +32,8 @@ export const SearchPage = () => { ) : searchView === 't2bs' ? ( + ) : searchView === 'embedding' ? ( + ) : (
Unknown searchView selected.
)} From 7c651d44672620acff9e59a6407c276c110fd137 Mon Sep 17 00:00:00 2001 From: Sam Park Date: Fri, 31 Oct 2025 20:01:36 -0400 Subject: [PATCH 08/76] replace 3d with embedding atlas component --- ui/package-lock.json | 8 +- ui/package.json | 2 +- .../bed-splash-components/bad-atlas.tsx | 55 +++--- ui/src/components/layout.tsx | 25 ++- ui/src/components/search/bed-atlas.tsx | 1 + ui/src/components/search/search-selector.tsx | 12 +- ui/src/main.tsx | 4 +- ui/src/pages/bed-atlas-full.tsx | 44 +++++ ui/src/pages/search.tsx | 5 +- ui/src/pages/visualization.tsx | 177 ------------------ 10 files changed, 104 insertions(+), 229 deletions(-) create mode 100644 ui/src/pages/bed-atlas-full.tsx delete mode 100644 ui/src/pages/visualization.tsx diff --git a/ui/package-lock.json b/ui/package-lock.json index b69667fb..aaa26af8 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -18,7 +18,7 @@ "chart.js": "^4.4.2", "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", - "embedding-atlas": "^0.11.0", + "embedding-atlas": "^0.12.0", "framer-motion": "^11.0.20", "js-yaml": "^4.1.0", "react": "^18.2.0", @@ -3748,9 +3748,9 @@ "license": "ISC" }, "node_modules/embedding-atlas": { - "version": "0.11.0", - "resolved": "https://registry.npmjs.org/embedding-atlas/-/embedding-atlas-0.11.0.tgz", - "integrity": "sha512-jA/mzhCOOmRfcU1wzqaToKPfFpHQ2V241sVchoF4fP8Br3wJf7bvM5PwjkIAc9fDxrx5RxQna76Vzr93ht2gyg==", + "version": "0.12.0", + "resolved": "https://registry.npmjs.org/embedding-atlas/-/embedding-atlas-0.12.0.tgz", + "integrity": "sha512-DPsKR4uTsMseCCb7xAl4z9daj6MYasXGfk4aXI3vCqF73q2kQ4oe1Pp4GCe6sYpbAR3WpHDlAU9reC52piepMw==", "license": "MIT", "peerDependencies": { "@uwdata/mosaic-core": ">=0.19.0", diff --git a/ui/package.json b/ui/package.json index a6a7caac..10433646 100644 --- a/ui/package.json +++ b/ui/package.json @@ -22,7 +22,7 @@ "chart.js": "^4.4.2", "chartjs-chart-error-bars": "^4.4.0", "chartjs-plugin-datalabels": "^2.2.0", - "embedding-atlas": "^0.11.0", + "embedding-atlas": "^0.12.0", "framer-motion": "^11.0.20", "js-yaml": "^4.1.0", "react": "^18.2.0", diff --git a/ui/src/components/bed-splash-components/bad-atlas.tsx b/ui/src/components/bed-splash-components/bad-atlas.tsx index bcbe8676..22e949a0 100644 --- a/ui/src/components/bed-splash-components/bad-atlas.tsx +++ b/ui/src/components/bed-splash-components/bad-atlas.tsx @@ -125,6 +125,11 @@ export const BADAtlas = (props: Props) => { let result; + // Build filter clause if a legend filter is active + const filterClause = filterSelection + ? ` AND ${colorGrouping} = '${filterSelection.category}'` + : ''; + // Check if rectangle selection (bounding box) if (typeof value === 'object' && 'xMin' in value) { result = await coordinator.query( @@ -135,7 +140,7 @@ export const BADAtlas = (props: Props) => { id as identifier, {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields FROM data - WHERE x >= ${value.xMin} AND x <= ${value.xMax} AND y >= ${value.yMin} AND y <= ${value.yMax}`, + WHERE x >= ${value.xMin} AND x <= ${value.xMax} AND y >= ${value.yMin} AND y <= ${value.yMax}${filterClause}`, { type: 'json' } ) as any[]; } @@ -152,7 +157,7 @@ export const BADAtlas = (props: Props) => { // Only fetch x, y, identifier for filtering, then get full data for matches const candidates: any = await coordinator.query( `SELECT x, y, id as identifier FROM data - WHERE x >= ${xMin} AND x <= ${xMax} AND y >= ${yMin} AND y <= ${yMax}`, + WHERE x >= ${xMin} AND x <= ${xMax} AND y >= ${yMin} AND y <= ${yMax}${filterClause}`, { type: 'json' } ); @@ -171,7 +176,7 @@ export const BADAtlas = (props: Props) => { id as identifier, {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields FROM data - WHERE id IN (${filteredIds})`, + WHERE id IN (${filteredIds})${filterClause}`, { type: 'json' } ) as any[]; } else { @@ -179,33 +184,31 @@ export const BADAtlas = (props: Props) => { } } - if (result && result.length > 0) { - // Always ensure initialPoint is included - const hasInitialPoint = result.some((p: any) => p.identifier === initialPoint?.identifier); - let finalPoints = hasInitialPoint ? result : (initialPoint ? [initialPoint, ...result] : result); + const resultArray = result || []; + const hasInitialPoint = resultArray.length > 0 && resultArray.some((p: any) => p.identifier === initialPoint?.identifier); + let finalPoints = hasInitialPoint ? resultArray : (initialPoint ? [initialPoint, ...resultArray] : resultArray); - if (showNeighbors && neighborIDs && neighborIDs.length > 0) { - const selectedIds = new Set(finalPoints.map((p: any) => p.identifier)); - const missingNeighborIds = neighborIDs.filter(id => !selectedIds.has(id)); + if (showNeighbors && neighborIDs && neighborIDs.length > 0) { + const selectedIds = new Set(finalPoints.map((p: any) => p.identifier)); + const missingNeighborIds = neighborIDs.filter(id => !selectedIds.has(id)); - if (missingNeighborIds.length > 0) { // fetch missing neighbor points - const neighborPoints = await coordinator.query( - `SELECT - x, y, - ${colorGrouping} as category, - name as text, - id as identifier, - {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields - FROM data - WHERE id IN (${missingNeighborIds.map(id => `'${id}'`).join(',')})`, - { type: 'json' } - ) as any[]; - finalPoints = [...finalPoints, ...neighborPoints]; - } + if (missingNeighborIds.length > 0) { // fetch missing neighbor points + const neighborPoints = await coordinator.query( + `SELECT + x, y, + ${colorGrouping} as category, + name as text, + id as identifier, + {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields + FROM data + WHERE id IN (${missingNeighborIds.map(id => `'${id}'`).join(',')})`, + { type: 'json' } + ) as any[]; + finalPoints = [...finalPoints, ...neighborPoints]; } - - setSelectedPoints(finalPoints); } + + setSelectedPoints(finalPoints); }; const fetchLegendItems = async (coordinator: any) => { diff --git a/ui/src/components/layout.tsx b/ui/src/components/layout.tsx index f006bcec..df2db937 100644 --- a/ui/src/components/layout.tsx +++ b/ui/src/components/layout.tsx @@ -12,6 +12,7 @@ type LayoutProps = { fullWidth?: boolean; footer?: boolean; fullHeight?: boolean; + flexLayout?: boolean; }; const Footer = () => { @@ -67,16 +68,32 @@ const Footer = () => { }; export const Layout = (props: LayoutProps) => { - const { children, title, description, image, footer, fullHeight } = props; - const mainContainerClass = fullHeight ? 'container min-h-screen' : 'container'; + const { children, title, description, image, footer, fullHeight, fullWidth, flexLayout } = props; + + if (flexLayout) { + return ( + + +
+
+
+
{children}
+
+ {!!footer &&
} + + ); + } + + const fluidContainer = `${fullWidth ? 'container-fluid' : 'container'}` return (
-
{children}
- {footer === true &&
} +
{children}
+ {!!footer &&
} ); }; diff --git a/ui/src/components/search/bed-atlas.tsx b/ui/src/components/search/bed-atlas.tsx index d7799159..ded5e8b5 100644 --- a/ui/src/components/search/bed-atlas.tsx +++ b/ui/src/components/search/bed-atlas.tsx @@ -1,6 +1,7 @@ import { EmbeddingAtlas } from 'embedding-atlas/react'; import { useEffect, useState } from 'react'; import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context'; + type Props = { bedId?: string; neighbors?: any; diff --git a/ui/src/components/search/search-selector.tsx b/ui/src/components/search/search-selector.tsx index 94ffa07f..41cef61c 100644 --- a/ui/src/components/search/search-selector.tsx +++ b/ui/src/components/search/search-selector.tsx @@ -1,7 +1,7 @@ import Nav from 'react-bootstrap/Nav'; import { useSearchParams } from 'react-router-dom'; -type SearchView = 't2b' | 'b2b' | 't2bs' | 'embedding'; +type SearchView = 't2b' | 'b2b' | 't2bs'; type Props = { view: SearchView; @@ -45,16 +45,6 @@ export const SearchSelector = (props: Props) => { > Text-to-BEDset - { - params.set('view', 'embedding'); - params.delete('q'); - setParams(params); - setView('embedding'); - }} - > - Embedding Atlas - diff --git a/ui/src/main.tsx b/ui/src/main.tsx index 548e1cb3..5443ea04 100644 --- a/ui/src/main.tsx +++ b/ui/src/main.tsx @@ -8,7 +8,7 @@ import { BedCartProvider } from './contexts/bedcart-context.tsx'; 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 { BEDAtlasFull } from './pages/bed-atlas-full.tsx'; import { HelmetProvider } from 'react-helmet-async'; import { MosaicCoordinatorProvider } from './contexts/mosaic-coordinator-context.tsx'; @@ -78,7 +78,7 @@ const router = createBrowserRouter([ }, { path: '/umap', - element: , + element: , }, ]); diff --git a/ui/src/pages/bed-atlas-full.tsx b/ui/src/pages/bed-atlas-full.tsx new file mode 100644 index 00000000..ac94e22b --- /dev/null +++ b/ui/src/pages/bed-atlas-full.tsx @@ -0,0 +1,44 @@ +import { EmbeddingAtlas } from 'embedding-atlas/react'; +import { useEffect, useState } from 'react'; +import { useMosaicCoordinator } from '../contexts/mosaic-coordinator-context'; +import { Layout } from '../components/layout'; + + +export const BEDAtlasFull: React.FC = () => { + const [isReady, setIsReady] = useState(false); + const { coordinator, initializeData } = useMosaicCoordinator(); + + useEffect(() => { + initializeData().then(() => setIsReady(true)); + }, []); + + return ( + + {isReady ? ( +
+
+ +
+
+ ) : ( +
+
+ Loading... +
+
+ )} + + + ); +}; \ No newline at end of file diff --git a/ui/src/pages/search.tsx b/ui/src/pages/search.tsx index ab1da7ab..d2c2f49b 100644 --- a/ui/src/pages/search.tsx +++ b/ui/src/pages/search.tsx @@ -7,11 +7,10 @@ import { SearchSelector } from '../components/search/search-selector'; import { Text2Bed } from '../components/search/text2bed/text2bed'; import { Bed2Bed } from '../components/search/bed2bed/bed2bed'; import { Text2BedSet } from '../components/search/text2bedset'; -import { BEDAtlas } from '../components/search/bed-atlas.tsx'; import { SearchViewProvider } from '../contexts/search-view-context.tsx'; -type SearchView = 't2b' | 'b2b' | 't2bs' | 'embedding'; +type SearchView = 't2b' | 'b2b' | 't2bs'; export const SearchPage = () => { const [searchParams] = useSearchParams(); @@ -32,8 +31,6 @@ export const SearchPage = () => { ) : searchView === 't2bs' ? ( - ) : searchView === 'embedding' ? ( - ) : (
Unknown searchView selected.
)} diff --git a/ui/src/pages/visualization.tsx b/ui/src/pages/visualization.tsx deleted file mode 100644 index fa5434df..00000000 --- a/ui/src/pages/visualization.tsx +++ /dev/null @@ -1,177 +0,0 @@ -import React, { useRef, useState, useEffect } from 'react'; -import ForceGraph3D from 'react-force-graph-3d'; -// import graphData from './output.json'; -import { Link } from 'react-router-dom'; -import { useUmapEmbeddings } from '../queries/useUmapEmbeddings.ts'; -import { useNavigate, useLocation } from 'react-router-dom'; - -export interface GraphNode { - id: string; - name: string; - description: string; - cell_line: string; - assay?: string; - x: number; - y: number; - z: number; -} - -type ColorBy = 'cell_line' | 'assay'; - -export const UMAPGraph: React.FC = () => { - const { data: umap_data, isLoading, error } = useUmapEmbeddings(); - const fgRef = useRef(); - const [searchId, setSearchId] = useState(''); - const [message, setMessage] = useState(''); - const navigate = useNavigate(); - const location = useLocation(); - const [colorByOption, setColorByOption] = useState('cell_line'); - - - useEffect(() => { - const queryParams = new URLSearchParams(location.search); - const initialSearchId = queryParams.get('searchId'); - if (initialSearchId) { - setSearchId(initialSearchId); - const timer = setTimeout(() => { - handleSearch(); - }, 1000); // Give time for the graph to initialize - return () => clearTimeout(timer); - } - }, [location.search, umap_data]); - - const handleSearch = () => { - - if (!umap_data) return; - const node = graphDataWithoutLinks.nodes.find((n: GraphNode) => n.id === searchId); - - if (node && fgRef.current) { - fgRef.current.cameraPosition( - { x: node.x, y: node.y, z: node.z + 300 }, // zoom in 300 units away - node, - 2000, // animate over 2 seconds - ); - setMessage(`Found: ${node.id}`); - navigate(`?searchId=${node.id}`); - } else { - - fgRef.current.cameraPosition( - { x: 0, y: 0, z: 1000 }, // reset to default center position - { x: 0, y: 0, z: 0 }, // look at the center - 2000, // animate over 2 seconds - ); - if (!searchId) { - setMessage(''); - } else { - setMessage(`Node with ID ${searchId} not found.`); - } - // setMessage('BED file not found or search is empty.'); - navigate(`?searchId=${node.id}`); - } - }; - - if (isLoading) { - return
Loading data...
; - } - - if (error) { - return
Error loading data: {error.message}
; - } - - const graphDataWithoutLinks = { - nodes: umap_data.nodes.map((node: GraphNode) => ({ - ...node, - x: node.x, - y: node.y, - z: node.z, - })), - links: [], - }; - - return ( -
- -
-
-
- setColorByOption('cell_line')} - /> - - - setColorByOption('assay')} - /> - -
-
-
- setSearchId(e.target.value)} - onKeyDown={e => e.key === 'Enter' && handleSearch()} - className="form-control me-2" - /> - -
- -
- {message &&

{message}

} -
-
- - ( - `
${node.id}
cell_line: ${node.cell_line}
assay: ${node.assay}
${node.description}
` - )} - nodeAutoColorBy={colorByOption} - nodeRelSize={60} - enableNodeDrag={false} - onNodeClick={(node: GraphNode) => { - if (node.id) { - // const url = `https://bedbase.org/bed/${node.id}`; - // window.open(url, '_blank'); - // navigator.clipboard.writeText(url).catch(console.error); - setSearchId(node.id); - handleSearch(); - setMessage(`Clicked on: ${node.id} \n ${node.cell_line} <\n ${node.assay}`); - } - }} - /> -
- - BEDbase Logo - - -
-
- - ); -}; \ No newline at end of file From 85cec759132e4269bbfe629cbed59c78af4ff2cf Mon Sep 17 00:00:00 2001 From: Sam Park Date: Fri, 7 Nov 2025 11:10:17 -0500 Subject: [PATCH 09/76] rename some files and components --- ui/src/components/search/bed-atlas.tsx | 52 ----------- .../components/umap/bed-embedding-atlas.tsx | 88 +++++++++++++++++++ .../bed-embedding-view.tsx} | 8 +- ui/src/main.tsx | 4 +- ui/src/pages/bed-atlas-full.tsx | 44 ---------- ui/src/pages/bed-splash.tsx | 6 +- ui/src/pages/bed-umap.tsx | 16 ++++ 7 files changed, 112 insertions(+), 106 deletions(-) delete mode 100644 ui/src/components/search/bed-atlas.tsx create mode 100644 ui/src/components/umap/bed-embedding-atlas.tsx rename ui/src/components/{bed-splash-components/bad-atlas.tsx => umap/bed-embedding-view.tsx} (98%) delete mode 100644 ui/src/pages/bed-atlas-full.tsx create mode 100644 ui/src/pages/bed-umap.tsx diff --git a/ui/src/components/search/bed-atlas.tsx b/ui/src/components/search/bed-atlas.tsx deleted file mode 100644 index ded5e8b5..00000000 --- a/ui/src/components/search/bed-atlas.tsx +++ /dev/null @@ -1,52 +0,0 @@ -import { EmbeddingAtlas } from 'embedding-atlas/react'; -import { useEffect, useState } from 'react'; -import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context'; - -type Props = { - bedId?: string; - neighbors?: any; -} - -export const BEDAtlas = (props: Props) => { - const {} = props; - - const [isReady, setIsReady] = useState(false); - const { coordinator, initializeData } = useMosaicCoordinator(); - - useEffect(() => { - initializeData().then(() => setIsReady(true)); - }, []); - - return ( - <> - {isReady ? ( -
-
-
-
- -
-
-
-
- ) : ( -
-
- Loading... -
-
- )} - - ); -} \ No newline at end of file diff --git a/ui/src/components/umap/bed-embedding-atlas.tsx b/ui/src/components/umap/bed-embedding-atlas.tsx new file mode 100644 index 00000000..39701d2d --- /dev/null +++ b/ui/src/components/umap/bed-embedding-atlas.tsx @@ -0,0 +1,88 @@ +import { EmbeddingAtlas } from 'embedding-atlas/react'; +import { useEffect, useState } from 'react'; +import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context'; + +type Props = { + bedId?: string; + neighbors?: any; + container?: boolean; + width?: string; + height?: string; +} + +export const BEDEmbeddingAtlas = (props: Props) => { + const {container, width, height} = props; + + const [isReady, setIsReady] = useState(false); + const { coordinator, initializeData } = useMosaicCoordinator(); + + useEffect(() => { + initializeData().then(() => setIsReady(true)); + }, []); + + return ( + container ? ( + <> + {isReady ? ( +
+
+
+
+ +
+
+
+
+ ) : ( +
+
+ Loading... +
+
+ )} + + ) : ( + <> + {isReady ? ( +
+
+ console.log(e)} + onExportSelection={async (predicate, format) => { + console.log('Export selection:', predicate, format); + }} + /> +
+
+ ) : ( +
+
+ Loading... +
+
+ )} + + ) + ); +} diff --git a/ui/src/components/bed-splash-components/bad-atlas.tsx b/ui/src/components/umap/bed-embedding-view.tsx similarity index 98% rename from ui/src/components/bed-splash-components/bad-atlas.tsx rename to ui/src/components/umap/bed-embedding-view.tsx index 22e949a0..40ae689b 100644 --- a/ui/src/components/bed-splash-components/bad-atlas.tsx +++ b/ui/src/components/umap/bed-embedding-view.tsx @@ -5,7 +5,7 @@ import * as vg from '@uwdata/vgplot' import { isPointInPolygon, tableau20 } from '../../utils'; import { useBedCart } from '../../contexts/bedcart-context'; import { components } from '../../../bedbase-types'; -import { AtlasTooltip } from './atlas-tooltip'; +import { AtlasTooltip } from '../bed-splash-components/atlas-tooltip'; import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context'; type SearchResponse = components['schemas']['BedListSearchResult']; @@ -16,7 +16,7 @@ type Props = { showNeighbors?: boolean; } -export const BADAtlas = (props: Props) => { +export const BEDEmbeddingView = (props: Props) => { const { bedId, neighbors, showNeighbors } = props; const { coordinator, initializeData } = useMosaicCoordinator(); const { addBedToCart } = useBedCart(); @@ -125,7 +125,7 @@ export const BADAtlas = (props: Props) => { let result; - // Build filter clause if a legend filter is active + // filter clause prevents selecting points that are not within a selected legend category const filterClause = filterSelection ? ` AND ${colorGrouping} = '${filterSelection.category}'` : ''; @@ -454,4 +454,4 @@ export const BADAtlas = (props: Props) => { )} ); -} \ No newline at end of file +} diff --git a/ui/src/main.tsx b/ui/src/main.tsx index 5443ea04..5bf18a37 100644 --- a/ui/src/main.tsx +++ b/ui/src/main.tsx @@ -8,7 +8,7 @@ import { BedCartProvider } from './contexts/bedcart-context.tsx'; import toast, { Toaster } from 'react-hot-toast'; import { Home } from './pages/home.tsx'; import { Metrics } from './pages/metrics.tsx'; -import { BEDAtlasFull } from './pages/bed-atlas-full.tsx'; +import { BEDUmap } from './pages/bed-umap.tsx'; import { HelmetProvider } from 'react-helmet-async'; import { MosaicCoordinatorProvider } from './contexts/mosaic-coordinator-context.tsx'; @@ -78,7 +78,7 @@ const router = createBrowserRouter([ }, { path: '/umap', - element: , + element: , }, ]); diff --git a/ui/src/pages/bed-atlas-full.tsx b/ui/src/pages/bed-atlas-full.tsx deleted file mode 100644 index ac94e22b..00000000 --- a/ui/src/pages/bed-atlas-full.tsx +++ /dev/null @@ -1,44 +0,0 @@ -import { EmbeddingAtlas } from 'embedding-atlas/react'; -import { useEffect, useState } from 'react'; -import { useMosaicCoordinator } from '../contexts/mosaic-coordinator-context'; -import { Layout } from '../components/layout'; - - -export const BEDAtlasFull: React.FC = () => { - const [isReady, setIsReady] = useState(false); - const { coordinator, initializeData } = useMosaicCoordinator(); - - useEffect(() => { - initializeData().then(() => setIsReady(true)); - }, []); - - return ( - - {isReady ? ( -
-
- -
-
- ) : ( -
-
- Loading... -
-
- )} - - - ); -}; \ No newline at end of file diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx index c3bb980a..704df8fb 100644 --- a/ui/src/pages/bed-splash.tsx +++ b/ui/src/pages/bed-splash.tsx @@ -17,8 +17,7 @@ import { snakeToTitleCase } from '../utils'; import { Text2BedSearchResultsTable } from '../components/search/text2bed/t2b-search-results-table'; import { useBedNeighbours } from '../queries/useBedNeighbours'; import type { components } from '../../bedbase-types.d.ts'; -// import { BEDAtlas } from '../components/bed-splash-components/bed-atlas.tsx'; -import { BADAtlas } from '../components/bed-splash-components/bad-atlas.tsx'; +import { BEDEmbeddingView } from '../components/umap/bed-embedding-view.tsx'; import { useState } from 'react'; // Use the response type to properly type the metadata @@ -277,8 +276,7 @@ export const BedSplash = () => { {bedId && metadata?.name?.includes('encode') && ( <> - - {/* */} + )} diff --git a/ui/src/pages/bed-umap.tsx b/ui/src/pages/bed-umap.tsx new file mode 100644 index 00000000..3544e2ea --- /dev/null +++ b/ui/src/pages/bed-umap.tsx @@ -0,0 +1,16 @@ +// import { useSearchParams } from 'react-router-dom'; +import { Layout } from '../components/layout'; +import { BEDEmbeddingAtlas } from '../components/umap/bed-embedding-atlas'; + +export const BEDUmap: React.FC = () => { + // const [searchParams] = useSearchParams(); + + // const bedId = searchParams.get('searchId'); + // console.log(bedId); + + return ( + + + + ); +}; From 995df0f62a27f4d8b4dd68e5222b971853129adf Mon Sep 17 00:00:00 2001 From: Sam Park Date: Thu, 13 Nov 2025 18:05:20 -0500 Subject: [PATCH 10/76] rudimentary bed umap upload functionality --- .../atlas-tooltip.tsx | 12 +- ui/src/components/umap/bed-embedding-view.tsx | 110 ++++++++++++++++-- .../contexts/mosaic-coordinator-context.tsx | 51 +++++++- ui/src/queries/useBedUmap.ts | 29 +++++ ui/vite.config.ts | 10 ++ 5 files changed, 198 insertions(+), 14 deletions(-) rename ui/src/components/{bed-splash-components => umap}/atlas-tooltip.tsx (79%) create mode 100644 ui/src/queries/useBedUmap.ts diff --git a/ui/src/components/bed-splash-components/atlas-tooltip.tsx b/ui/src/components/umap/atlas-tooltip.tsx similarity index 79% rename from ui/src/components/bed-splash-components/atlas-tooltip.tsx rename to ui/src/components/umap/atlas-tooltip.tsx index a9168114..0fa0e7a7 100644 --- a/ui/src/components/bed-splash-components/atlas-tooltip.tsx +++ b/ui/src/components/umap/atlas-tooltip.tsx @@ -9,13 +9,17 @@ interface TooltipProps { 'Cell Line': string; Description: string; }; - category?: string; + category?: number; + x?: number; + y?: number; }; } const TooltipContent = ({ tooltip }: { tooltip: TooltipProps['tooltip'] }) => { if (!tooltip) return null; + console.log(tooltip) + return (
{ id:{' '}{tooltip.identifier || 'N/A'} + + x:{' '}{tooltip.x ? tooltip.x.toFixed(6) : 'N/A'} + + + y:{' '}{tooltip.y ? tooltip.y.toFixed(6) : 'N/A'} +
)} diff --git a/ui/src/components/umap/bed-embedding-view.tsx b/ui/src/components/umap/bed-embedding-view.tsx index 40ae689b..0cc2da44 100644 --- a/ui/src/components/umap/bed-embedding-view.tsx +++ b/ui/src/components/umap/bed-embedding-view.tsx @@ -5,8 +5,9 @@ import * as vg from '@uwdata/vgplot' import { isPointInPolygon, tableau20 } from '../../utils'; import { useBedCart } from '../../contexts/bedcart-context'; import { components } from '../../../bedbase-types'; -import { AtlasTooltip } from '../bed-splash-components/atlas-tooltip'; +import { AtlasTooltip } from './atlas-tooltip'; import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context'; +import { useBedUmap } from '../../queries/useBedUmap'; type SearchResponse = components['schemas']['BedListSearchResult']; @@ -14,14 +15,19 @@ type Props = { bedId: string; neighbors?: SearchResponse; showNeighbors?: boolean; + enableUpload?: boolean; } export const BEDEmbeddingView = (props: Props) => { const { bedId, neighbors, showNeighbors } = props; - const { coordinator, initializeData } = useMosaicCoordinator(); + const { coordinator, initializeData, addCustomPoint, deleteCustomPoint } = useMosaicCoordinator(); const { addBedToCart } = useBedCart(); + const { mutateAsync: getUmapCoordinates } = useBedUmap(); + + const enableUpload = true; const containerRef = useRef(null); + const fileInputRef = useRef(null); const [containerWidth, setContainerWidth] = useState(900); const [isReady, setIsReady] = useState(false); @@ -33,6 +39,8 @@ export const BEDEmbeddingView = (props: Props) => { const [filterSelection, setFilterSelection] = useState(null); const [addedToCart, setAddedToCart] = useState(false); const [tooltipPoint, setTooltipPoint] = useState(null); + const [uploadedFilename, setUploadedFilename] = useState(''); + const [dataVersion, setDataVersion] = useState(0); const filter = useMemo(() => vg.Selection.intersect(), []); const legendFilterSource = useMemo(() => ({}), []); @@ -115,6 +123,47 @@ export const BEDEmbeddingView = (props: Props) => { setSelectedPoints(finalPoints); }; + const handleFileRemove = async () => { + try { + await deleteCustomPoint(); + setUploadedFilename('') + + coordinator.clear(); + const updatedLegend = await fetchLegendItems(coordinator); + setLegendItems(updatedLegend); + setDataVersion(v => v + 1); + } catch (error) { + console.error('Error deleting file'); + } + } + + const handleFileUpload = async (event: React.ChangeEvent) => { + const file = event.target.files?.[0]; + if (!file) return; + + try { + const coordinates = await getUmapCoordinates(file); + + if (coordinates.length >= 2) { + await addCustomPoint(coordinates[0], coordinates[1]); + setUploadedFilename(file.name) + + // Clear coordinator cache and refresh legend + coordinator.clear(); + const updatedLegend = await fetchLegendItems(coordinator); + setLegendItems(updatedLegend); + setDataVersion(v => v + 1); + centerOnPoint({x: coordinates[0], y: coordinates[1]}, 0.3) + } + } catch (error) { + console.error('Error getting UMAP coordinates:', error); + } + }; + + const handleUploadClick = () => { + fileInputRef.current?.click(); + }; + // Range selection (for rectangle/lasso) const handleRangeSelection = async (coordinator: any, value: any) => { // console.log('Range selection updated:', value); @@ -212,14 +261,15 @@ export const BEDEmbeddingView = (props: Props) => { }; const fetchLegendItems = async (coordinator: any) => { - const result = await coordinator.query( - `SELECT DISTINCT + const query = `SELECT DISTINCT ${colorGrouping.replace('_category', '')} as name, ${colorGrouping} as category FROM data - ORDER BY ${colorGrouping}`, - { type: 'json' } - ) as any[]; + ORDER BY ${colorGrouping}`; + + console.log('Legend query:', query); + const result = await coordinator.query(query, { type: 'json' }) as any[]; + console.log('Legend results:', result); return result } @@ -230,6 +280,11 @@ export const BEDEmbeddingView = (props: Props) => { }); }, []); + // useEffect(() => { // add point + // addPoint(20, 20).then(() => { + // }); + // }, []); + useEffect(() => { // resize width of view if (containerRef.current) { setContainerWidth(containerRef.current.offsetWidth); @@ -285,9 +340,41 @@ export const BEDEmbeddingView = (props: Props) => { return ( <>
-
-
BED Embedding Atlas
-
+ { + enableUpload ? ( +
+
+
BED Embedding Atlas
+ + + {!!uploadedFilename && ( + + {uploadedFilename} + + + )} +
+
+ ) : ( +
+
BED Embedding Atlas
+
+ ) + }
{isReady ? (
@@ -295,6 +382,7 @@ export const BEDEmbeddingView = (props: Props) => {
{
{getSortedSelectedPoints().map((point: any, index: number) => ( - centerOnPoint(point, 0.3)} key={index}> + centerOnPoint(point, 0.3)} key={point.identifier + '_' + index}> diff --git a/ui/src/contexts/mosaic-coordinator-context.tsx b/ui/src/contexts/mosaic-coordinator-context.tsx index 0da56cc1..8dc1879f 100644 --- a/ui/src/contexts/mosaic-coordinator-context.tsx +++ b/ui/src/contexts/mosaic-coordinator-context.tsx @@ -4,6 +4,8 @@ import * as vg from '@uwdata/vgplot'; interface MosaicCoordinatorContextType { getCoordinator: () => vg.Coordinator; initializeData: () => Promise; + addCustomPoint: (x: number, y: number) => Promise; + deleteCustomPoint: () => Promise; } const MosaicCoordinatorContext = createContext(null); @@ -43,7 +45,50 @@ export const MosaicCoordinatorProvider = ({ children }: { children: ReactNode }) dataInitializedRef.current = true; }; - const value = useMemo(() => ({ getCoordinator, initializeData }), []); + const deleteCustomPoint = async () => { + const coordinator = getCoordinator(); + + await coordinator.exec([ + vg.sql`DELETE FROM data WHERE id = 'custom_point'` as any + ]); + } + + const addCustomPoint = async (x: number, y: number) => { + const coordinator = getCoordinator(); + + await coordinator.exec([ + vg.sql`DELETE FROM data WHERE id = 'custom_point'` as any + ]); + + // Get max category indices for uploaded points (after deletion to ensure clean state) + const maxCategories = await coordinator.query( + `SELECT + MAX(assay_category) as max_assay_category, + MAX(cell_line_category) as max_cell_line_category + FROM data`, + { type: 'json' } + ) as any[]; + + const assayCategory = (maxCategories[0]?.max_assay_category ?? -1) + 1; + const cellLineCategory = (maxCategories[0]?.max_cell_line_category ?? -1) + 1; + + await coordinator.exec([ + vg.sql`INSERT INTO data VALUES ( + ${x}, + ${y}, + 0, + 'custom_point', + 'Your uploaded file', + 'User uploaded BED file', + 'Uploaded BED', + 'Uploaded BED', + ${assayCategory}, + ${cellLineCategory} + )` as any, + ]); + }; + + const value = useMemo(() => ({ getCoordinator, initializeData, addCustomPoint, deleteCustomPoint }), []); return ( {children} @@ -58,7 +103,9 @@ export const useMosaicCoordinator = () => { } return { coordinator: context.getCoordinator(), - initializeData: context.initializeData + initializeData: context.initializeData, + addCustomPoint: context.addCustomPoint, + deleteCustomPoint: context.deleteCustomPoint }; }; diff --git a/ui/src/queries/useBedUmap.ts b/ui/src/queries/useBedUmap.ts new file mode 100644 index 00000000..6d9c8ed1 --- /dev/null +++ b/ui/src/queries/useBedUmap.ts @@ -0,0 +1,29 @@ +import { useMutation, useQueryClient } from '@tanstack/react-query'; +import { AxiosInstance } from 'axios'; +import { useBedbaseApi } from '../contexts/api-context'; + +type UmapResponse = number[]; + +const getBedUmap = async (file: File, axiosInstance: AxiosInstance) => { + const formData = new FormData(); + formData.append('file', file); + + const { data } = await axiosInstance.post('/bed/umap', formData, { + headers: { + 'Content-Type': 'multipart/form-data', + }, + }); + return data; +}; + +export const useBedUmap = () => { + const queryClient = useQueryClient(); + const { api } = useBedbaseApi(); + + return useMutation({ + mutationFn: (file: File) => getBedUmap(file, api), + onSuccess: () => { + queryClient.invalidateQueries({ queryKey: ['bed-umap'] }); + }, + }); +}; diff --git a/ui/vite.config.ts b/ui/vite.config.ts index 5a33944a..3b1a7fee 100644 --- a/ui/vite.config.ts +++ b/ui/vite.config.ts @@ -4,4 +4,14 @@ import react from '@vitejs/plugin-react' // https://vitejs.dev/config/ export default defineConfig({ plugins: [react()], + server: { + proxy: { + '/api': { + target: 'https://api-dev.bedbase.org/v1', + changeOrigin: true, + rewrite: (path) => path.replace(/^\/api/, ''), + secure: false, + } + } + } }) From a86037fa97966e2b1f7b880f24db52827b2ede54 Mon Sep 17 00:00:00 2001 From: Sam Park Date: Fri, 14 Nov 2025 12:44:04 -0500 Subject: [PATCH 11/76] highlight uploaded bed file on umap --- ui/src/components/umap/bed-embedding-view.tsx | 152 +++++++++++------- ui/src/pages/bed-splash.tsx | 2 +- 2 files changed, 99 insertions(+), 55 deletions(-) diff --git a/ui/src/components/umap/bed-embedding-view.tsx b/ui/src/components/umap/bed-embedding-view.tsx index 0cc2da44..f0c76c64 100644 --- a/ui/src/components/umap/bed-embedding-view.tsx +++ b/ui/src/components/umap/bed-embedding-view.tsx @@ -19,13 +19,11 @@ type Props = { } export const BEDEmbeddingView = (props: Props) => { - const { bedId, neighbors, showNeighbors } = props; + const { bedId, neighbors, showNeighbors, enableUpload } = props; const { coordinator, initializeData, addCustomPoint, deleteCustomPoint } = useMosaicCoordinator(); const { addBedToCart } = useBedCart(); const { mutateAsync: getUmapCoordinates } = useBedUmap(); - const enableUpload = true; - const containerRef = useRef(null); const fileInputRef = useRef(null); @@ -41,6 +39,7 @@ export const BEDEmbeddingView = (props: Props) => { const [tooltipPoint, setTooltipPoint] = useState(null); const [uploadedFilename, setUploadedFilename] = useState(''); const [dataVersion, setDataVersion] = useState(0); + const [pendingSelection, setPendingSelection] = useState(null); const filter = useMemo(() => vg.Selection.intersect(), []); const legendFilterSource = useMemo(() => ({}), []); @@ -55,6 +54,82 @@ export const BEDEmbeddingView = (props: Props) => { }); }; + const handleFileRemove = async () => { + try { + await deleteCustomPoint(); + setUploadedFilename('') + + coordinator.clear(); + const updatedLegend = await fetchLegendItems(coordinator); + setLegendItems(updatedLegend); + + // Prepare selection without custom point + const newSelection = selectedPoints.filter((p: any) => p.identifier !== 'custom_point'); + setPendingSelection(newSelection); + + // Force remount to remove point from map + setDataVersion(v => v + 1); + } catch (error) { + console.error('Error deleting file'); + } + } + + const handleFileUpload = async (event: React.ChangeEvent) => { + const file = event.target.files?.[0]; + if (!file) return; + + try { + const coordinates = await getUmapCoordinates(file); + + if (coordinates.length >= 2) { + await addCustomPoint(coordinates[0], coordinates[1]); + setUploadedFilename(file.name) + + // Clear coordinator cache and refresh legend + coordinator.clear(); + const updatedLegend = await fetchLegendItems(coordinator); + setLegendItems(updatedLegend); + + // await new Promise(resolve => setTimeout(resolve, 150)); + + // Query the uploaded point + const customPoint: any = await coordinator.query( + `SELECT + x, y, + ${colorGrouping} as category, + name as text, + id as identifier, + {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields + FROM data + WHERE id = 'custom_point'`, + { type: 'json' } + ); + + if (customPoint && customPoint.length > 0) { + // console.log('Custom point queried:', customPoint[0]); + + // Prepare selection to apply after remount + const newSelection = selectedPoints.filter((p: any) => p.identifier !== 'custom_point'); + newSelection.push(customPoint[0]); + setPendingSelection(newSelection); + + // Force remount to show new point + setDataVersion(v => v + 1); + } + } + } catch (error) { + console.error('Error getting UMAP coordinates:', error); + } finally { + if (fileInputRef.current) { + fileInputRef.current.value = ''; + } + } + }; + + const handleUploadClick = () => { + fileInputRef.current?.click(); + }; + const getSortedSelectedPoints = () => { if (!selectedPoints || selectedPoints.length === 0) return []; @@ -123,47 +198,6 @@ export const BEDEmbeddingView = (props: Props) => { setSelectedPoints(finalPoints); }; - const handleFileRemove = async () => { - try { - await deleteCustomPoint(); - setUploadedFilename('') - - coordinator.clear(); - const updatedLegend = await fetchLegendItems(coordinator); - setLegendItems(updatedLegend); - setDataVersion(v => v + 1); - } catch (error) { - console.error('Error deleting file'); - } - } - - const handleFileUpload = async (event: React.ChangeEvent) => { - const file = event.target.files?.[0]; - if (!file) return; - - try { - const coordinates = await getUmapCoordinates(file); - - if (coordinates.length >= 2) { - await addCustomPoint(coordinates[0], coordinates[1]); - setUploadedFilename(file.name) - - // Clear coordinator cache and refresh legend - coordinator.clear(); - const updatedLegend = await fetchLegendItems(coordinator); - setLegendItems(updatedLegend); - setDataVersion(v => v + 1); - centerOnPoint({x: coordinates[0], y: coordinates[1]}, 0.3) - } - } catch (error) { - console.error('Error getting UMAP coordinates:', error); - } - }; - - const handleUploadClick = () => { - fileInputRef.current?.click(); - }; - // Range selection (for rectangle/lasso) const handleRangeSelection = async (coordinator: any, value: any) => { // console.log('Range selection updated:', value); @@ -267,10 +301,7 @@ export const BEDEmbeddingView = (props: Props) => { FROM data ORDER BY ${colorGrouping}`; - console.log('Legend query:', query); const result = await coordinator.query(query, { type: 'json' }) as any[]; - console.log('Legend results:', result); - return result } @@ -280,11 +311,6 @@ export const BEDEmbeddingView = (props: Props) => { }); }, []); - // useEffect(() => { // add point - // addPoint(20, 20).then(() => { - // }); - // }, []); - useEffect(() => { // resize width of view if (containerRef.current) { setContainerWidth(containerRef.current.offsetWidth); @@ -299,6 +325,22 @@ export const BEDEmbeddingView = (props: Props) => { } }, [isReady, colorGrouping]) + useEffect(() => { // apply pending selection after dataVersion change + if (pendingSelection !== null) { + setTimeout(() => { + setSelectedPoints(pendingSelection); + // If there's an uploaded file, center on it and set tooltip + if (uploadedFilename) { + const uploadedPoint = pendingSelection.find((point: any) => point.identifier === 'custom_point'); + if (uploadedPoint) { + centerOnPoint(uploadedPoint, 0.3); + } + } + setPendingSelection(null); + }, 200); + } + }, [dataVersion, pendingSelection]) + useEffect(() => { // fetch initial bed id and neighbors if (isReady) { setTimeout(async () => { @@ -330,6 +372,8 @@ export const BEDEmbeddingView = (props: Props) => { { type: 'json' } ); setSelectedPoints([currentBed[0], ...neighborPoints]); + } else if (showNeighbors && enableUpload) { + setSelectedPoints([currentBed[0]]); } else { setSelectedPoints([currentBed[0]]); } @@ -355,7 +399,7 @@ export const BEDEmbeddingView = (props: Props) => { ref={fileInputRef} className="d-none" type="file" - accept=".bed,.bed.gz" + accept=".bed,.gz,application/gzip,application/x-gzip" onChange={handleFileUpload} /> {!!uploadedFilename && ( @@ -484,7 +528,7 @@ export const BEDEmbeddingView = (props: Props) => { {/* */} */} + -
- {/*Or, explore an example BED file*/} - Or, explore an example BED file - or an{' '} example BEDset -
-
- - -
-
- -
+ {searchOptions && ( +
+ test
- -
-
-

Statistics

-
- -
-
-
-

BED sets

-
- -
-
-
-

Embeddings

-
- + )} + +
+ +
+
+ explore the BED file embedding space above, or visit a random BED file + or BEDset +
+ +
+ + {(bedbaseStats?.bedfiles_number || '-').toLocaleString()} BED files + + • + + {(bedbaseStats?.bedsets_number || '-').toLocaleString()} BEDsets + + • + + {(bedbaseStats?.genomes_number || '-').toLocaleString()} genomes + + • + + more metrics + + +
+ +
+
+
+
+
+
+
+ +
Vector Search
+
+

+ Search by text, upload BED files for similarity matching, or browse BEDsets. Explore results directly within their region embedding space. +

+ + +
+
+ +
+
+
+ +
BED Analyzer
+
+

+ Analyze any BED file in your browser with our gtars-wasm integration. Get file statistics, region distributions, and chromosome coverage instantly. +

+ + BED Analyzer + +
+
-
-
-
- -
-

Web Server and API

-

- The BEDbase web server and API are designed to provide a user-friendly interface for exploring and - working with genomic region data. The web server allows users to search for BED files and BED sets, view - detailed information about specific files, and create collections of files. -

- - -
- -
- +
- +
{CODE_SNIPPETS.map((snippet) => ( - - +
+ {snippet.code} -
- -
- +
))} - - -
- - - -
-

BED Embedding Visualization

-

- BEDbase supports 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. -

- - - - - - - -

Search for BED Files

-

- BEDbase offers three search endpoints for discovering BED files and BEDsets, distinguishing itself from - other platforms by utilizing vector search to index and search through bed file regions. This approach - enhances search accuracy and efficiency compared to platforms relying on unstructured user-provided - metadata, which can be ambiguous and less reliable. User can search for BED files by providing a query - string, or a BED file. -

- - -
- setSearchTermSmall(e.target.value)} - onKeyDown={(e) => { - if (e.key === 'Enter') { - if (searchTermSmall.length === 0) { - return; - } - navigate(`/search?q=${searchTermSmall}`); - } - }} - className="p-2 rounded border w-100 shadow-sm" - /> - +
+
+ +
+ +
+
+ +
REST API
+
+

+ Programmatic access to the BEDbase web server with a RESTful API. Query, retrieve, and analyze genomic regions with simple HTTP requests from any language. +

+ + API Docs + +
- - - {/*
*/} - - -

BEDbase Client

-

- BEDbase provides a Python an R client for interacting with the BEDbase API. The client allows users to - download, cache, and analyze BED files and BED sets programmatically, without the need to interact with - the native API. BBclient is available on PyPI in geniml package with other useful tools for genomic data - analysis. Python Geniml package:{' '} - - {' '} - PyPI geniml - - . - R package:{' '} - - {' '} - BEDbaser - - . -

- + - -
- -
- +
- +
{BBCONF_SNIPPETS.map((snippet) => ( - - +
+ {snippet.code} -
- -
- +
))} - - -
- - - -
-

Data Availability Summary

-

- Comprehensive metrics about BEDbase file statistics is available on the {' '} - metrics page. -

- - -
-
    -
  • - Number of bed files available: - {(bedbaseStats?.bedfiles_number || 0).toLocaleString()} -
    • -
  • - Number of bed sets available: - {(bedbaseStats?.bedsets_number || 0).toLocaleString()} -
    • -
  • - Number of genomes available: - {(bedbaseStats?.genomes_number || 0).toLocaleString()} -
    • -
+
+
+ +
+ +
+
+ +
BEDbase Clients
+
+

+ Download, cache, and analyze BED files programmatically with native Python and R packages. Simplifies API interaction through high-level interfaces. +

+ +
- - + + + From 1a201b8981e89200cbc44a89f7daccc289cd4ccd Mon Sep 17 00:00:00 2001 From: Sam Park Date: Sat, 15 Nov 2025 00:56:25 -0500 Subject: [PATCH 16/76] color adjustment --- ui/src/components/layout.tsx | 18 ++++++++++-------- ui/src/components/nav/nav.tsx | 3 +-- ui/src/components/umap/bed-embedding-plot.tsx | 2 +- ui/src/custom.scss | 4 ++++ ui/src/pages/home.tsx | 12 ++++++------ 5 files changed, 22 insertions(+), 17 deletions(-) diff --git a/ui/src/components/layout.tsx b/ui/src/components/layout.tsx index df2db937..59e3529c 100644 --- a/ui/src/components/layout.tsx +++ b/ui/src/components/layout.tsx @@ -18,7 +18,7 @@ type LayoutProps = { const Footer = () => { const { data, isLoading, isFetching } = useServiceInfo(); return ( -
+
+ { }); return ( -
+
{ const renderTooltip = () => {tooltip || 'No tooltip available'}; return ( - -
-
-
{title}
-
{children}
+ +
+
+
{title}
+
{children}
 diff --git a/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx b/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx index c820a99e..795e96f0 100644 --- a/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx +++ b/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx @@ -193,7 +193,7 @@ export const GenomicFeatureBar = (props: Props) => { } return ( -
+

Genomic Features

diff --git a/ui/src/components/bedset-splash-components/plots.tsx b/ui/src/components/bedset-splash-components/plots.tsx index 86fddb90..422508c0 100644 --- a/ui/src/components/bedset-splash-components/plots.tsx +++ b/ui/src/components/bedset-splash-components/plots.tsx @@ -29,7 +29,7 @@ const Plot = (props: PlotProps) => { setShow(true); } }} - className="h-100 border rounded p-1 shadow-sm hover-border-primary transition-all" + className="h-100 border rounded p-1 shadow-sm hover-border-primary transition-all bg-white" >
{title} 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..1de5b36b 100644 --- a/ui/src/components/search/bed2bed/b2b-search-results-table.tsx +++ b/ui/src/components/search/bed2bed/b2b-search-results-table.tsx @@ -30,10 +30,10 @@ const columnHelper = createColumnHelper(); const scoreTooltip = ( - 
+      
+          
             Cosine similarity between files.
             Score is between 0 an 100, where 100 is a perfect match.
           

@@ -64,8 +64,8 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
         const bedId = info.getValue()?.id;
         const bedName = info.getValue()?.name;
         return (
-          
-            {bedName}
+          
+            {bedName}
           
         );
       },
@@ -74,31 +74,31 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
       id: 'name',
     }),
     columnHelper.accessor('metadata.genome_alias', {
-      cell: (info) => {info.getValue()},
+      cell: (info) => {info.getValue()},
       footer: (info) => info.column.id,
       header: 'Genome',
       id: 'genome',
     }),
     columnHelper.accessor('metadata.annotation.tissue', {
-      cell: (info) => {info.getValue() || 'N/A'},
+      cell: (info) => {info.getValue() || 'N/A'},
       footer: (info) => info.column.id,
       header: 'Tissue',
       id: 'tissue',
     }),
     columnHelper.accessor('metadata.annotation.cell_line', {
-      cell: (info) => {info.getValue() || 'N/A'},
+      cell: (info) => {info.getValue() || 'N/A'},
       footer: (info) => info.column.id,
       header: 'Cell line',
       id: 'cell-line',
     }),
     columnHelper.accessor('metadata.annotation.cell_type', {
-      cell: (info) => {info.getValue() || 'N/A'},
+      cell: (info) => {info.getValue() || 'N/A'},
       footer: (info) => info.column.id,
       header: 'Cell type',
       id: 'cell-type',
     }),
     columnHelper.accessor('metadata.description', {
-      cell: (info) => {info.getValue()},
+      cell: (info) => {info.getValue()},
       footer: (info) => info.column.id,
       header: 'Description',
       id: 'description',
@@ -106,10 +106,10 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
     columnHelper.accessor('metadata', {
       cell: (info) => (
         
-              
+            
+              
                 {YAML.dump(info.getValue(), {
                   indent: 2,
                   noRefs: true,
@@ -118,7 +118,7 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
             
           }
         >
-          
+          
         
       ),
       footer: (info) => info.column.id,
@@ -127,12 +127,12 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
     }),
     columnHelper.accessor('score', {
       cell: (info) => (
-        
+        
           
         
       ),
@@ -149,7 +149,7 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
           

             {cart[bedId || ''] ? (
               
             ) : (
               
             )}
           

@@ -226,21 +226,21 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
   };
 
   return (
-    

-      

+    

+      

          setGlobalFilter(e.target.value)}
         />
       

-
{point.text} {point.fields.Assay} {point.fields['Cell Line']}
+
{table.getHeaderGroups().map((headerGroup) => ( {headerGroup.headers.map((header) => ( - {table.getRowModel().rows.map((row) => ( - + {row.getVisibleCells().map((cell) => ( ))} @@ -277,11 +277,11 @@ export const Bed2BedSearchResultsTable = (props: Props) => { ))}
+ {header.isPlaceholder ? null : (
{ > {flexRender(header.column.columnDef.header, header.getContext())} {{ - asc: , - desc: , + asc: , + desc: , }[header.column.getIsSorted() as string] ?? null}
)} @@ -269,7 +269,7 @@ export const Bed2BedSearchResultsTable = (props: Props) => {
{flexRender(cell.column.columnDef.cell, cell.getContext())}
-
-
-
+
+
+
Showing - + {table.getState().pagination.pageSize * table.getState().pagination.pageIndex + 1} to{' '} {Math.min( table.getState().pagination.pageSize * (table.getState().pagination.pageIndex + 1), @@ -290,39 +290,39 @@ export const Bed2BedSearchResultsTable = (props: Props) => { of {table.getRowCount().toLocaleString()} files
-
-
+
+
{ - if (e.target.value === '') { - setSearchParams({}); - } else { - setSearchParams({ q: e.target.value }); - } - onChange(e.target.value); - }} - className="form-control" - type="text" - placeholder={placeholder} - onKeyDown={(e) => { - if (e.key === 'Enter') { - if (value === '') { - toast.error('Please enter a search term', { - position: 'top-center', - }); - return; +
+
+ { + if (e.target.value === '') { + setSearchParams({}); + } else { + setSearchParams({ q: e.target.value }); } - onSearch(); - } - }} - /> + onChange(e.target.value); + }} + className="form-control" + type="text" + placeholder={placeholder} + onKeyDown={(e) => { + if (e.key === 'Enter') { + if (value === '') { + toast.error('Please enter a search term', { + position: 'top-center', + }); + return; + } + onSearch(); + } + }} + /> - - {searchView === 't2b' && ( - + )} +
+ +
{showOptions && ( diff --git a/ui/src/components/search/search-selector.tsx b/ui/src/components/search/search-selector.tsx index 41cef61c..7dcb2126 100644 --- a/ui/src/components/search/search-selector.tsx +++ b/ui/src/components/search/search-selector.tsx @@ -1,4 +1,3 @@ -import Nav from 'react-bootstrap/Nav'; import { useSearchParams } from 'react-router-dom'; type SearchView = 't2b' | 'b2b' | 't2bs'; @@ -12,40 +11,49 @@ export const SearchSelector = (props: Props) => { const { view, setView } = props; const [params, setParams] = useSearchParams(); return ( -
-
- +
+
+
    +
  • + +
    • +
  • + +
    • +
  • + +
    • +
); diff --git a/ui/src/components/search/text2bed/text2bed.tsx b/ui/src/components/search/text2bed/text2bed.tsx index b3a5f92b..3b939ab0 100644 --- a/ui/src/components/search/text2bed/text2bed.tsx +++ b/ui/src/components/search/text2bed/text2bed.tsx @@ -81,7 +81,7 @@ export const Text2Bed = () => { ) : (
{results ? ( -
+
{' '} diff --git a/ui/src/components/search/text2bedset.tsx b/ui/src/components/search/text2bedset.tsx index a0213bce..81c920bd 100644 --- a/ui/src/components/search/text2bedset.tsx +++ b/ui/src/components/search/text2bedset.tsx @@ -66,7 +66,7 @@ export const Text2BedSet = () => { ) : (
{results ? ( -
+
diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx index 6230ef73..304b22dc 100644 --- a/ui/src/pages/bed-splash.tsx +++ b/ui/src/pages/bed-splash.tsx @@ -68,28 +68,28 @@ export const BedSplash = () => { if (isLoading) { return ( -
+
-
- +
+
-
- +
+
-
- +
+
-
- +
+
- +
@@ -100,32 +100,32 @@ export const BedSplash = () => { return (
-

Oh no!

-
-
+

Oh no!

+
+
We could not find BED with record identifier:
- {bedId} + {bedId}
-
-

+

+

Are you sure you have the correct record identifier? If you believe this is an error, please open an - issue: on GitHub + issue: on GitHub

-
- - - - @@ -139,25 +139,25 @@ export const BedSplash = () => { } else { return ( - - + + {metadata !== undefined ? : null} - + -
Overview
-
-
- +
Overview
+
+
+
- - + + - + {Object.keys(metadata?.annotation || {}).map((k) => { if (k === 'input_file' || k === 'file_name' || k === 'sample_name') { return null; @@ -170,10 +170,10 @@ export const BedSplash = () => { return ( - - -
BEDsets
-
-
-
KeyValueKeyValue
+ {snakeToTitleCase(k)} + { k === 'global_sample_id' ? (Array.isArray(value) && value.length > 0) ? value.map((v, i) => ( @@ -204,29 +204,29 @@ export const BedSplash = () => {
+
BEDsets
+
+
+
- - - - + + + + {[ ...(metadata?.bedsets || []).map((bedset) => ( - - + - - + )} - + - -
Plots
+ +
Plots
 @@ -281,9 +281,9 @@ export const BedSplash = () => { )} {neighbours && ( - +
-
Similar BED Files
+
Similar BED Files
{
- + diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx index 2b9052c7..c5df76ce 100644 --- a/ui/src/pages/home.tsx +++ b/ui/src/pages/home.tsx @@ -11,12 +11,14 @@ import { BEDEmbeddingPlot } from '../components/umap/bed-embedding-plot.tsx'; export const Home = () => { const [searchTerm, setSearchTerm] = useState(''); + const [uploadedFile, setUploadedFile] = useState(null); const [copiedAPI, setCopiedAPI] = useState(false); const [copiedClient, setCopiedClient] = useState(false); - // const [searchOptions, setSearchOptions] = useState(false); + const [searchType, setSearchType] = useState('t2b'); const [activeApiTab, setActiveApiTab] = useState(CODE_SNIPPETS[0].language); const [activeClientTab, setActiveClientTab] = useState(BBCONF_SNIPPETS[0].language); + const navigate = useNavigate(); // const { data: exampleBedMetadata } = useExampleBed(); # if example will be dynamic again @@ -24,66 +26,121 @@ export const Home = () => { const { data: exampleBedSetMetadata } = useExampleBedSet(); const { data: bedbaseStats } = useStats(); + const handleSearch = () => { + if (searchType === 'b2b') { + if (!uploadedFile) return; + navigate(`/search?view=${searchType}`, { state: { file: uploadedFile } }); + } else { + if (!searchTerm) return; + navigate(`/search?q=${searchTerm}&view=${searchType}`); + } + }; + return (

BEDbase

-
-

- The open access platform for aggregating, analyzing, and serving genomic regions. +

+

+ The open access platform for aggregating, analyzing, and serving genomic region data. +

+

+ Explore thousands of BED files (including {' '} + + .bed + ,{' '} + + .bigbed + ,{' '} + + .wig + ,{' '} + + .bw + ,{' '} + + .bdg + + ) from ENCODE, GEO, and more.

-
-
- setSearchTerm(e.target.value)} - onKeyDown={(e) => { - if (e.key === 'Enter') { - if (searchTerm.length === 0) { - return; +
+
+ {searchType === 'b2b' ? ( + { + const file = e.target.files?.[0]; + if (file) { + setUploadedFile(file); } - navigate(`/search?q=${searchTerm}`); - } - }} - /> - {/*
- {/* {searchOptions && ( -
- test -
- )} */} -
- explore the BED file embedding space above, or visit a random BED file + explore the BED file region embedding space above, or visit a random BED file or BEDset
@@ -107,9 +164,9 @@ export const Home = () => {
-
+
-
+
@@ -117,7 +174,7 @@ export const Home = () => {
Vector Search

- Search by text, upload BED files for similarity matching, or browse BEDsets. Explore results directly within their region embedding space. + Search by text, upload BED files for similarity matching, or browse BEDsets. Explore results directly in their region embedding space.

setMetricModalProps({ title: 'BEDset Search Term', type: 'bar', diff --git a/ui/src/pages/search.tsx b/ui/src/pages/search.tsx index d2c2f49b..278ec77f 100644 --- a/ui/src/pages/search.tsx +++ b/ui/src/pages/search.tsx @@ -1,7 +1,7 @@ import { Layout } from '../components/layout'; import { useState } from 'react'; -import { useSearchParams } from 'react-router-dom'; +import { useSearchParams, useLocation } from 'react-router-dom'; import { SearchSelector } from '../components/search/search-selector'; import { Text2Bed } from '../components/search/text2bed/text2bed'; @@ -14,8 +14,11 @@ type SearchView = 't2b' | 'b2b' | 't2bs'; export const SearchPage = () => { const [searchParams] = useSearchParams(); + const location = useLocation(); const [searchView, setSearchView] = useState((searchParams.get('view') as SearchView) || 't2b'); + const uploadedFile = location.state?.file as File | undefined; + return ( @@ -28,7 +31,7 @@ export const SearchPage = () => { {searchView === 't2b' ? ( ) : searchView === 'b2b' ? ( - + ) : searchView === 't2bs' ? ( ) : ( From 7317e4e9b540eaecf3d19e17d7ceff10b65dd253 Mon Sep 17 00:00:00 2001 From: Sam Park Date: Sat, 15 Nov 2025 18:28:58 -0500 Subject: [PATCH 18/76] add umap to t2b search --- .gitignore | 2 + ui/src/components/search/search-bar.tsx | 6 +- ui/src/components/search/search-selector.tsx | 10 +- .../text2bed/t2b-search-results-table.tsx | 201 +++++++++--------- .../components/search/text2bed/text2bed.tsx | 51 ++++- ui/src/components/umap/bed-embedding-plot.tsx | 58 ++++- ui/src/pages/home.tsx | 2 +- 7 files changed, 199 insertions(+), 131 deletions(-) diff --git a/.gitignore b/.gitignore index 118f812c..71244524 100644 --- a/.gitignore +++ b/.gitignore @@ -38,3 +38,5 @@ ENV/ env.bak/ venv.bak/ .DS_store + +ui/package-lock.json diff --git a/ui/src/components/search/search-bar.tsx b/ui/src/components/search/search-bar.tsx index 99e45cd9..ad45cbe3 100644 --- a/ui/src/components/search/search-bar.tsx +++ b/ui/src/components/search/search-bar.tsx @@ -109,10 +109,10 @@ export const SearchBar = (props: Props) => {
{searchView === 't2b' &&
-
Search Options
+
Search Options
Genome:
-
Assay:
-
BEDset IDNameDescriptionViewBEDset IDNameDescriptionView
+
{bedset.id} + {bedset.name || 'No name'} + {bedset.description || 'No description'} @@ -252,23 +252,23 @@ export const BedSplash = () => { - -
Statistics
+ +
Statistics
{metadata && ( -
- - - - - - - - - - - - - - - - {results.results?.map((result) => ( - - - - - - - - - - - - - ))} - -
NameGenomeTissueCell LineCell TypeDescriptionAssayInfo - - 
-                      Cosine similarity between search term and bedfile.
-                      Score is between 0 an 100, where 100 is a perfect match.
-
- - } + <> + {results.results?.map((result) => ( +
+
+
onCardClick?.(result.metadata?.id || '')} > - - Score* +
+
+

+ {result?.metadata?.name || 'No name'} +

+ + 
+                          {YAML.dump(result?.metadata, {
+                            indent: 2,
+                            noRefs: true,
+                          }) || 'No metadata'}
+
+ + } + > + e.stopPropagation()}> + +
+ +
+ {IsUnique(result.id, search_query || '')} + +
Match score
+
+ } + > + + {roundToTwoDecimals((result.score ?? 0) * 100)}% + + +
+
+

+ {result?.metadata?.description || 'No description'} +

+ +
+ + genome:{' '}{result?.metadata?.genome_alias || 'N/A'} + + + tissue:{' '}{result?.metadata?.annotation?.tissue || 'N/A'} + + + cell_line:{' '}{result?.metadata?.annotation?.cell_line || 'N/A'} - -
- Actions -
{IsUnique(result?.metadata?.name || 'No name', result.id, search_query || '') || 'No name'} - {result?.metadata?.genome_alias || 'N/A'} - {result?.metadata?.annotation?.tissue || 'N/A'}{result?.metadata?.annotation?.cell_line || 'N/A'}{result?.metadata?.annotation?.cell_type || 'N/A'}{result?.metadata?.description || ''}{result?.metadata?.annotation?.assay || 'N/A'} - - 
-                      {YAML.dump(result?.metadata, {
-                        indent: 2,
-                        noRefs: true,
-                      }) || 'No description'}
-
- - } + + cell_type:{' '}{result?.metadata?.annotation?.cell_type || 'N/A'} + + + assay:{' '}{result?.metadata?.annotation?.assay || 'N/A'} + + + + +
+
- - + + {cart[result?.metadata?.id || ''] ? ( ) : ( )} -
-
+
+
+
+ ))} + ); }; \ No newline at end of file diff --git a/ui/src/components/search/text2bed/text2bed.tsx b/ui/src/components/search/text2bed/text2bed.tsx index 3b939ab0..5d8315ab 100644 --- a/ui/src/components/search/text2bed/text2bed.tsx +++ b/ui/src/components/search/text2bed/text2bed.tsx @@ -4,12 +4,13 @@ import { SearchBar } from '../search-bar'; import { Text2BedSearchResultsTable } from './t2b-search-results-table'; import { SearchingJumper } from '../searching-jumper'; import { useSearchParams } from 'react-router-dom'; -import { useEffect, useState } from 'react'; +import { useEffect, useState, useRef } from 'react'; import { useText2BedSearch } from '../../../queries/useText2BedSearch'; import { TableToolbar } from '../table-toolbar'; import { PaginationBar } from '../pagination-bar'; import { SearchError } from '../search-error'; import { AxiosError } from 'axios'; +import { BEDEmbeddingPlot, BEDEmbeddingPlotRef } from '../../../components/umap/bed-embedding-plot.tsx'; export const Text2Bed = () => { const [searchParams, setSearchParams] = useSearchParams(); @@ -18,6 +19,9 @@ export const Text2Bed = () => { const [assay, setAssay] = useState(searchParams.get('assay') || ''); const [limit, setLimit] = useState(20); const [offset, setOffset] = useState(0); + const [containerHeight, setContainerHeight] = useState(660); + const embeddingPlotRef = useRef(null); + const containerRef = useRef(null); const { isFetching: isSearching, @@ -33,6 +37,8 @@ export const Text2Bed = () => { autoRun: false, }); + console.log(results) + useEffect(() => { const params = new URLSearchParams(); if (searchTerm) params.set('q', searchTerm); @@ -47,6 +53,20 @@ export const Text2Bed = () => { } }, [limit, offset, genome, assay, onSearch]); + useEffect(() => { + const calculateHeight = () => { + if (containerRef.current) { + const rect = containerRef.current.getBoundingClientRect(); + const availableHeight = window.innerHeight - rect.top; // 40px margin from bottom + setContainerHeight(Math.max(400, Math.min(availableHeight, 800))); // min 400px, max 800px + } + }; + + calculateHeight(); + window.addEventListener('resize', calculateHeight); + return () => window.removeEventListener('resize', calculateHeight); + }, []); + if (error) { if (error) { return ; @@ -79,12 +99,31 @@ export const Text2Bed = () => { {isSearching ? ( ) : ( -
+
{results ? ( -
- - {' '} - +
+
+
+ result.id)} + height={containerHeight} + /> +
+
+
+
+ + { + embeddingPlotRef.current?.centerOnBedId(bedId); + }} + />{' '} + +
+
) : (
diff --git a/ui/src/components/umap/bed-embedding-plot.tsx b/ui/src/components/umap/bed-embedding-plot.tsx index eed7950b..04959444 100644 --- a/ui/src/components/umap/bed-embedding-plot.tsx +++ b/ui/src/components/umap/bed-embedding-plot.tsx @@ -1,5 +1,5 @@ import { EmbeddingViewMosaic } from 'embedding-atlas/react'; -import { useEffect, useState, useRef, useMemo } from 'react'; +import { useEffect, useState, useRef, useMemo, forwardRef, useImperativeHandle } from 'react'; import * as vg from '@uwdata/vgplot' import { tableau20 } from '../../utils'; @@ -7,12 +7,16 @@ import { AtlasTooltip } from './atlas-tooltip'; import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context'; type Props = { - bedId?: string, + bedIds?: string[], height?: number; } -export const BEDEmbeddingPlot = (props: Props) => { - const { bedId, height } = props; +export interface BEDEmbeddingPlotRef { + centerOnBedId: (bedId: string, scale?: number) => Promise; +} + +export const BEDEmbeddingPlot = forwardRef((props, ref) => { + const { bedIds, height } = props; const { coordinator, initializeData } = useMosaicCoordinator(); const containerRef = useRef(null); @@ -26,6 +30,40 @@ export const BEDEmbeddingPlot = (props: Props) => { const filter = useMemo(() => vg.Selection.intersect(), []); + const centerOnPoint = (point: any, scale: number = 1) => { + setTooltipPoint(point); + setViewportState({ + x: point.x, + y: point.y, + scale: scale + }); + }; + + const centerOnBedId = async (bedId: string, scale: number = 1) => { + if (!isReady) return; + + const bedData: any = await coordinator.query( + `SELECT + x, y, + ${colorGrouping} as category, + name as text, + id as identifier, + {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields + FROM data + WHERE id = '${bedId}'`, + { type: 'json' } + ); + + if (bedData && bedData.length > 0) { + centerOnPoint(bedData[0], scale); + // setSelectedPoints([bedData[0]]); + } + }; + + useImperativeHandle(ref, () => ({ + centerOnBedId + })); + useEffect(() => { // initialize data initializeData().then(() => { setIsReady(true); @@ -38,8 +76,8 @@ export const BEDEmbeddingPlot = (props: Props) => { } }, [isReady]); - useEffect(() => { // fetch initial bed id and neighbors - if (isReady && !!bedId) { + useEffect(() => { // fetch provided bed ids + if (isReady && bedIds && bedIds.length > 0) { setTimeout(async () => { const currentBed: any = await coordinator.query( `SELECT @@ -49,15 +87,15 @@ export const BEDEmbeddingPlot = (props: Props) => { id as identifier, {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields FROM data - WHERE id = '${bedId}'`, + WHERE id IN ('${bedIds.join("','")}')`, { type: 'json' } ); if (!currentBed || currentBed.length === 0) return; setTooltipPoint(currentBed[0]); - setSelectedPoints([currentBed[0]]); + setSelectedPoints(currentBed); }, 200); } - }, [isReady, bedId, coordinator]); + }, [isReady, bedIds, coordinator, colorGrouping]); return ( <> @@ -102,4 +140,4 @@ export const BEDEmbeddingPlot = (props: Props) => { )} ); -} +}); diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx index c5df76ce..41605d92 100644 --- a/ui/src/pages/home.tsx +++ b/ui/src/pages/home.tsx @@ -137,7 +137,7 @@ export const Home = () => {
- +
explore the BED file region embedding space above, or visit a random BED file From 48e5a19911315cc9e8c0d9d6027bfb2b6c4a139a Mon Sep 17 00:00:00 2001 From: Sam Park Date: Sat, 15 Nov 2025 19:24:20 -0500 Subject: [PATCH 19/76] t2b search layout options --- ui/src/components/search/search-bar.tsx | 48 ++++++++++++++++--- .../text2bed/t2b-search-results-table.tsx | 15 ++++-- .../components/search/text2bed/text2bed.tsx | 28 +++++++---- 3 files changed, 69 insertions(+), 22 deletions(-) diff --git a/ui/src/components/search/search-bar.tsx b/ui/src/components/search/search-bar.tsx index ad45cbe3..9c4190cd 100644 --- a/ui/src/components/search/search-bar.tsx +++ b/ui/src/components/search/search-bar.tsx @@ -11,10 +11,12 @@ type Props = { setLimit: (limit: number) => void; genome: string; assay: string; + layout?: string; setGenome: (assay: string) => void; setAssay: (assay: string) => void; onChange: (value: string) => void; onSearch: () => void; + setLayout?: (layout: string) => void; }; const placeholders = [ @@ -27,7 +29,7 @@ const placeholders = [ ]; export const SearchBar = (props: Props) => { - const { value, onChange, onSearch, limit, setLimit, genome, setGenome, assay, setAssay } = props; + const { value, onChange, onSearch, limit, setLimit, genome, setGenome, assay, setAssay, layout, setLayout } = props; const [, setSearchParams] = useSearchParams(); const { searchView } = useSearchView(); const { data: genomes } = useAvailableGenomes(); @@ -107,12 +109,44 @@ export const SearchBar = (props: Props) => {
{showOptions && (
- {searchView === 't2b' && + {(searchView === 't2b') && !!layout && !!setLayout &&
-
Search Options
+
Layout:
+
+ setLayout('split')} + /> + + setLayout('table')} + /> + +
-
Genome:
- setGenome(String(e.target.value))}> {genomes?.results.map((genomeItem, index) => ( @@ -122,8 +156,8 @@ export const SearchBar = (props: Props) => { ))} -
Assay:
- setAssay(String(e.target.value))}> {assays?.results.map((assayItem, index) => ( 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 0d3258d8..bbc787b0 100644 --- a/ui/src/components/search/text2bed/t2b-search-results-table.tsx +++ b/ui/src/components/search/text2bed/t2b-search-results-table.tsx @@ -13,6 +13,7 @@ type SearchResponse = components['schemas']['BedListSearchResult']; type Props = { results: SearchResponse; search_query?: string | undefined; + layout?: string; onCardClick?: (bedId: string) => void; }; @@ -38,7 +39,7 @@ const IsUnique = (found_id: string, search_id: string) => { }; export const Text2BedSearchResultsTable = (props: Props) => { - const { results, search_query, onCardClick } = props; + const { results, search_query, layout, onCardClick } = props; const { cart, addBedToCart, removeBedFromCart } = useBedCart(); const navigate = useNavigate(); @@ -48,8 +49,12 @@ export const Text2BedSearchResultsTable = (props: Props) => {
onCardClick?.(result.metadata?.id || '')} + className={`card-body position-relative flex-1 ${(layout === 'split') && 'cursor-pointer'}`} + onClick={() => { + if (layout === 'split') { + onCardClick?.(result.metadata?.id || '') + } + }} >
@@ -57,7 +62,7 @@ export const Text2BedSearchResultsTable = (props: Props) => { {result?.metadata?.name || 'No name'} 

@@ -83,7 +88,7 @@ export const Text2BedSearchResultsTable = (props: Props) => {
} > - + 0.5 ? 'bg-primary' : 'bg-warning'}`} style={{ fontSize: '10px' }}> {roundToTwoDecimals((result.score ?? 0) * 100)}% diff --git a/ui/src/components/search/text2bed/text2bed.tsx b/ui/src/components/search/text2bed/text2bed.tsx index 5d8315ab..2847ee01 100644 --- a/ui/src/components/search/text2bed/text2bed.tsx +++ b/ui/src/components/search/text2bed/text2bed.tsx @@ -20,6 +20,8 @@ export const Text2Bed = () => { const [limit, setLimit] = useState(20); const [offset, setOffset] = useState(0); const [containerHeight, setContainerHeight] = useState(660); + const [layout, setLayout] = useState('split'); + const embeddingPlotRef = useRef(null); const containerRef = useRef(null); @@ -92,6 +94,8 @@ export const Text2Bed = () => { onSearch(); }, 100); }} + layout={layout} + setLayout={setLayout} /> @@ -102,21 +106,25 @@ export const Text2Bed = () => {
{results ? (
-
-
- result.id)} - height={containerHeight} - /> + {(layout === 'split') && ( +
+
+ result.id)} + height={containerHeight} + /> +
-
-
-
+ )} + +
+
{ embeddingPlotRef.current?.centerOnBedId(bedId); }} From c91fda737d016dbbd1d77b46e6f187273312cc15 Mon Sep 17 00:00:00 2001 From: Sam Park Date: Sun, 16 Nov 2025 01:25:47 -0500 Subject: [PATCH 20/76] b2b search page progress --- .../bed2bed/b2b-search-results-cards.tsx | 176 +++++++++++++++ ui/src/components/search/bed2bed/bed2bed.tsx | 127 ++++++----- ui/src/components/search/search-bar.tsx | 204 ++++++++++-------- .../text2bed/t2b-search-results-table.tsx | 10 +- .../components/search/text2bed/text2bed.tsx | 74 +++---- ui/src/components/search/text2bedset.tsx | 59 +++-- ui/src/components/umap/atlas-tooltip.tsx | 73 +++---- ui/src/components/umap/bed-embedding-plot.tsx | 5 +- ui/src/pages/bed-splash.tsx | 107 +++++---- ui/src/pages/home.tsx | 2 +- ui/src/pages/search.tsx | 73 ++++++- 11 files changed, 569 insertions(+), 341 deletions(-) create mode 100644 ui/src/components/search/bed2bed/b2b-search-results-cards.tsx diff --git a/ui/src/components/search/bed2bed/b2b-search-results-cards.tsx b/ui/src/components/search/bed2bed/b2b-search-results-cards.tsx new file mode 100644 index 00000000..05c18bd2 --- /dev/null +++ b/ui/src/components/search/bed2bed/b2b-search-results-cards.tsx @@ -0,0 +1,176 @@ +// import { useState } from 'react'; +import { useNavigate } from 'react-router-dom'; + +import { components } from '../../../../bedbase-types'; +import { OverlayTrigger, Tooltip } from 'react-bootstrap'; +import { roundToTwoDecimals } from '../../../utils'; +import YAML from 'js-yaml'; +import { useBedCart } from '../../../contexts/bedcart-context'; +import toast from 'react-hot-toast'; + +type Bed = components['schemas']['QdrantSearchResult']; + +type Props = { + results: Bed[]; + layout?: string; + onCardClick?: (bedId: string) => void; +}; + +// const scoreTooltip = ( +// +// 
+//             Cosine similarity between files.
+//             Score is between 0 an 100, where 100 is a perfect match.
+//
+// +// } +// > +// +// Score* +// + +// +// ); + +export const Bed2BedSearchResultsCards = (props: Props) => { + const { results, layout, onCardClick } = props; + const { cart, addBedToCart, removeBedFromCart } = useBedCart(); + const navigate = useNavigate(); + + // const [sorting, setSorting] = useState([]); + // const [pagination, setPagination] = useState({ + // pageIndex: 0, + // pageSize: 20, + // }); + + return ( + <> + {results?.map((result) => ( +
+
+
{ + if (layout === 'split') { + onCardClick?.(result.metadata?.id || '') + } + }} + > +
+
+

+ {result?.metadata?.name || 'No name'} +

+ + 
+                          {YAML.dump(result?.metadata, {
+                            indent: 2,
+                            noRefs: true,
+                          }) || 'No metadata'}
+
+ + } + > + e.stopPropagation()}> + +
+ +
+ {/* {IsUnique(result.id, search_query || '')} */} + +
Match score
+
+ } + > + 0.5 ? 'bg-primary' : 'bg-secondary'}`} style={{ fontSize: '10px' }}> + {roundToTwoDecimals((result.score ?? 0) * 100)}% + + +
+
+

+ {result?.metadata?.description || 'No description'} +

+ +
+ + genome:{' '}{result?.metadata?.genome_alias || 'N/A'} + + + tissue:{' '}{result?.metadata?.annotation?.tissue || 'N/A'} + + + cell_line:{' '}{result?.metadata?.annotation?.cell_line || 'N/A'} + + + cell_type:{' '}{result?.metadata?.annotation?.cell_type || 'N/A'} + + + assay:{' '}{result?.metadata?.annotation?.assay || 'N/A'} + +
+
+ +
+ + {cart[result?.metadata?.id || ''] ? ( + + ) : ( + + )} +
+
+
+ ))} + + ); +}; diff --git a/ui/src/components/search/bed2bed/bed2bed.tsx b/ui/src/components/search/bed2bed/bed2bed.tsx index 664e3c03..48f75f1c 100644 --- a/ui/src/components/search/bed2bed/bed2bed.tsx +++ b/ui/src/components/search/bed2bed/bed2bed.tsx @@ -1,23 +1,21 @@ -import { useRef, useCallback, Fragment, useEffect, useState } from 'react'; -import { useDropzone } from 'react-dropzone'; +import { useEffect, useState, useRef } from 'react'; import { SearchingJumper } from '../searching-jumper'; import { useBed2BedSearch } from '../../../queries/useBed2BedSearch'; -import { Bed2BedSearchResultsTable } from './b2b-search-results-table'; +// import { Bed2BedSearchResultsTable } from './b2b-search-results-table'; +import { BEDEmbeddingPlot, BEDEmbeddingPlotRef } from '../../../components/umap/bed-embedding-plot.tsx'; +import { Bed2BedSearchResultsCards } from './b2b-search-results-cards.tsx'; type Props = { - uploadedFile?: File; + file: File | null; + layout: string; }; export const Bed2Bed = (props: Props) => { - const { uploadedFile } = props; - const [file, setFile] = useState(uploadedFile || null); - - const inputRef = useRef(null); - const onDrop = useCallback((acceptedFiles: File[]) => { - setFile(acceptedFiles[0]); - }, []); - - const { isDragActive, getRootProps, getInputProps } = useDropzone({ onDrop }); + const { file, layout } = props; + const [containerHeight, setContainerHeight] = useState(660); + + const embeddingPlotRef = useRef(null); + const containerRef = useRef(null); const { isFetching: isSearching, @@ -28,6 +26,8 @@ export const Bed2Bed = (props: Props) => { autoRun: false, }); + console.log(results) + useEffect(() => { if (file) { if (document.activeElement instanceof HTMLElement) { @@ -39,59 +39,56 @@ export const Bed2Bed = (props: Props) => { } }, [file, onSearch]); + useEffect(() => { + const calculateHeight = () => { + if (containerRef.current) { + const rect = containerRef.current.getBoundingClientRect(); + const availableHeight = window.innerHeight - rect.top; + setContainerHeight(Math.max(400, Math.min(availableHeight, 800))); + } + }; + + calculateHeight(); + window.addEventListener('resize', calculateHeight); + return () => window.removeEventListener('resize', calculateHeight); + }, []); + return ( -
-
{ - if (inputRef.current) { - inputRef.current.click(); - } - }} - className={ - isDragActive - ? 'w-100 rounded border p-3 shadow-sm border-dashed b2b-drop-zone transition-all border-primary' - : 'w-100 rounded border p-3 shadow-sm border-dashed b2b-drop-zone transition-all' - } - > - {file ? ( - -

- Selected file: - {file.name} -

- - - ) : ( - -

Select a file or drag and drop one

-

- *Provided file should be aligned to hg38 assembly. -

- - - ) - } -
- -
- {isSearching ? ( - - ) : ( -
{results ? : null}
- )} -
+
+ {isSearching ? ( + + ) : ( +
+ {results ? ( +
+ {(layout === 'split') && ( +
+
+ result.payload.id)} + height={containerHeight} + preselectPoint={false} + /> +
+
+ )} + +
+
+ +
+
+
+ ) : ( +
+

Try uploading a BED file above to find similar files!

+

Note: provided file should be aligned to hg38 assembly.

+
+ )} +
+ + )}
); }; diff --git a/ui/src/components/search/search-bar.tsx b/ui/src/components/search/search-bar.tsx index 9c4190cd..025438f8 100644 --- a/ui/src/components/search/search-bar.tsx +++ b/ui/src/components/search/search-bar.tsx @@ -1,6 +1,6 @@ import toast from 'react-hot-toast'; -import { useSearchParams } from 'react-router-dom'; -import { useMemo, useState } from 'react'; +// import { useSearchParams } from 'react-router-dom'; +import { useMemo, useState, useRef } from 'react'; import { useSearchView } from '../../contexts/search-view-context.tsx'; import { useAvailableGenomes } from '../../queries/useAvailableGenomes.ts'; import { useAvailableAssays } from '../../queries/useAvailableAssays.ts'; @@ -17,6 +17,8 @@ type Props = { onChange: (value: string) => void; onSearch: () => void; setLayout?: (layout: string) => void; + file: File | null; + setFile: (file: File | null) => void; }; const placeholders = [ @@ -29,49 +31,102 @@ const placeholders = [ ]; export const SearchBar = (props: Props) => { - const { value, onChange, onSearch, limit, setLimit, genome, setGenome, assay, setAssay, layout, setLayout } = props; - const [, setSearchParams] = useSearchParams(); + const { value, onChange, onSearch, limit, setLimit, genome, setGenome, assay, setAssay, layout, setLayout, file, setFile } = props; + // const [, setSearchParams] = useSearchParams(); const { searchView } = useSearchView(); const { data: genomes } = useAvailableGenomes(); const { data: assays } = useAvailableAssays(); const [showOptions, setShowOptions] = useState(false); - // const assays = ['ATAC-seq', 'ChIP-Seq']; + const fileInputRef = useRef(null); const placeholder = useMemo(() => placeholders[Math.floor(Math.random() * placeholders.length)], []); return ( <> -
+
- { - if (e.target.value === '') { - setSearchParams({}); - } else { - setSearchParams({ q: e.target.value }); - } - onChange(e.target.value); - }} - className="form-control" - type="text" - placeholder={placeholder} - onKeyDown={(e) => { - if (e.key === 'Enter') { - if (value === '') { - toast.error('Please enter a search term', { - position: 'top-center', - }); - return; + {searchView === 'b2b' ? ( + <> + {file ? ( + <> + fileInputRef.current?.click()} + readOnly + /> + { + const selectedFile = e.target.files?.[0]; + if (selectedFile) { + setFile(selectedFile); + } + }} + /> + + + ) : ( + { + const selectedFile = e.target.files?.[0]; + if (selectedFile) { + setFile(selectedFile); + } + }} + /> + )} + + ) : ( + { + // if (e.target.value === '') { + // setSearchParams({}); + // } else { + // setSearchParams({ q: e.target.value }); + // } + onChange(e.target.value); + }} + placeholder={placeholder} + onKeyDown={(e) => { + if (e.key === 'Enter') { + if (value === '') { + toast.error('Please enter a search term', { + position: 'top-center', + }); + return; + } + onSearch(); } - onSearch(); - } - }} - /> + }} + /> + )} setLayout('split')} - /> - - setLayout('table')} - /> - -
+
+
Layout:
+ -
Genome:
- setGenome(String(e.target.value))}> {genomes?.results.map((genomeItem, index) => ( @@ -156,8 +186,8 @@ export const SearchBar = (props: Props) => { ))} -
Assay:
- setAssay(String(e.target.value))}> {assays?.results.map((assayItem, index) => ( 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 bbc787b0..798b16ac 100644 --- a/ui/src/components/search/text2bed/t2b-search-results-table.tsx +++ b/ui/src/components/search/text2bed/t2b-search-results-table.tsx @@ -49,7 +49,7 @@ export const Text2BedSearchResultsTable = (props: Props) => {
{ if (layout === 'split') { onCardClick?.(result.metadata?.id || '') @@ -57,8 +57,8 @@ export const Text2BedSearchResultsTable = (props: Props) => { }} >
-
-

+

+

{result?.metadata?.name || 'No name'}

{
} > - 0.5 ? 'bg-primary' : 'bg-warning'}`} style={{ fontSize: '10px' }}> + 0.5 ? 'bg-primary' : 'bg-secondary'}`} style={{ fontSize: '10px' }}> {roundToTwoDecimals((result.score ?? 0) * 100)}%
-

+

{result?.metadata?.description || 'No description'}

diff --git a/ui/src/components/search/text2bed/text2bed.tsx b/ui/src/components/search/text2bed/text2bed.tsx index 2847ee01..bba93974 100644 --- a/ui/src/components/search/text2bed/text2bed.tsx +++ b/ui/src/components/search/text2bed/text2bed.tsx @@ -1,9 +1,6 @@ /* eslint-disable react-hooks/exhaustive-deps */ -import { Col, Row } from 'react-bootstrap'; -import { SearchBar } from '../search-bar'; import { Text2BedSearchResultsTable } from './t2b-search-results-table'; import { SearchingJumper } from '../searching-jumper'; -import { useSearchParams } from 'react-router-dom'; import { useEffect, useState, useRef } from 'react'; import { useText2BedSearch } from '../../../queries/useText2BedSearch'; import { TableToolbar } from '../table-toolbar'; @@ -12,15 +9,21 @@ import { SearchError } from '../search-error'; import { AxiosError } from 'axios'; import { BEDEmbeddingPlot, BEDEmbeddingPlotRef } from '../../../components/umap/bed-embedding-plot.tsx'; -export const Text2Bed = () => { - const [searchParams, setSearchParams] = useSearchParams(); - const [searchTerm, setSearchTerm] = useState(searchParams.get('q') || ''); - const [genome, setGenome] = useState(searchParams.get('genome') || ''); - const [assay, setAssay] = useState(searchParams.get('assay') || ''); - const [limit, setLimit] = useState(20); - const [offset, setOffset] = useState(0); +type Props = { + searchTerm: string; + genome: string; + assay: string; + limit: number; + setLimit: (limit: number) => void; + offset: number; + setOffset: (offset: number) => void; + layout: string; + triggerSearch: number; +}; + +export const Text2Bed = (props: Props) => { + const { searchTerm, genome, assay, limit, setLimit, offset, setOffset, layout, triggerSearch } = props; const [containerHeight, setContainerHeight] = useState(660); - const [layout, setLayout] = useState('split'); const embeddingPlotRef = useRef(null); const containerRef = useRef(null); @@ -34,20 +37,16 @@ export const Text2Bed = () => { q: searchTerm, genome: genome, assay: assay, - limit: limit, // TODO: make this a variable + limit: limit, offset: offset, autoRun: false, }); - console.log(results) - useEffect(() => { - const params = new URLSearchParams(); - if (searchTerm) params.set('q', searchTerm); - if (genome) params.set('genome', genome); - if (assay) params.set('assay', assay); - setSearchParams(params); - }, [searchTerm, genome, assay]); + if (triggerSearch > 0) { + onSearch(); + } + }, [triggerSearch, onSearch]); useEffect(() => { if (searchTerm || genome || assay) { @@ -59,8 +58,8 @@ export const Text2Bed = () => { const calculateHeight = () => { if (containerRef.current) { const rect = containerRef.current.getBoundingClientRect(); - const availableHeight = window.innerHeight - rect.top; // 40px margin from bottom - setContainerHeight(Math.max(400, Math.min(availableHeight, 800))); // min 400px, max 800px + const availableHeight = window.innerHeight - rect.top; + setContainerHeight(Math.max(400, Math.min(availableHeight, 800))); } }; @@ -71,39 +70,17 @@ export const Text2Bed = () => { if (error) { if (error) { - return ; + return ; } } return ( -
- - - { - setOffset(0); - setTimeout(() => { - onSearch(); - }, 100); - }} - layout={layout} - setLayout={setLayout} - /> - - +
{isSearching ? ( ) : ( -
+
{results ? (
{(layout === 'split') && ( @@ -113,6 +90,7 @@ export const Text2Bed = () => { ref={embeddingPlotRef} bedIds={results?.results?.map((result: any) => result.id)} height={containerHeight} + preselectPoint={false} />
@@ -134,7 +112,7 @@ export const Text2Bed = () => {
) : ( -
+
Try searching for some BED files! e.g. K562
)} diff --git a/ui/src/components/search/text2bedset.tsx b/ui/src/components/search/text2bedset.tsx index 81c920bd..2737b717 100644 --- a/ui/src/components/search/text2bedset.tsx +++ b/ui/src/components/search/text2bedset.tsx @@ -1,8 +1,5 @@ -import { Col, Row } from 'react-bootstrap'; -import { SearchBar } from './search-bar'; import { SearchingJumper } from './searching-jumper'; -import { useSearchParams } from 'react-router-dom'; -import { useEffect, useState } from 'react'; +import { useEffect } from 'react'; import { useText2BedSetSearch } from '../../queries/useText2BedSetSearch'; import { ErrorPage } from '../common/error-page'; import { TableToolbar } from './table-toolbar'; @@ -10,13 +7,17 @@ import { PaginationBar } from './pagination-bar'; import { SearchBedSetResultTable } from './search-bedset-table.tsx'; import { AxiosError } from 'axios'; -export const Text2BedSet = () => { - const [searchParams] = useSearchParams(); - const [searchTerm, setSearchTerm] = useState(searchParams.get('q') || ''); - const [limit, setLimit] = useState(50); - const [offset, setOffset] = useState(0); - const [genome, setGenome] = useState(searchParams.get('genome') || ''); - const [assay, setAssay] = useState(searchParams.get('assay') || ''); +type Props = { + searchTerm: string; + limit: number; + setLimit: (limit: number) => void; + offset: number; + setOffset: (offset: number) => void; + triggerSearch: number; +}; + +export const Text2BedSet = (props: Props) => { + const { searchTerm, limit, setLimit, offset, setOffset, triggerSearch } = props; const { isFetching: isSearching, @@ -30,51 +31,43 @@ export const Text2BedSet = () => { autoRun: false, }); + useEffect(() => { + if (triggerSearch > 0) { + onSearch(); + } + // eslint-disable-next-line react-hooks/exhaustive-deps + }, [triggerSearch]); + useEffect(() => { if (searchTerm) { onSearch(); } // eslint-disable-next-line react-hooks/exhaustive-deps - }, [limit, offset, onSearch]); + }, [limit, offset]); if (error) { if (error) { - return ; + return ; } } return ( -
- - - onSearch()} - /> - - +
{isSearching ? ( ) : ( -
+
{results ? ( -
-
+
+
{' '}
) : ( -
+
Try searching for some BEDsets! e.g. K562 or excluderanges
)} diff --git a/ui/src/components/umap/atlas-tooltip.tsx b/ui/src/components/umap/atlas-tooltip.tsx index 46764c85..09a4ce4b 100644 --- a/ui/src/components/umap/atlas-tooltip.tsx +++ b/ui/src/components/umap/atlas-tooltip.tsx @@ -18,10 +18,9 @@ interface TooltipProps { const TooltipContent = ({ tooltip, showLink }: { tooltip: TooltipProps['tooltip'], showLink?: boolean }) => { if (!tooltip) return null; - console.log(tooltip) return (
-
{tooltip.text || 'Unnamed BED'}
- {tooltip.fields && ( - <> -

- {tooltip.fields.Description || 'No description available'} -

-
- - cell_line:{' '}{tooltip.fields['Cell Line'] || 'N/A'} - - - assay:{' '}{tooltip.fields.Assay || 'N/A'} - - - id:{' '}{tooltip.identifier || 'N/A'} - - - x:{' '}{tooltip.x ? tooltip.x.toFixed(6) : 'N/A'} - - - y:{' '}{tooltip.y ? tooltip.y.toFixed(6) : 'N/A'} - -
- {showLink && ( - - Go! - - )} - - )} +
+
{tooltip.text || 'Unnamed BED'}
+ {tooltip.fields && ( + <> +

+ {tooltip.fields.Description || 'No description available'} +

+
+ + cell_line:{' '}{tooltip.fields['Cell Line'] || 'N/A'} + + + assay:{' '}{tooltip.fields.Assay || 'N/A'} + + + id:{' '}{tooltip.identifier || 'N/A'} + + + x:{' '}{tooltip.x ? tooltip.x.toFixed(6) : 'N/A'} + + + y:{' '}{tooltip.y ? tooltip.y.toFixed(6) : 'N/A'} + +
+ + )} + {showLink && ( + + Go! + + )} +
); }; diff --git a/ui/src/components/umap/bed-embedding-plot.tsx b/ui/src/components/umap/bed-embedding-plot.tsx index 04959444..16fb0403 100644 --- a/ui/src/components/umap/bed-embedding-plot.tsx +++ b/ui/src/components/umap/bed-embedding-plot.tsx @@ -9,6 +9,7 @@ import { useMosaicCoordinator } from '../../contexts/mosaic-coordinator-context' type Props = { bedIds?: string[], height?: number; + preselectPoint?: boolean; } export interface BEDEmbeddingPlotRef { @@ -16,7 +17,7 @@ export interface BEDEmbeddingPlotRef { } export const BEDEmbeddingPlot = forwardRef((props, ref) => { - const { bedIds, height } = props; + const { bedIds, height, preselectPoint } = props; const { coordinator, initializeData } = useMosaicCoordinator(); const containerRef = useRef(null); @@ -91,7 +92,7 @@ export const BEDEmbeddingPlot = forwardRef((props, r { type: 'json' } ); if (!currentBed || currentBed.length === 0) return; - setTooltipPoint(currentBed[0]); + if (preselectPoint) setTooltipPoint(currentBed[0]); setSelectedPoints(currentBed); }, 200); } diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx index 304b22dc..39eedea2 100644 --- a/ui/src/pages/bed-splash.tsx +++ b/ui/src/pages/bed-splash.tsx @@ -2,7 +2,6 @@ import { useParams } from 'react-router-dom'; import { useBedMetadata } from '../queries/useBedMetadata'; import { useBedGenomeStats } from '../queries/useBedGenomeStats'; import { Layout } from '../components/layout'; -import { Col, Container, Row } from 'react-bootstrap'; import { BedSplashHeader } from '../components/bed-splash-components/header'; import { CardSkeleton } from '../components/skeletons/card-skeleton'; import { ErrorPage } from '../components/common/error-page'; @@ -69,15 +68,15 @@ export const BedSplash = () => { return (
- - +
+
- - - - +
+
+
+
@@ -87,11 +86,11 @@ export const BedSplash = () => {
- - +
+
- - +
+
); @@ -139,14 +138,14 @@ export const BedSplash = () => { } else { return ( - - - +
+
+
{metadata !== undefined ? : null} - - - - +
+
+
+
Overview
@@ -202,8 +201,8 @@ export const BedSplash = () => {
- - +
+
BEDsets
@@ -249,30 +248,30 @@ export const BedSplash = () => {
- - +
+
- +
Statistics
{metadata && ( - +
- +
)} - +
- - +
+
- +
Plots
- +
- - +
+
{bedId && metadata?.name?.includes('encode') && ( <> @@ -281,31 +280,31 @@ export const BedSplash = () => { )} {neighbours && ( - -
-
Similar BED Files
-
- setShowNeighbors(!showNeighbors)} - /> - +
+
+
+
Similar BED Files
+
+ setShowNeighbors(!showNeighbors)} + /> + +
-
- - - +
+
)} - +
); } diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx index 41605d92..3c55c491 100644 --- a/ui/src/pages/home.tsx +++ b/ui/src/pages/home.tsx @@ -137,7 +137,7 @@ export const Home = () => {
- +
explore the BED file region embedding space above, or visit a random BED file diff --git a/ui/src/pages/search.tsx b/ui/src/pages/search.tsx index 278ec77f..10c8d273 100644 --- a/ui/src/pages/search.tsx +++ b/ui/src/pages/search.tsx @@ -1,26 +1,47 @@ -import { Layout } from '../components/layout'; - -import { useState } from 'react'; +import { useState, useEffect } from 'react'; import { useSearchParams, useLocation } from 'react-router-dom'; import { SearchSelector } from '../components/search/search-selector'; +import { SearchBar } from '../components/search/search-bar'; import { Text2Bed } from '../components/search/text2bed/text2bed'; import { Bed2Bed } from '../components/search/bed2bed/bed2bed'; import { Text2BedSet } from '../components/search/text2bedset'; - +import { Layout } from '../components/layout'; import { SearchViewProvider } from '../contexts/search-view-context.tsx'; type SearchView = 't2b' | 'b2b' | 't2bs'; export const SearchPage = () => { - const [searchParams] = useSearchParams(); const location = useLocation(); + const uploadedFile = location.state?.file as File | undefined; + + const [searchParams, setSearchParams] = useSearchParams(); const [searchView, setSearchView] = useState((searchParams.get('view') as SearchView) || 't2b'); + const [searchTerm, setSearchTerm] = useState(searchParams.get('q') || ''); + const [genome, setGenome] = useState(searchParams.get('genome') || ''); + const [assay, setAssay] = useState(searchParams.get('assay') || ''); + const [limit, setLimit] = useState(20); + const [offset, setOffset] = useState(0); + const [layout, setLayout] = useState('split'); + const [triggerSearch, setTriggerSearch] = useState(0); + const [file, setFile] = useState(uploadedFile || null); - const uploadedFile = location.state?.file as File | undefined; + useEffect(() => { + const params = new URLSearchParams(); + if (searchView) params.set('view', searchView); + if (searchTerm) params.set('q', searchTerm); + if (genome) params.set('genome', genome); + if (assay) params.set('assay', assay); + setSearchParams(params); + }, [searchTerm, genome, assay, searchView, setSearchParams]); + + const handleSearch = () => { + setOffset(0); + setTriggerSearch(prev => prev + 1); + }; return ( - + { setSearchView(view); }} /> + {searchView === 't2b' ? ( - + ) : searchView === 'b2b' ? ( - + ) : searchView === 't2bs' ? ( - + ) : (
Unknown searchView selected.
)} From 3b6c3e95ff9c9249fcd3ff9b9df3c93e3f4874ba Mon Sep 17 00:00:00 2001 From: Sam Park Date: Sun, 16 Nov 2025 18:23:58 -0500 Subject: [PATCH 21/76] locate uploaded bed file on atlas on b2b search --- .../bed2bed/b2b-search-results-cards.tsx | 36 ++++------------ ui/src/components/search/bed2bed/bed2bed.tsx | 23 ++++++---- ui/src/components/search/search-bar.tsx | 40 +++++++++++++----- .../text2bed/t2b-search-results-table.tsx | 38 +++++------------ ui/src/components/umap/atlas-tooltip.tsx | 24 ++++++----- ui/src/components/umap/bed-embedding-plot.tsx | 39 +++++++++++++---- ui/src/custom.scss | 3 ++ ui/src/pages/home.tsx | 14 +++---- ui/src/pages/search.tsx | 42 +++++++++++++++---- 9 files changed, 149 insertions(+), 110 deletions(-) diff --git a/ui/src/components/search/bed2bed/b2b-search-results-cards.tsx b/ui/src/components/search/bed2bed/b2b-search-results-cards.tsx index 05c18bd2..3de9e86b 100644 --- a/ui/src/components/search/bed2bed/b2b-search-results-cards.tsx +++ b/ui/src/components/search/bed2bed/b2b-search-results-cards.tsx @@ -16,25 +16,6 @@ type Props = { onCardClick?: (bedId: string) => void; }; -// const scoreTooltip = ( -// -// 
-//             Cosine similarity between files.
-//             Score is between 0 an 100, where 100 is a perfect match.
-//
-// -// } -// > -// -// Score* -// - -// -// ); - export const Bed2BedSearchResultsCards = (props: Props) => { const { results, layout, onCardClick } = props; const { cart, addBedToCart, removeBedFromCart } = useBedCart(); @@ -52,14 +33,14 @@ export const Bed2BedSearchResultsCards = (props: Props) => {
{ if (layout === 'split') { onCardClick?.(result.metadata?.id || '') } }} > -
+

{result?.metadata?.name || 'No name'} @@ -82,13 +63,14 @@ export const Bed2BedSearchResultsCards = (props: Props) => {

- {/* {IsUnique(result.id, search_query || '')} */} -
Match score
-
+ + 
Cosine similarity between files.
+ 
Score is between 0 and 100,
+ 
where 100 is a perfect match.
+ } > 0.5 ? 'bg-primary' : 'bg-secondary'}`} style={{ fontSize: '10px' }}> @@ -97,11 +79,11 @@ export const Bed2BedSearchResultsCards = (props: Props) => {
-

+

{result?.metadata?.description || 'No description'}

-
+
genome:{' '}{result?.metadata?.genome_alias || 'N/A'} diff --git a/ui/src/components/search/bed2bed/bed2bed.tsx b/ui/src/components/search/bed2bed/bed2bed.tsx index 48f75f1c..bf9c3e35 100644 --- a/ui/src/components/search/bed2bed/bed2bed.tsx +++ b/ui/src/components/search/bed2bed/bed2bed.tsx @@ -1,4 +1,4 @@ -import { useEffect, useState, useRef } from 'react'; +import { useEffect, useState, useRef, RefObject } from 'react'; import { SearchingJumper } from '../searching-jumper'; import { useBed2BedSearch } from '../../../queries/useBed2BedSearch'; // import { Bed2BedSearchResultsTable } from './b2b-search-results-table'; @@ -8,14 +8,14 @@ import { Bed2BedSearchResultsCards } from './b2b-search-results-cards.tsx'; type Props = { file: File | null; layout: string; + customCoordinates: number[] | null; + embeddingPlotRef: RefObject; }; export const Bed2Bed = (props: Props) => { - const { file, layout } = props; - const [containerHeight, setContainerHeight] = useState(660); - - const embeddingPlotRef = useRef(null); + const { file, layout, customCoordinates, embeddingPlotRef } = props; const containerRef = useRef(null); + const [containerHeight, setContainerHeight] = useState(660); const { isFetching: isSearching, @@ -26,8 +26,6 @@ export const Bed2Bed = (props: Props) => { autoRun: false, }); - console.log(results) - useEffect(() => { if (file) { if (document.activeElement instanceof HTMLElement) { @@ -68,7 +66,8 @@ export const Bed2Bed = (props: Props) => { ref={embeddingPlotRef} bedIds={results?.results?.map((result: any) => result.payload.id)} height={containerHeight} - preselectPoint={false} + preselectPoint={true} + customCoordinates={customCoordinates} />
@@ -76,7 +75,13 @@ export const Bed2Bed = (props: Props) => {
- + { + embeddingPlotRef.current?.centerOnBedId(bedId); + }} + />
diff --git a/ui/src/components/search/search-bar.tsx b/ui/src/components/search/search-bar.tsx index 025438f8..7c985f5b 100644 --- a/ui/src/components/search/search-bar.tsx +++ b/ui/src/components/search/search-bar.tsx @@ -1,9 +1,10 @@ import toast from 'react-hot-toast'; // import { useSearchParams } from 'react-router-dom'; -import { useMemo, useState, useRef } from 'react'; +import { useMemo, useState, useRef, RefObject } from 'react'; import { useSearchView } from '../../contexts/search-view-context.tsx'; import { useAvailableGenomes } from '../../queries/useAvailableGenomes.ts'; import { useAvailableAssays } from '../../queries/useAvailableAssays.ts'; +import { BEDEmbeddingPlotRef } from '../umap/bed-embedding-plot.tsx'; type Props = { value: string; @@ -19,6 +20,7 @@ type Props = { setLayout?: (layout: string) => void; file: File | null; setFile: (file: File | null) => void; + embeddingPlotRef: RefObject; }; const placeholders = [ @@ -31,7 +33,7 @@ const placeholders = [ ]; export const SearchBar = (props: Props) => { - const { value, onChange, onSearch, limit, setLimit, genome, setGenome, assay, setAssay, layout, setLayout, file, setFile } = props; + const { value, onChange, onSearch, limit, setLimit, genome, setGenome, assay, setAssay, layout, setLayout, file, setFile, embeddingPlotRef } = props; // const [, setSearchParams] = useSearchParams(); const { searchView } = useSearchView(); const { data: genomes } = useAvailableGenomes(); @@ -75,11 +77,27 @@ export const SearchBar = (props: Props) => { if (fileInputRef.current) { fileInputRef.current.value = ''; } + if (typeof embeddingPlotRef.current?.handleFileRemove === 'function') { + embeddingPlotRef.current.handleFileRemove(); + } }} title='Remove file' > + {(layout === 'split') && + + } ) : ( { /> )} + {searchView === 't2b' && ( + + )} + - - {searchView === 't2b' && ( - - )}
{searchView !== 'b2b' && ( 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 798b16ac..5b789ed7 100644 --- a/ui/src/components/search/text2bed/t2b-search-results-table.tsx +++ b/ui/src/components/search/text2bed/t2b-search-results-table.tsx @@ -17,26 +17,6 @@ type Props = { onCardClick?: (bedId: string) => void; }; -const IsUnique = (found_id: string, search_id: string) => { - if (found_id === search_id) { - return ( -
- -
Perfect match
-
- } - > - - -
- ); - } else { - return; - } -}; export const Text2BedSearchResultsTable = (props: Props) => { const { results, search_query, layout, onCardClick } = props; @@ -49,14 +29,14 @@ export const Text2BedSearchResultsTable = (props: Props) => {
{ if (layout === 'split') { onCardClick?.(result.metadata?.id || '') } }} > -
+

{result?.metadata?.name || 'No name'} @@ -79,13 +59,15 @@ export const Text2BedSearchResultsTable = (props: Props) => {

- {IsUnique(result.id, search_query || '')} + {(result.id === (search_query || '')) && } -
Match score
-
+ + 
Cosine similarity between files.
+ 
Score is between 0 and 100,
+ 
where 100 is a perfect match.
+ } > 0.5 ? 'bg-primary' : 'bg-secondary'}`} style={{ fontSize: '10px' }}> @@ -94,11 +76,11 @@ export const Text2BedSearchResultsTable = (props: Props) => {
-

+

{result?.metadata?.description || 'No description'}

-
+
genome:{' '}{result?.metadata?.genome_alias || 'N/A'} diff --git a/ui/src/components/umap/atlas-tooltip.tsx b/ui/src/components/umap/atlas-tooltip.tsx index 09a4ce4b..450ab7db 100644 --- a/ui/src/components/umap/atlas-tooltip.tsx +++ b/ui/src/components/umap/atlas-tooltip.tsx @@ -36,15 +36,19 @@ const TooltipContent = ({ tooltip, showLink }: { tooltip: TooltipProps['tooltip' {tooltip.fields.Description || 'No description available'}

- - cell_line:{' '}{tooltip.fields['Cell Line'] || 'N/A'} - - - assay:{' '}{tooltip.fields.Assay || 'N/A'} - - - id:{' '}{tooltip.identifier || 'N/A'} - + {(tooltip.identifier !== 'custom_point') && ( + <> + + cell_line:{' '}{tooltip.fields['Cell Line'] || 'N/A'} + + + assay:{' '}{tooltip.fields.Assay || 'N/A'} + + + id:{' '}{tooltip.identifier || 'N/A'} + + + )} x:{' '}{tooltip.x ? tooltip.x.toFixed(6) : 'N/A'} @@ -54,7 +58,7 @@ const TooltipContent = ({ tooltip, showLink }: { tooltip: TooltipProps['tooltip'
)} - {showLink && ( + {showLink && (tooltip.identifier !== 'custom_point') && ( Promise; + handleFileRemove: () => Promise; } export const BEDEmbeddingPlot = forwardRef((props, ref) => { - const { bedIds, height, preselectPoint } = props; - const { coordinator, initializeData } = useMosaicCoordinator(); + const { bedIds, height, preselectPoint, customCoordinates } = props; + const { coordinator, initializeData, addCustomPoint, deleteCustomPoint } = useMosaicCoordinator(); const containerRef = useRef(null); @@ -57,16 +59,29 @@ export const BEDEmbeddingPlot = forwardRef((props, r if (bedData && bedData.length > 0) { centerOnPoint(bedData[0], scale); - // setSelectedPoints([bedData[0]]); + setSelectedPoints([bedData[0]]); } }; + const handleFileRemove = async () => { + try { + await deleteCustomPoint(); + coordinator.clear(); + } catch (error) { + console.error('Error removing file'); + } + } + useImperativeHandle(ref, () => ({ - centerOnBedId + centerOnBedId, + handleFileRemove, })); useEffect(() => { // initialize data initializeData().then(() => { + if (!!customCoordinates) { + addCustomPoint(customCoordinates[0], customCoordinates[1]); + } setIsReady(true); }); }, []); @@ -80,6 +95,7 @@ export const BEDEmbeddingPlot = forwardRef((props, r useEffect(() => { // fetch provided bed ids if (isReady && bedIds && bedIds.length > 0) { setTimeout(async () => { + const idsToQuery = customCoordinates ? ['custom_point', ...bedIds] : bedIds; const currentBed: any = await coordinator.query( `SELECT x, y, @@ -88,15 +104,24 @@ export const BEDEmbeddingPlot = forwardRef((props, r id as identifier, {'Description': description, 'Assay': assay, 'Cell Line': cell_line} as fields FROM data - WHERE id IN ('${bedIds.join("','")}')`, + WHERE id IN ('${idsToQuery.join("','")}')`, { type: 'json' } ); if (!currentBed || currentBed.length === 0) return; - if (preselectPoint) setTooltipPoint(currentBed[0]); + if (preselectPoint) { + const pointToSelect = customCoordinates + ? currentBed.find((bed: any) => bed.identifier === 'custom_point') || currentBed[0] + : currentBed[0]; + if (!!customCoordinates) { + centerOnPoint(pointToSelect); + } else { + setTooltipPoint(pointToSelect); + } + } setSelectedPoints(currentBed); }, 200); } - }, [isReady, bedIds, coordinator, colorGrouping]); + }, [isReady, bedIds, coordinator, colorGrouping, customCoordinates]); return ( <> diff --git a/ui/src/custom.scss b/ui/src/custom.scss index 36ab1116..1b220218 100644 --- a/ui/src/custom.scss +++ b/ui/src/custom.scss @@ -371,3 +371,6 @@ td { transform: translateX(-3rem) !important; } +.btn-card { + transition: color 0.15s ease-in-out, background-color 0.15s ease-in-out, border-color 0.15s ease-in-out, box-shadow 0.15s ease-in-out; +} diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx index 3c55c491..d09ee4a2 100644 --- a/ui/src/pages/home.tsx +++ b/ui/src/pages/home.tsx @@ -11,7 +11,6 @@ import { BEDEmbeddingPlot } from '../components/umap/bed-embedding-plot.tsx'; export const Home = () => { const [searchTerm, setSearchTerm] = useState(''); - const [uploadedFile, setUploadedFile] = useState(null); const [copiedAPI, setCopiedAPI] = useState(false); const [copiedClient, setCopiedClient] = useState(false); @@ -27,13 +26,8 @@ export const Home = () => { const { data: bedbaseStats } = useStats(); const handleSearch = () => { - if (searchType === 'b2b') { - if (!uploadedFile) return; - navigate(`/search?view=${searchType}`, { state: { file: uploadedFile } }); - } else { - if (!searchTerm) return; - navigate(`/search?q=${searchTerm}&view=${searchType}`); - } + if (!searchTerm) return; + navigate(`/search?q=${searchTerm}&view=${searchType}`); }; return ( @@ -94,18 +88,20 @@ export const Home = () => {
{searchType === 'b2b' ? ( { const file = e.target.files?.[0]; if (file) { - setUploadedFile(file); + navigate(`/search?view=b2b`, { state: { file: file } }); } }} /> ) : ( { const location = useLocation(); + const embeddingPlotRef = useRef(null); const uploadedFile = location.state?.file as File | undefined; const [searchParams, setSearchParams] = useSearchParams(); @@ -25,20 +28,35 @@ export const SearchPage = () => { const [layout, setLayout] = useState('split'); const [triggerSearch, setTriggerSearch] = useState(0); const [file, setFile] = useState(uploadedFile || null); + const [customCoordinates, setCustomCoordinates] = useState(null); + + const { mutateAsync: getUmapCoordinates } = useBedUmap(); + + const handleSearch = () => { + setOffset(0); + setTriggerSearch(prev => prev + 1); + }; useEffect(() => { const params = new URLSearchParams(); if (searchView) params.set('view', searchView); - if (searchTerm) params.set('q', searchTerm); - if (genome) params.set('genome', genome); - if (assay) params.set('assay', assay); + if (searchView !== 'b2b') { + if (searchTerm) params.set('q', searchTerm); + } + if (searchView === 't2b') { + if (genome) params.set('genome', genome); + if (assay) params.set('assay', assay); + } setSearchParams(params); }, [searchTerm, genome, assay, searchView, setSearchParams]); - const handleSearch = () => { - setOffset(0); - setTriggerSearch(prev => prev + 1); - }; + useEffect(() => { + if (!file) return; + (async () => { + const coordinates = await getUmapCoordinates(file); + setCustomCoordinates(coordinates); + })(); + }, [file]) return ( @@ -63,6 +81,7 @@ export const SearchPage = () => { onSearch={handleSearch} file={file} setFile={setFile} + embeddingPlotRef={embeddingPlotRef} /> {searchView === 't2b' ? ( { triggerSearch={triggerSearch} /> ) : searchView === 'b2b' ? ( - + ) : searchView === 't2bs' ? ( Date: Sun, 16 Nov 2025 21:34:52 -0500 Subject: [PATCH 22/76] details in b2b search atlas --- ui/src/components/search/bed2bed/bed2bed.tsx | 2 ++ .../components/search/text2bed/text2bed.tsx | 1 + ui/src/components/umap/bed-embedding-plot.tsx | 29 +++++++++++++++---- .../contexts/mosaic-coordinator-context.tsx | 6 ++-- ui/src/pages/bed-splash.tsx | 2 +- 5 files changed, 31 insertions(+), 9 deletions(-) diff --git a/ui/src/components/search/bed2bed/bed2bed.tsx b/ui/src/components/search/bed2bed/bed2bed.tsx index bf9c3e35..a254a8c9 100644 --- a/ui/src/components/search/bed2bed/bed2bed.tsx +++ b/ui/src/components/search/bed2bed/bed2bed.tsx @@ -67,7 +67,9 @@ export const Bed2Bed = (props: Props) => { bedIds={results?.results?.map((result: any) => result.payload.id)} height={containerHeight} preselectPoint={true} + stickyBaseline={true} customCoordinates={customCoordinates} + customFilename={file?.name || undefined} />
diff --git a/ui/src/components/search/text2bed/text2bed.tsx b/ui/src/components/search/text2bed/text2bed.tsx index bba93974..1c86a9b3 100644 --- a/ui/src/components/search/text2bed/text2bed.tsx +++ b/ui/src/components/search/text2bed/text2bed.tsx @@ -91,6 +91,7 @@ export const Text2Bed = (props: Props) => { bedIds={results?.results?.map((result: any) => result.id)} height={containerHeight} preselectPoint={false} + stickyBaseline={true} />
diff --git a/ui/src/components/umap/bed-embedding-plot.tsx b/ui/src/components/umap/bed-embedding-plot.tsx index e88c8ddc..eb2cbf37 100644 --- a/ui/src/components/umap/bed-embedding-plot.tsx +++ b/ui/src/components/umap/bed-embedding-plot.tsx @@ -1,5 +1,6 @@ import { EmbeddingViewMosaic } from 'embedding-atlas/react'; import { useEffect, useState, useRef, useMemo, forwardRef, useImperativeHandle } from 'react'; +import toast from 'react-hot-toast'; import * as vg from '@uwdata/vgplot' import { tableau20 } from '../../utils'; @@ -10,7 +11,9 @@ type Props = { bedIds?: string[], height?: number; preselectPoint?: boolean; + stickyBaseline?: boolean; customCoordinates?: number[] | null; + customFilename?: string; } export interface BEDEmbeddingPlotRef { @@ -19,10 +22,11 @@ export interface BEDEmbeddingPlotRef { } export const BEDEmbeddingPlot = forwardRef((props, ref) => { - const { bedIds, height, preselectPoint, customCoordinates } = props; + const { bedIds, height, preselectPoint, stickyBaseline, customCoordinates, customFilename } = props; const { coordinator, initializeData, addCustomPoint, deleteCustomPoint } = useMosaicCoordinator(); const containerRef = useRef(null); + const baselinePointsRef = useRef([]); const [containerWidth, setContainerWidth] = useState(900); const [isReady, setIsReady] = useState(false); @@ -60,6 +64,8 @@ export const BEDEmbeddingPlot = forwardRef((props, r if (bedData && bedData.length > 0) { centerOnPoint(bedData[0], scale); setSelectedPoints([bedData[0]]); + } else { + toast.error('Error: BED file not present in embeddings.'); } }; @@ -78,9 +84,10 @@ export const BEDEmbeddingPlot = forwardRef((props, r })); useEffect(() => { // initialize data - initializeData().then(() => { + initializeData().then(async () => { if (!!customCoordinates) { - addCustomPoint(customCoordinates[0], customCoordinates[1]); + await addCustomPoint(customCoordinates[0], customCoordinates[1], customFilename); + coordinator.clear(); } setIsReady(true); }); @@ -92,8 +99,8 @@ export const BEDEmbeddingPlot = forwardRef((props, r } }, [isReady]); - useEffect(() => { // fetch provided bed ids - if (isReady && bedIds && bedIds.length > 0) { + useEffect(() => { // fetch provided bed ids + if (isReady && bedIds && (bedIds.length > 0)) { setTimeout(async () => { const idsToQuery = customCoordinates ? ['custom_point', ...bedIds] : bedIds; const currentBed: any = await coordinator.query( @@ -118,6 +125,7 @@ export const BEDEmbeddingPlot = forwardRef((props, r setTooltipPoint(pointToSelect); } } + baselinePointsRef.current = currentBed; setSelectedPoints(currentBed); }, 200); } @@ -154,6 +162,17 @@ export const BEDEmbeddingPlot = forwardRef((props, r } }} selection={selectedPoints} + onSelection={(dataPoints) => { + if (!dataPoints || dataPoints.length === 0 && stickyBaseline) { + setTimeout(() => { + if (baselinePointsRef.current.length > 0) { + setSelectedPoints([...baselinePointsRef.current]); + } + }, 0); + return; + } + setSelectedPoints(dataPoints); + }} theme={{ statusBar: false }} diff --git a/ui/src/contexts/mosaic-coordinator-context.tsx b/ui/src/contexts/mosaic-coordinator-context.tsx index 8dc1879f..1e3042ec 100644 --- a/ui/src/contexts/mosaic-coordinator-context.tsx +++ b/ui/src/contexts/mosaic-coordinator-context.tsx @@ -4,7 +4,7 @@ import * as vg from '@uwdata/vgplot'; interface MosaicCoordinatorContextType { getCoordinator: () => vg.Coordinator; initializeData: () => Promise; - addCustomPoint: (x: number, y: number) => Promise; + addCustomPoint: (x: number, y: number, description?: string) => Promise; deleteCustomPoint: () => Promise; } @@ -53,7 +53,7 @@ export const MosaicCoordinatorProvider = ({ children }: { children: ReactNode }) ]); } - const addCustomPoint = async (x: number, y: number) => { + const addCustomPoint = async (x: number, y: number, description: string = 'User uploaded BED file') => { const coordinator = getCoordinator(); await coordinator.exec([ @@ -79,7 +79,7 @@ export const MosaicCoordinatorProvider = ({ children }: { children: ReactNode }) 0, 'custom_point', 'Your uploaded file', - 'User uploaded BED file', + '${description}', 'Uploaded BED', 'Uploaded BED', ${assayCategory}, diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx index 39eedea2..d9cc005e 100644 --- a/ui/src/pages/bed-splash.tsx +++ b/ui/src/pages/bed-splash.tsx @@ -275,7 +275,7 @@ export const BedSplash = () => { {bedId && metadata?.name?.includes('encode') && ( <> - + )} From a195d4d07bf93b4b2d86dc9e58b366a9265e2b97 Mon Sep 17 00:00:00 2001 From: Sam Park Date: Tue, 18 Nov 2025 22:52:34 -0500 Subject: [PATCH 23/76] switch back to api pagination for b2b, vibe code sticky scroll for search page embeddings --- ui/src/components/search/bed2bed/bed2bed.tsx | 210 ++++++++++++++---- .../search/{ => bed2bed}/search-bar.tsx | 60 ++--- ui/src/components/search/pagination-bar.tsx | 20 +- ui/src/components/search/search-selector.tsx | 6 +- .../components/search/text2bed/text2bed.tsx | 158 ++++++++++--- ui/src/custom.scss | 20 +- ui/src/pages/home.tsx | 18 +- ui/src/pages/search.tsx | 9 +- ui/src/queries/useBed2BedSearchPaginate.ts | 42 ++++ 9 files changed, 404 insertions(+), 139 deletions(-) rename ui/src/components/search/{ => bed2bed}/search-bar.tsx (78%) create mode 100644 ui/src/queries/useBed2BedSearchPaginate.ts diff --git a/ui/src/components/search/bed2bed/bed2bed.tsx b/ui/src/components/search/bed2bed/bed2bed.tsx index a254a8c9..1498de4a 100644 --- a/ui/src/components/search/bed2bed/bed2bed.tsx +++ b/ui/src/components/search/bed2bed/bed2bed.tsx @@ -1,31 +1,49 @@ import { useEffect, useState, useRef, RefObject } from 'react'; import { SearchingJumper } from '../searching-jumper'; -import { useBed2BedSearch } from '../../../queries/useBed2BedSearch'; +// import { useBed2BedSearch } from '../../../queries/useBed2BedSearch'; +import { useBed2BedSearchPaginate } from '../../../queries/useBed2BedSearchPaginate.ts'; // import { Bed2BedSearchResultsTable } from './b2b-search-results-table'; import { BEDEmbeddingPlot, BEDEmbeddingPlotRef } from '../../../components/umap/bed-embedding-plot.tsx'; import { Bed2BedSearchResultsCards } from './b2b-search-results-cards.tsx'; +import { PaginationBar } from '../pagination-bar'; type Props = { - file: File | null; + limit: number; + offset: number; + setOffset: (offset: number) => void; layout: string; + file: File | null; customCoordinates: number[] | null; embeddingPlotRef: RefObject; }; export const Bed2Bed = (props: Props) => { - const { file, layout, customCoordinates, embeddingPlotRef } = props; - const containerRef = useRef(null); + const { limit, offset, setOffset, layout, file, customCoordinates, embeddingPlotRef } = props; const [containerHeight, setContainerHeight] = useState(660); + const [stickyState, setStickyState] = useState<'normal' | 'sticky' | 'bottom'>('normal'); + const [stickyWidth, setStickyWidth] = useState(undefined); + const [stickyLeft, setStickyLeft] = useState(undefined); + + const containerRef = useRef(null); + const stickyDivRef = useRef(null); + const colRef = useRef(null); + const placeholderRef = useRef(null); + const stickyStateRef = useRef<'normal' | 'sticky' | 'bottom'>('normal'); const { isFetching: isSearching, data: results, refetch: onSearch, - } = useBed2BedSearch({ + } = useBed2BedSearchPaginate({ q: file, + limit: limit, + offset: offset, autoRun: false, }); + console.log(offset) + console.log(results) + useEffect(() => { if (file) { if (document.activeElement instanceof HTMLElement) { @@ -35,13 +53,13 @@ export const Bed2Bed = (props: Props) => { onSearch(); }, 50); } - }, [file, onSearch]); + }, [file, limit, offset, onSearch]); useEffect(() => { const calculateHeight = () => { if (containerRef.current) { - const rect = containerRef.current.getBoundingClientRect(); - const availableHeight = window.innerHeight - rect.top; + // const rect = containerRef.current.getBoundingClientRect(); + const availableHeight = window.innerHeight*0.9; setContainerHeight(Math.max(400, Math.min(availableHeight, 800))); } }; @@ -51,51 +69,149 @@ export const Bed2Bed = (props: Props) => { return () => window.removeEventListener('resize', calculateHeight); }, []); + useEffect(() => { + let rafId: number; + + const handleScroll = () => { + if (rafId) { + cancelAnimationFrame(rafId); + } + + rafId = requestAnimationFrame(() => { + if (stickyDivRef.current && colRef.current) { + const currentState = stickyStateRef.current; + + // Capture the exact dimensions from the sticky div itself when in normal state + if (currentState === 'normal') { + const stickyRect = stickyDivRef.current.getBoundingClientRect(); + setStickyWidth(stickyRect.width); + setStickyLeft(stickyRect.left); + } + + // Use the sticky div's position when in normal state, otherwise use placeholder + let divMiddle: number; + if (currentState === 'normal') { + const rect = stickyDivRef.current.getBoundingClientRect(); + divMiddle = rect.top + rect.height / 2; + } else if (placeholderRef.current) { + const rect = placeholderRef.current.getBoundingClientRect(); + divMiddle = rect.top + rect.height / 2; + } else { + return; + } + + const viewportMiddle = window.innerHeight / 2; + + // Get the column (parent) boundaries + const colRect = colRef.current.getBoundingClientRect(); + const colBottom = colRect.bottom; + + // Calculate if sticky div would go past the bottom of parent + const stickyDivHeight = containerHeight; + const wouldExceedBottom = colBottom < viewportMiddle + (stickyDivHeight / 2); + + // Determine state + let newState: 'normal' | 'sticky' | 'bottom'; + if (wouldExceedBottom) { + newState = 'bottom'; + } else if (divMiddle <= viewportMiddle) { + newState = 'sticky'; + } else { + newState = 'normal'; + } + + if (newState !== currentState) { + stickyStateRef.current = newState; + setStickyState(newState); + } + } + }); + }; + + window.addEventListener('scroll', handleScroll, { passive: true }); + window.addEventListener('resize', handleScroll); + handleScroll(); // Check initial position + return () => { + if (rafId) { + cancelAnimationFrame(rafId); + } + window.removeEventListener('scroll', handleScroll); + window.removeEventListener('resize', handleScroll); + }; + }, [layout, containerHeight]); + return (
- {isSearching ? ( - - ) : ( -
- {results ? ( -
- {(layout === 'split') && ( -
-
- result.payload.id)} - height={containerHeight} - preselectPoint={true} - stickyBaseline={true} - customCoordinates={customCoordinates} - customFilename={file?.name || undefined} - /> +
+ {isSearching ? ( + + ) : ( +
+ {results ? ( + <> +
+ {(layout === 'split') && ( +
+
+
+ result.payload.id)} + height={containerHeight} + preselectPoint={true} + stickyBaseline={true} + customCoordinates={customCoordinates} + customFilename={file?.name || undefined} + /> +
+
+ )} + +
+
+ { + embeddingPlotRef.current?.centerOnBedId(bedId); + }} + /> +
- )} - -
-
- { - embeddingPlotRef.current?.centerOnBedId(bedId); - }} - /> +
+
+ +
+ + ) : ( +
+

Try uploading a BED file above to find similar files!

+

Note: provided file should be aligned to hg38 assembly.

-
- ) : ( -
-

Try uploading a BED file above to find similar files!

-

Note: provided file should be aligned to hg38 assembly.

-
- )} -
- - )} + )} +
+ )} +
); }; diff --git a/ui/src/components/search/search-bar.tsx b/ui/src/components/search/bed2bed/search-bar.tsx similarity index 78% rename from ui/src/components/search/search-bar.tsx rename to ui/src/components/search/bed2bed/search-bar.tsx index 7c985f5b..1faeeec4 100644 --- a/ui/src/components/search/search-bar.tsx +++ b/ui/src/components/search/bed2bed/search-bar.tsx @@ -1,10 +1,10 @@ import toast from 'react-hot-toast'; // import { useSearchParams } from 'react-router-dom'; import { useMemo, useState, useRef, RefObject } from 'react'; -import { useSearchView } from '../../contexts/search-view-context.tsx'; -import { useAvailableGenomes } from '../../queries/useAvailableGenomes.ts'; -import { useAvailableAssays } from '../../queries/useAvailableAssays.ts'; -import { BEDEmbeddingPlotRef } from '../umap/bed-embedding-plot.tsx'; +import { useSearchView } from '../../../contexts/search-view-context.tsx'; +import { useAvailableGenomes } from '../../../queries/useAvailableGenomes.ts'; +import { useAvailableAssays } from '../../../queries/useAvailableAssays.ts'; +import { BEDEmbeddingPlotRef } from '../../umap/bed-embedding-plot.tsx'; type Props = { value: string; @@ -131,7 +131,7 @@ export const SearchBar = (props: Props) => { onKeyDown={(e) => { if (e.key === 'Enter') { if (value === '') { - toast.error('Please enter a search term', { + toast.error('Please enter a search term.', { position: 'top-center', }); return; @@ -142,10 +142,11 @@ export const SearchBar = (props: Props) => { /> )} - {searchView === 't2b' && ( + {['t2b', 'b2b'].includes(searchView) && ( @@ -184,7 +185,7 @@ export const SearchBar = (props: Props) => { {showOptions && (
- {(searchView === 't2b') && !!layout && !!setLayout && + {['t2b', 'b2b'].includes(searchView) && !!layout && !!setLayout &&
Layout:
-
Genome:
- + {(searchView === 't2b') && ( + <> +
Genome:
+ -
Assay:
- +
Assay:
+ + + )} +
}
diff --git a/ui/src/components/search/pagination-bar.tsx b/ui/src/components/search/pagination-bar.tsx index b8130d95..4c4b288a 100644 --- a/ui/src/components/search/pagination-bar.tsx +++ b/ui/src/components/search/pagination-bar.tsx @@ -8,10 +8,10 @@ type Props = { export const PaginationBar = (props: Props) => { const { total, limit, offset, setOffset } = props; return ( -
-
+
+
-
- Viewing results {offset + 1} - {Math.min(offset + limit, total)} of {total} results. +
+ Viewing results {offset + 1} - {Math.min(offset + limit, total)} of {total} results
); diff --git a/ui/src/components/search/search-selector.tsx b/ui/src/components/search/search-selector.tsx index fa18e095..0a2d9c92 100644 --- a/ui/src/components/search/search-selector.tsx +++ b/ui/src/components/search/search-selector.tsx @@ -5,10 +5,11 @@ type SearchView = 't2b' | 'b2b' | 't2bs'; type Props = { view: SearchView; setView: (view: SearchView) => void; + setOffset: (offset: number) => void; }; export const SearchSelector = (props: Props) => { - const { view, setView } = props; + const { view, setView, setOffset } = props; const [params, setParams] = useSearchParams(); return (
@@ -22,6 +23,7 @@ export const SearchSelector = (props: Props) => { params.delete('q'); setParams(params); setView('t2b'); + setOffset(0); }} > Text-to-BED @@ -35,6 +37,7 @@ export const SearchSelector = (props: Props) => { params.delete('q'); setParams(params); setView('b2b'); + setOffset(0); }} > BED-to-BED @@ -48,6 +51,7 @@ export const SearchSelector = (props: Props) => { params.delete('q'); setParams(params); setView('t2bs'); + setOffset(0); }} > Text-to-BEDset diff --git a/ui/src/components/search/text2bed/text2bed.tsx b/ui/src/components/search/text2bed/text2bed.tsx index 1c86a9b3..f3fd3503 100644 --- a/ui/src/components/search/text2bed/text2bed.tsx +++ b/ui/src/components/search/text2bed/text2bed.tsx @@ -3,7 +3,6 @@ import { Text2BedSearchResultsTable } from './t2b-search-results-table'; import { SearchingJumper } from '../searching-jumper'; import { useEffect, useState, useRef } from 'react'; import { useText2BedSearch } from '../../../queries/useText2BedSearch'; -import { TableToolbar } from '../table-toolbar'; import { PaginationBar } from '../pagination-bar'; import { SearchError } from '../search-error'; import { AxiosError } from 'axios'; @@ -14,7 +13,6 @@ type Props = { genome: string; assay: string; limit: number; - setLimit: (limit: number) => void; offset: number; setOffset: (offset: number) => void; layout: string; @@ -22,11 +20,18 @@ type Props = { }; export const Text2Bed = (props: Props) => { - const { searchTerm, genome, assay, limit, setLimit, offset, setOffset, layout, triggerSearch } = props; + const { searchTerm, genome, assay, limit, offset, setOffset, layout, triggerSearch } = props; const [containerHeight, setContainerHeight] = useState(660); + const [stickyState, setStickyState] = useState<'normal' | 'sticky' | 'bottom'>('normal'); + const [stickyWidth, setStickyWidth] = useState(undefined); + const [stickyLeft, setStickyLeft] = useState(undefined); const embeddingPlotRef = useRef(null); const containerRef = useRef(null); + const stickyDivRef = useRef(null); + const colRef = useRef(null); + const placeholderRef = useRef(null); + const stickyStateRef = useRef<'normal' | 'sticky' | 'bottom'>('normal'); const { isFetching: isSearching, @@ -57,8 +62,8 @@ export const Text2Bed = (props: Props) => { useEffect(() => { const calculateHeight = () => { if (containerRef.current) { - const rect = containerRef.current.getBoundingClientRect(); - const availableHeight = window.innerHeight - rect.top; + // const rect = containerRef.current.getBoundingClientRect(); + const availableHeight = window.innerHeight*0.9; setContainerHeight(Math.max(400, Math.min(availableHeight, 800))); } }; @@ -68,6 +73,77 @@ export const Text2Bed = (props: Props) => { return () => window.removeEventListener('resize', calculateHeight); }, []); + useEffect(() => { + let rafId: number; + + const handleScroll = () => { + if (rafId) { + cancelAnimationFrame(rafId); + } + + rafId = requestAnimationFrame(() => { + if (stickyDivRef.current && colRef.current) { + const currentState = stickyStateRef.current; + + // Capture the exact dimensions from the sticky div itself when in normal state + if (currentState === 'normal') { + const stickyRect = stickyDivRef.current.getBoundingClientRect(); + setStickyWidth(stickyRect.width); + setStickyLeft(stickyRect.left); + } + + // Use the sticky div's position when in normal state, otherwise use placeholder + let divMiddle: number; + if (currentState === 'normal') { + const rect = stickyDivRef.current.getBoundingClientRect(); + divMiddle = rect.top + rect.height / 2; + } else if (placeholderRef.current) { + const rect = placeholderRef.current.getBoundingClientRect(); + divMiddle = rect.top + rect.height / 2; + } else { + return; + } + + const viewportMiddle = window.innerHeight / 2; + + // Get the column (parent) boundaries + const colRect = colRef.current.getBoundingClientRect(); + const colBottom = colRect.bottom; + + // Calculate if sticky div would go past the bottom of parent + const stickyDivHeight = containerHeight; + const wouldExceedBottom = colBottom < viewportMiddle + (stickyDivHeight / 2); + + // Determine state + let newState: 'normal' | 'sticky' | 'bottom'; + if (wouldExceedBottom) { + newState = 'bottom'; + } else if (divMiddle <= viewportMiddle) { + newState = 'sticky'; + } else { + newState = 'normal'; + } + + if (newState !== currentState) { + stickyStateRef.current = newState; + setStickyState(newState); + } + } + }); + }; + + window.addEventListener('scroll', handleScroll, { passive: true }); + window.addEventListener('resize', handleScroll); + handleScroll(); // Check initial position + return () => { + if (rafId) { + cancelAnimationFrame(rafId); + } + window.removeEventListener('scroll', handleScroll); + window.removeEventListener('resize', handleScroll); + }; + }, [layout, containerHeight]); + if (error) { if (error) { return ; @@ -82,36 +158,60 @@ export const Text2Bed = (props: Props) => { ) : (
{results ? ( -
- {(layout === 'split') && ( -
-
- result.id)} - height={containerHeight} - preselectPoint={false} - stickyBaseline={true} + <> +
+ {(layout === 'split') && ( +
+
+
+ result.id)} + height={containerHeight} + preselectPoint={false} + stickyBaseline={true} + /> +
+
+ )} + +
+
+ { + embeddingPlotRef.current?.centerOnBedId(bedId); + }} + />{' '}
- )} - -
-
- - { - embeddingPlotRef.current?.centerOnBedId(bedId); - }} - />{' '} +
+
+
-
+ ) : (
Try searching for some BED files! e.g. K562 diff --git a/ui/src/custom.scss b/ui/src/custom.scss index 1b220218..7f5a55cd 100644 --- a/ui/src/custom.scss +++ b/ui/src/custom.scss @@ -1,16 +1,7 @@ -@import 'bootstrap/scss/functions'; -@import 'bootstrap/scss/variables'; - -$primary: #008080; -// $secondary: #f97316; - -// merge with existing $theme-colors map -$theme-colors: map-merge( - $theme-colors, - ( - 'primary': $primary, - // 'secondary': $secondary, - ) +// Import Bootstrap with @use instead of @import +@use 'bootstrap/scss/bootstrap' as * with ( + $primary: #008080, + // $secondary: #f97316, ); // override btn-outline-primary hover bg-color @@ -22,9 +13,6 @@ $theme-colors: map-merge( } } -// set changes -@import 'bootstrap'; - body { background-color: var(--bs-body-tertiary-bg) !important; } diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx index d09ee4a2..c961d19d 100644 --- a/ui/src/pages/home.tsx +++ b/ui/src/pages/home.tsx @@ -3,6 +3,7 @@ import { Layout } from '../components/layout'; import { useNavigate } from 'react-router-dom'; import Markdown from 'react-markdown'; import rehypeHighlight from 'rehype-highlight'; +import toast from 'react-hot-toast'; import { CODE_SNIPPETS, BBCONF_SNIPPETS } from '../const'; // import { useExampleBed } from '../queries/useExampleBed'; import { useExampleBedSet } from '../queries/useExampleBedSet'; @@ -26,7 +27,12 @@ export const Home = () => { const { data: bedbaseStats } = useStats(); const handleSearch = () => { - if (!searchTerm) return; + if (!searchTerm) { + toast.error('Please enter a search term.', { + position: 'top-center', + }); + return; + } navigate(`/search?q=${searchTerm}&view=${searchType}`); }; @@ -35,7 +41,7 @@ export const Home = () => {

BEDbase

-
+

The open access platform for aggregating, analyzing, and serving genomic region data.

@@ -251,9 +257,9 @@ export const Home = () => {
-
REST API
+
REST API
-

+

Programmatic access to the BEDbase web server with a RESTful API. Query, retrieve, and analyze genomic regions with simple HTTP requests from any language.

@@ -313,9 +319,9 @@ export const Home = () => {
-
BEDbase Clients
+
BEDbase Clients
-

+

Download, cache, and analyze BED files programmatically with native Python and R packages. Simplifies API interaction through high-level interfaces.

diff --git a/ui/src/pages/search.tsx b/ui/src/pages/search.tsx index f32eef65..436748bd 100644 --- a/ui/src/pages/search.tsx +++ b/ui/src/pages/search.tsx @@ -2,7 +2,7 @@ import { useState, useEffect, useRef } from 'react'; import { useSearchParams, useLocation } from 'react-router-dom'; import { SearchSelector } from '../components/search/search-selector'; -import { SearchBar } from '../components/search/search-bar'; +import { SearchBar } from '../components/search/bed2bed/search-bar.tsx'; import { Text2Bed } from '../components/search/text2bed/text2bed'; import { Bed2Bed } from '../components/search/bed2bed/bed2bed'; import { Text2BedSet } from '../components/search/text2bedset'; @@ -66,6 +66,7 @@ export const SearchPage = () => { setView={(view) => { setSearchView(view); }} + setOffset={setOffset} /> { genome={genome} assay={assay} limit={limit} - setLimit={setLimit} offset={offset} setOffset={setOffset} layout={layout} @@ -97,8 +97,11 @@ export const SearchPage = () => { /> ) : searchView === 'b2b' ? ( diff --git a/ui/src/queries/useBed2BedSearchPaginate.ts b/ui/src/queries/useBed2BedSearchPaginate.ts new file mode 100644 index 00000000..c45e557a --- /dev/null +++ b/ui/src/queries/useBed2BedSearchPaginate.ts @@ -0,0 +1,42 @@ +import { useQuery } from '@tanstack/react-query'; +import { useBedbaseApi } from '../contexts/api-context'; +import { components } from '../../bedbase-types'; + +type SearchResponse = components['schemas']['BedListSearchResult']; +type SearchQuery = { + q: File | null; + limit?: number; + offset?: number; + autoRun?: boolean; +}; + +export const useBed2BedSearchPaginate = (query: SearchQuery) => { + const { api } = useBedbaseApi(); + const { q, limit, offset, autoRun } = query; + let enabled = false; + if (autoRun !== undefined && autoRun === true && !!q) { + enabled = true; + } + + return useQuery({ + queryKey: ['search', q, limit, offset], + queryFn: async () => { + if (!q) { + return { + count: 0, + results: [], + }; + } + const formData = new FormData(); + formData.append('file', q); + const { data } = await api.post(`/bed/search/bed?limit=${limit || 20}&offset=${offset || 0}`, formData, { + headers: { + 'Content-Type': 'multipart/form-data', + }, + }); + return data; + }, + enabled: enabled, + staleTime: 0, + }); +}; From b2972a2517387cc9bab77caf623867d531ddcc4c Mon Sep 17 00:00:00 2001 From: Sam Park Date: Wed, 19 Nov 2025 13:03:11 -0500 Subject: [PATCH 24/76] ui details --- .../bed2bed/b2b-search-results-cards.tsx | 16 +++--- ui/src/components/search/search-selector.tsx | 6 +-- .../text2bed/t2b-search-results-table.tsx | 16 +++--- ui/src/pages/home.tsx | 33 ++++++------ ui/src/pages/search.tsx | 53 +++++++++++-------- 5 files changed, 66 insertions(+), 58 deletions(-) diff --git a/ui/src/components/search/bed2bed/b2b-search-results-cards.tsx b/ui/src/components/search/bed2bed/b2b-search-results-cards.tsx index 3de9e86b..0766ae2a 100644 --- a/ui/src/components/search/bed2bed/b2b-search-results-cards.tsx +++ b/ui/src/components/search/bed2bed/b2b-search-results-cards.tsx @@ -62,7 +62,7 @@ export const Bed2BedSearchResultsCards = (props: Props) => {
-
+
{ } > - 0.5 ? 'bg-primary' : 'bg-secondary'}`} style={{ fontSize: '10px' }}> + 0.5 ? 'bg-primary' : 'bg-secondary'}`}> {roundToTwoDecimals((result.score ?? 0) * 100)}% @@ -83,20 +83,20 @@ export const Bed2BedSearchResultsCards = (props: Props) => { {result?.metadata?.description || 'No description'}

-
- +
+ genome:{' '}{result?.metadata?.genome_alias || 'N/A'} - + tissue:{' '}{result?.metadata?.annotation?.tissue || 'N/A'} - + cell_line:{' '}{result?.metadata?.annotation?.cell_line || 'N/A'} - + cell_type:{' '}{result?.metadata?.annotation?.cell_type || 'N/A'} - + assay:{' '}{result?.metadata?.annotation?.assay || 'N/A'}
diff --git a/ui/src/components/search/search-selector.tsx b/ui/src/components/search/search-selector.tsx index 0a2d9c92..fa18e095 100644 --- a/ui/src/components/search/search-selector.tsx +++ b/ui/src/components/search/search-selector.tsx @@ -5,11 +5,10 @@ type SearchView = 't2b' | 'b2b' | 't2bs'; type Props = { view: SearchView; setView: (view: SearchView) => void; - setOffset: (offset: number) => void; }; export const SearchSelector = (props: Props) => { - const { view, setView, setOffset } = props; + const { view, setView } = props; const [params, setParams] = useSearchParams(); return (
@@ -23,7 +22,6 @@ export const SearchSelector = (props: Props) => { params.delete('q'); setParams(params); setView('t2b'); - setOffset(0); }} > Text-to-BED @@ -37,7 +35,6 @@ export const SearchSelector = (props: Props) => { params.delete('q'); setParams(params); setView('b2b'); - setOffset(0); }} > BED-to-BED @@ -51,7 +48,6 @@ export const SearchSelector = (props: Props) => { params.delete('q'); setParams(params); setView('t2bs'); - setOffset(0); }} > Text-to-BEDset 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 5b789ed7..fec8947d 100644 --- a/ui/src/components/search/text2bed/t2b-search-results-table.tsx +++ b/ui/src/components/search/text2bed/t2b-search-results-table.tsx @@ -58,7 +58,7 @@ export const Text2BedSearchResultsTable = (props: Props) => {
-
+
{(result.id === (search_query || '')) && } { } > - 0.5 ? 'bg-primary' : 'bg-secondary'}`} style={{ fontSize: '10px' }}> + 0.5 ? 'bg-primary' : 'bg-secondary'}`}> {roundToTwoDecimals((result.score ?? 0) * 100)}% @@ -80,20 +80,20 @@ export const Text2BedSearchResultsTable = (props: Props) => { {result?.metadata?.description || 'No description'}

-
- +
+ genome:{' '}{result?.metadata?.genome_alias || 'N/A'} - + tissue:{' '}{result?.metadata?.annotation?.tissue || 'N/A'} - + cell_line:{' '}{result?.metadata?.annotation?.cell_line || 'N/A'} - + cell_type:{' '}{result?.metadata?.annotation?.cell_type || 'N/A'} - + assay:{' '}{result?.metadata?.annotation?.assay || 'N/A'}
diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx index c961d19d..0dbf963a 100644 --- a/ui/src/pages/home.tsx +++ b/ui/src/pages/home.tsx @@ -39,13 +39,13 @@ export const Home = () => { return (
-
-

BEDbase

-
+
+

BEDbase

+

The open access platform for aggregating, analyzing, and serving genomic region data.

-

+

Explore thousands of BED files (including {' '} { > .bdg - ) from ENCODE, GEO, and more. + ) from ENCODE, GEO, and more.

+ {/*
*/}
{searchType === 'b2b' ? ( @@ -141,7 +142,7 @@ export const Home = () => {
-
+ @@ -173,9 +174,9 @@ export const Home = () => {
-
Vector Search
+
Vector Search
-

+

Search by text, upload BED files for similarity matching, or browse BEDsets. Explore results directly in their region embedding space.

@@ -194,9 +195,9 @@ export const Home = () => {
-
BED Analyzer
+
BED Analyzer
-

+

Analyze any BED file in your browser with our gtars-wasm integration. Get file statistics, region distributions, and chromosome coverage instantly.

@@ -211,7 +212,7 @@ export const Home = () => {
-
{!metadata?.processed && (

+ This file has not been processed by the BedBoss pipeline yet. } > - + Not Processed

)} -
+
{(metadata?.processed && metadata?.genome_alias == 'hg38') && - } - - {!addedToCart && cart[record_identifier || ''] ? ( ) : ( )} - - + + Downloads { // If there are no files to download, disable the dropdown noFilesToDownload ? ( - + There are no files to download ) : ( - + {metadata.files?.bed_file && ( {(metadata.files?.bed_file?.access_methods || []).map((method, index) => { @@ -163,9 +163,9 @@ export const BedSplashHeader = (props: Props) => { return null; } return ( - + {method.access_id ? 'BED file' : 'No download link available'} ( - {bytesToSize(metadata.files?.bed_file?.size || 0)}) + {bytesToSize(metadata.files?.bed_file?.size || 0)}) ); })} @@ -178,9 +178,9 @@ export const BedSplashHeader = (props: Props) => { return null; } return ( - + {method.access_id ? 'BigBED file' : 'No download link available'} ( - {bytesToSize(metadata.files?.bigbed_file?.size || 0)}) + {bytesToSize(metadata.files?.bigbed_file?.size || 0)}) ); })} @@ -193,38 +193,38 @@ export const BedSplashHeader = (props: Props) => {
-
{metadata.name}
-

{metadata?.description || 'No description available'}

+
{metadata.name}
+

{metadata?.description || 'No description available'}

-
-
-
+ className='d-flex flex-column flex-xl-row align-items-start align-items-xl-end justify-content-xl-between mt-2 overflow-x-auto'> +
+
+
-
-
Genome assembly
+
+
+
Genome assembly
} > {metadata?.genome_digest ? ( <> + target='_blank'>
- + {metadata.genome_alias || 'No assembly available'}
) : ( <> -
- +
+ {metadata.genome_alias || 'No assembly available'}
@@ -232,82 +232,82 @@ export const BedSplashHeader = (props: Props) => { {genomeStats?.compared_genome && -
-
Genome compatibility details
+
+
+
Genome compatibility details
} >
{ if (showRefGenomeModal !== true) { setShowRefGenomeModal(true); } }} > - +
}
-
-
+
+
-
-
BED compliance
+
+
+
BED compliance
} > -
- +
+ {metadata?.bed_compliance || 'No compliance available'}
-
-
+
+
-
-
Data Format
+
+
+
Data Format
} > -
- +
+ {metadata?.data_format || 'No data format available'}
-
-
+
+
-
-
License
+
+
+
License
} > -
- +
+ {metadata?.license_id || 'DUO:0000042'}
@@ -315,19 +315,19 @@ export const BedSplashHeader = (props: Props) => {
{metadata?.is_universe && ( -
-
+
+
-
-
This BED file is part of the Universe
+
+
+
This BED file is part of the Universe
} > -
- +
+ Universe
@@ -335,24 +335,6 @@ export const BedSplashHeader = (props: Props) => {
)}
-
-
- -

- Created:{' '} - {metadata?.submission_date ? formatDateTime(metadata?.submission_date) : 'No date available'} -

-
- -
- -

- Updated:{' '} - {metadata?.last_update_date ? formatDateTime(metadata?.last_update_date) : 'No date available'} -

-
-
{genomeStats?.compared_genome && { setShow(true); } }} - className='h-100 border rounded p-2 shadow-sm hover-border-primary transition-all bg-white' + className='h-100 border rounded p-2 hover-border-primary transition-all bg-white' >

{title}

diff --git a/ui/src/components/bed-splash-components/refgenome-modal.tsx b/ui/src/components/bed-splash-components/refgenome-modal.tsx index 65cc4cec..48b6622d 100644 --- a/ui/src/components/bed-splash-components/refgenome-modal.tsx +++ b/ui/src/components/bed-splash-components/refgenome-modal.tsx @@ -70,7 +70,7 @@ export const RefGenomeModal = (props: Props) => { rel="noopener noreferrer" >
@@ -81,7 +81,7 @@ export const RefGenomeModal = (props: Props) => {

{genome.compared_genome}

-
+
{genome.xs ? <> { }
-
+
{genome.oobr ? <> { }
-
+
{genome.sequence_fit ? <> { }); return ( -
+
{ const renderTooltip = () => {tooltip || 'No tooltip available'}; return ( -
+
{title}
{children}
diff --git a/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx b/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx index 795e96f0..b29e6293 100644 --- a/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx +++ b/ui/src/components/bedset-splash-components/charts/genomic-feature-bar.tsx @@ -193,7 +193,7 @@ export const GenomicFeatureBar = (props: Props) => { } return ( -
+

Genomic Features

diff --git a/ui/src/components/bedset-splash-components/header.tsx b/ui/src/components/bedset-splash-components/header.tsx index 2896c572..1bb4204f 100644 --- a/ui/src/components/bedset-splash-components/header.tsx +++ b/ui/src/components/bedset-splash-components/header.tsx @@ -115,7 +115,7 @@ export const BedsetSplashHeader = (props: Props) => { Downloads - + setShowDownloadModal(true)}> Download BEDset diff --git a/ui/src/components/bedset-splash-components/plots.tsx b/ui/src/components/bedset-splash-components/plots.tsx index 422508c0..0a70725b 100644 --- a/ui/src/components/bedset-splash-components/plots.tsx +++ b/ui/src/components/bedset-splash-components/plots.tsx @@ -29,7 +29,7 @@ const Plot = (props: PlotProps) => { setShow(true); } }} - className="h-100 border rounded p-1 shadow-sm hover-border-primary transition-all bg-white" + className="h-100 border rounded p-1 hover-border-primary transition-all bg-white" >
{title} 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 1de5b36b..ae8f8624 100644 --- a/ui/src/components/search/bed2bed/b2b-search-results-table.tsx +++ b/ui/src/components/search/bed2bed/b2b-search-results-table.tsx @@ -226,7 +226,7 @@ export const Bed2BedSearchResultsTable = (props: Props) => { }; return ( -
+
{ - const { results } = props; - - const handleRowClick = (id?: string) => (e: React.MouseEvent) => { - if (!(e.target as HTMLElement).closest('button')) { - window.location.href = `/bedset/${id}`; - } - }; - - return ( - - - - - - - - - - - - {results.results?.map((result) => ( - - - - - - - - ))} - -
Bedset IDNameDescriptionNumber of Beds - Actions -
{result?.id || 'Unknown Id'}{result?.name || 'Unknown Name'}{result?.description || 'Unknown Description'}{result?.bed_ids?.length || 0} - - - -
- ); -}; diff --git a/ui/src/components/search/search-selector.tsx b/ui/src/components/search/search-selector.tsx index fa18e095..eac6c698 100644 --- a/ui/src/components/search/search-selector.tsx +++ b/ui/src/components/search/search-selector.tsx @@ -16,7 +16,7 @@ export const SearchSelector = (props: Props) => {
  • +
+
+
+ ))} + + ); +}; diff --git a/ui/src/components/search/text2bedset.tsx b/ui/src/components/search/text2bedset/text2bedset.tsx similarity index 71% rename from ui/src/components/search/text2bedset.tsx rename to ui/src/components/search/text2bedset/text2bedset.tsx index 2737b717..a8787ab1 100644 --- a/ui/src/components/search/text2bedset.tsx +++ b/ui/src/components/search/text2bedset/text2bedset.tsx @@ -1,10 +1,10 @@ -import { SearchingJumper } from './searching-jumper'; +import { SearchingJumper } from '../searching-jumper.tsx'; import { useEffect } from 'react'; -import { useText2BedSetSearch } from '../../queries/useText2BedSetSearch'; -import { ErrorPage } from '../common/error-page'; -import { TableToolbar } from './table-toolbar'; -import { PaginationBar } from './pagination-bar'; -import { SearchBedSetResultTable } from './search-bedset-table.tsx'; +import { useText2BedSetSearch } from '../../../queries/useText2BedSetSearch.ts'; +import { ErrorPage } from '../../common/error-page.tsx'; +// import { TableToolbar } from '../table-toolbar.tsx'; +import { PaginationBar } from '../pagination-bar.tsx'; +import { SearchBedSetResultTable } from './t2bs-search-results-table.tsx'; import { AxiosError } from 'axios'; type Props = { @@ -17,7 +17,7 @@ type Props = { }; export const Text2BedSet = (props: Props) => { - const { searchTerm, limit, setLimit, offset, setOffset, triggerSearch } = props; + const { searchTerm, limit, offset, setOffset, triggerSearch } = props; const { isFetching: isSearching, @@ -59,11 +59,11 @@ export const Text2BedSet = (props: Props) => { ) : (
{results ? ( -
-
+
+ {/*
-
- {' '} +
*/} +
) : ( diff --git a/ui/src/components/umap/atlas-tooltip.tsx b/ui/src/components/umap/atlas-tooltip.tsx index 450ab7db..787d85cb 100644 --- a/ui/src/components/umap/atlas-tooltip.tsx +++ b/ui/src/components/umap/atlas-tooltip.tsx @@ -20,7 +20,7 @@ const TooltipContent = ({ tooltip, showLink }: { tooltip: TooltipProps['tooltip' if (!tooltip) return null; return (
{ {isReady ? (
-
+
{ {isReady ? (
-
+
{
-
+
Legend
@@ -522,7 +522,7 @@ export const BEDEmbeddingView = (props: Props) => {
-
+
Selection {/* */} diff --git a/ui/src/custom.scss b/ui/src/custom.scss index 7f5a55cd..44f9a465 100644 --- a/ui/src/custom.scss +++ b/ui/src/custom.scss @@ -362,3 +362,13 @@ td { .btn-card { transition: color 0.15s ease-in-out, background-color 0.15s ease-in-out, border-color 0.15s ease-in-out, box-shadow 0.15s ease-in-out; } + +.table-transparent { + background-color: transparent; /* Makes the table background completely transparent */ + --bs-table-bg: transparent; +} + +.table-transparent tbody tr { + background-color: transparent; + --bs-table-bg: transparent; +} diff --git a/ui/src/pages/bed-analytics.tsx b/ui/src/pages/bed-analytics.tsx index ed053d70..80fa6a1f 100644 --- a/ui/src/pages/bed-analytics.tsx +++ b/ui/src/pages/bed-analytics.tsx @@ -134,7 +134,7 @@ export const BEDAnalytics = () => { { const file = e.target.files?.[0]; @@ -259,7 +259,7 @@ export const BEDAnalytics = () => {
{rs && (
-
+
@@ -289,7 +289,7 @@ export const BEDAnalytics = () => {
{rs && ( - //
+ //
//
Region Distribution Data
// 
diff --git a/ui/src/pages/bed-cart.tsx b/ui/src/pages/bed-cart.tsx
index ee1eea14..effb27b3 100644
--- a/ui/src/pages/bed-cart.tsx
+++ b/ui/src/pages/bed-cart.tsx
@@ -3,39 +3,36 @@ import { Layout } from '../components/layout';
 import { DownloadCartModal } from '../components/modals/download-cart-modal';
 import { CreateBedSetModal } from '../components/modals/create-bedset-modal';
 import { useState } from 'react';
+import { useNavigate } from 'react-router-dom';
+
 
 export const BedCart = () => {
   const [showDownloadModal, setShowDownloadModal] = useState(false);
   const [showCreateBedsetModal, setCreateBedSetModal] = useState(false);
   const { cart, removeBedFromCart } = useBedCart();
-
-  const handleRowClick = (id?: string) => (e: React.MouseEvent) => {
-    if (!(e.target as HTMLElement).closest('button')) {
-      window.location.href = `/bed/${id}`;
-    }
-  };
+  const navigate = useNavigate();
 
   if (Object.keys(cart).length === 0) {
     return (
-      
-        

-          
Your cart is empty

-          
Try searching for some bedfiles!

-          

-            
-              
             
-            
-              
             
-            
           

@@ -46,85 +43,96 @@ export const BedCart = () => {
   }
 
   return (
-    
-      

-        

-          

-            
Cart

+    
+      

+        

+          

+            
Cart

             {Object.keys(cart).length === 1 ? (
-              
You have 1 item in your cart

+              
You have 1 item in your cart.

             ) : (
-              
You have {Object.keys(cart).length} items in your cart

+              
You have {Object.keys(cart).length} items in your cart.

             )}
           

-          

-            
-            
-            
           

         

-        

-          

-
- - - - - - - - - - - - - - {Object.values(cart).map((item) => ( - ( +
+
+
{ + navigate(`/bed/${result.id}`) + }} + > +
+
+

+ {result?.name || 'No name'} +

+
+
+

+ {result?.description || 'No description'} +

+ +
+ + genome:{' '}{result?.genome || 'N/A'} + + + tissue:{' '}{result?.tissue || 'N/A'} + + + cell_line:{' '}{result?.cell_line || 'N/A'} + + + cell_type:{' '}{result?.cell_type || 'N/A'} + + + assay:{' '}{result?.assay || 'N/A'} + +
+
+ +
+
- - - - - - - - - ))} - -
NameGenomeTissueCell LineCell TypeDescriptionAssay - Actions -
{item.name || 'N/A'} - {item.genome || 'N/A'} - {item.tissue || 'N/A'}{item.cell_line || 'N/A'}{item.cell_type || 'N/A'}{item.description || ''}{item.assay || 'N/A'} - {cart[item.id || ''] && ( - - )} -
+ + + {cart[result?.id || ''] ? ( + + ) : (<> + )} +
+
-
+ ))}
diff --git a/ui/src/pages/bed-splash.tsx b/ui/src/pages/bed-splash.tsx index d9cc005e..c0946ea3 100644 --- a/ui/src/pages/bed-splash.tsx +++ b/ui/src/pages/bed-splash.tsx @@ -12,12 +12,13 @@ import { GenomicFeatureBar } from '../components/bed-splash-components/charts/ge import { Plots } from '../components/bed-splash-components/plots'; import { AxiosError } from 'axios'; import { GCContentCard } from '../components/bed-splash-components/cards/gc-content-card'; -import { snakeToTitleCase } from '../utils'; +import { snakeToTitleCase, formatDateTime } from '../utils'; import { Text2BedSearchResultsTable } from '../components/search/text2bed/t2b-search-results-table'; import { useBedNeighbours } from '../queries/useBedNeighbours'; import type { components } from '../../bedbase-types.d.ts'; -import { BEDEmbeddingView } from '../components/umap/bed-embedding-view.tsx'; -import { useState } from 'react'; +// import { BEDEmbeddingView } from '../components/umap/bed-embedding-view.tsx'; +// import { useState } from 'react'; +import { SearchBedSetResultTable } from '../components/search/text2bedset/t2bs-search-results-table.tsx'; // Use the response type to properly type the metadata type BedMetadata = components['schemas']['BedMetadataAll']; @@ -26,7 +27,7 @@ export const BedSplash = () => { const params = useParams(); const bedId = params.id; - const [showNeighbors, setShowNeighbors] = useState(false); + // const [showNeighbors, setShowNeighbors] = useState(false); const { isLoading, @@ -64,6 +65,74 @@ export const BedSplash = () => { ); }; + const filteredKeys = getFilteredKeys(metadata); + // Add created and updated at the end + const allKeys = [...filteredKeys, '_created', '_updated']; + const midpoint = Math.ceil(allKeys.length / 2); + const leftKeys = allKeys.slice(0, midpoint); + const rightKeys = allKeys.slice(midpoint); + + const metadataRow = (k: string) => { + if (k === '_created') { + return ( + + + File Created + + + {metadata?.submission_date ? formatDateTime(metadata?.submission_date) : 'N/A'} + + + ); + } + + if (k === '_updated') { + return ( + + + File Updated + + + {metadata?.last_update_date ? formatDateTime(metadata?.last_update_date) : 'N/A'} + + + ); + } + + const value = getAnnotationValue(metadata, k); + if (!value) return null; + + return ( + + + {snakeToTitleCase(k)} + + + { k === 'global_sample_id' ? + (Array.isArray(value) && value.length > 0) + ? value.map((v, i) => ( + v.includes('encode:') + ? {v} + : v.includes('geo:') + ? {v} + : v ?? 'N/A' + )).reduce((prev, curr) => <>{prev}, {curr}) + : value ?? 'N/A' + : + k === 'global_experiment_id' ? + (Array.isArray(value) && value.length > 0) ? value.map((v, i) => ( + v.includes('encode') ? {v} : + v.includes('geo:') ? {v} : + v ?? 'N/A' + )).reduce((prev, curr) => <>{prev}, {curr}) : value ?? 'N/A' + : + value ?? 'N/A' + } + + + ); + }; + if (isLoading) { return ( @@ -144,110 +213,29 @@ export const BedSplash = () => { {metadata !== undefined ? : null}
-
-
-
Overview
-
-
- - - - - - - - - {Object.keys(metadata?.annotation || {}).map((k) => { - if (k === 'input_file' || k === 'file_name' || k === 'sample_name') { - return null; - } - - const value = getAnnotationValue(metadata, k); - if (!value) { - return null; - } - - return ( - - - - - ); - })} - -
KeyValue
- {snakeToTitleCase(k)} - - { k === 'global_sample_id' ? - (Array.isArray(value) && value.length > 0) - ? value.map((v, i) => ( - v.includes('encode:') - ? {v} - : v.includes('geo:') - ? {v} - : v ?? 'N/A' - )).reduce((prev, curr) => <>{prev}, {curr}) - : value ?? 'N/A' - : - k === 'global_experiment_id' ? - (Array.isArray(value) && value.length > 0) ? value.map((v, i) => ( - v.includes('encode') ? {v} : - v.includes('geo:') ? {v} : - v ?? 'N/A' - )).reduce((prev, curr) => <>{prev}, {curr}) : value ?? 'N/A' - : - value ?? 'N/A' - } -
+
+
+
Metadata
+
+
+
+ + + {leftKeys.map(metadataRow)} + +
+
+
+
+
+ + + {rightKeys.map(metadataRow)} + +
+
+
-
-
-
-
BEDsets
-
-
- - - - - - - - - - - {[ - ...(metadata?.bedsets || []).map((bedset) => ( - - - - - - - )), - ...Array(Math.max(0, getFilteredKeys(metadata).length - (metadata?.bedsets?.length || 0))) - .fill(null) - .map((_, index) => ( - - - - - - - )), - ]} - -
BEDset IDNameDescriptionView
- {bedset.id} - - {bedset.name || 'No name'} - - {bedset.description || 'No description'} - - View -
    
-
-
@@ -273,10 +261,33 @@ export const BedSplash = () => {
- {bedId && metadata?.name?.includes('encode') && ( + {/* {bedId && metadata?.name?.includes('encode') && ( <> + )} */} + + {(metadata?.bedsets && metadata.bedsets.length > 0) && ( +
+
+
BEDsets
+ ({ + id: bedset.id, + name: bedset.name || '', + description: bedset.description || '', + md5sum: '', + bed_ids: [] + })) + }} + showBEDCount={false} + /> +
+
)} {neighbours && ( @@ -284,7 +295,7 @@ export const BedSplash = () => {
Similar BED Files
-
+ {/*
{ > Show in Atlas -
+
*/}
diff --git a/ui/src/pages/home.tsx b/ui/src/pages/home.tsx index 0dbf963a..5c6e46f7 100644 --- a/ui/src/pages/home.tsx +++ b/ui/src/pages/home.tsx @@ -172,7 +172,7 @@ export const Home = () => {
-
+
Vector Search
@@ -193,12 +193,12 @@ export const Home = () => {
-
+
BED Analyzer

- Analyze any BED file in your browser with our gtars-wasm integration. Get file statistics, region distributions, and chromosome coverage instantly. + Analyze any BED file in your browser with gtars-wasm. Get file statistics, region distributions, and chromosome coverage instantly.

BED Analyzer diff --git a/ui/src/pages/metrics.tsx b/ui/src/pages/metrics.tsx index b84a657e..dd995d66 100644 --- a/ui/src/pages/metrics.tsx +++ b/ui/src/pages/metrics.tsx @@ -122,7 +122,7 @@ export const Metrics = () => {

BEDbase File Statistics

-