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tristan-f-rtristan-f-r
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feat: dataset categories (#49)
* chore: fix up config, bump cores * chore: bump web dependencies * feat: use visjs * feat: categorization * chore: mv to type-category-dataset * chore: mv type category dataset slug * chore: mv again * feat: fully handle categories * feat: more prefix fixing * feat: type category * style: fmt * fix: up pnpm lock * fix: export datasets * style: fmt
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24 files changed

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‎configs/dmmm.yaml‎

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@@ -42,12 +42,12 @@ algorithms:
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datasets:
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# TODO: use old paramaters for datasets
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# HIV: https://github.com/Reed-CompBio/spras-benchmarking/blob/0293ae4dc0be59502fac06b42cfd9796a4b4413e/hiv-benchmarking/spras-config/config.yaml
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- label: dmmmhiv060
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- label: dmmmhiv_060
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node_files: ["processed_prize_060.txt"]
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edge_files: ["../../../databases/irefindex/phosphosite-irefindex13.0-uniprot.txt"]
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other_files: []
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data_dir: "datasets/hiv/processed"
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- label: dmmmhiv05
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- label: dmmmhiv_05
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node_files: ["processed_prize_05.txt"]
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edge_files: ["../../../databases/irefindex/phosphosite-irefindex13.0-uniprot.txt"]
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other_files: []
@@ -58,21 +58,21 @@ datasets:
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edge_files: ["network1.txt"]
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other_files: []
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data_dir: "datasets/yeast-osmotic-stress/processed"
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- label: dmmmalopecia_areata
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- label: dmmmdiseases_alopecia_areata
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data_dir: datasets/diseases
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edge_files:
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- raw/string_interactome.txt
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node_files:
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- prize_files/alopecia_areata_prizes.txt
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other_files: []
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- label: dmmmdiabetes_mellitus
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- label: dmmmdiseases_diabetes_mellitus
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data_dir: datasets/diseases
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edge_files:
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- raw/string_interactome.txt
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node_files:
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- prize_files/diabetes_mellitus_prizes.txt
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other_files: []
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- label: dmmmcellline_fadu
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- label: dmmmdepmap_cellline_fadu
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data_dir: datasets/depmap
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edge_files: ["../../databases/irefindex/phosphosite-irefindex13.0-uniprot.txt"]
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node_files: ["processed/FADU_cell_line_prizes_input_nonzero.txt"]
@@ -81,12 +81,12 @@ gold_standards:
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- label: gs0
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node_files: ['GS_files/Alopecia_areata_GS.txt']
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data_dir: "datasets/diseases"
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dataset_labels: ["dmmmalopecia_areata"]
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dataset_labels: ["dmmmdiseases_alopecia_areata"]
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- label: gs1
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node_files: ['GS_files/Diabetes_mellitus_GS.txt']
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data_dir: "datasets/diseases"
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dataset_labels: ["dmmmdiabetes_mellitus"]
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dataset_labels: ["dmmmdiseases_diabetes_mellitus"]
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- label: gs_fadu
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node_files: ["processed/FADU_gold_standard.txt"]
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data_dir: datasets/depmap
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dataset_labels: ["dmmmcellline_fadu"]
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dataset_labels: ["dmmmdepmap_cellline_fadu"]

‎configs/pra.yaml‎

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@@ -49,7 +49,7 @@ algorithms:
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include: true
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datasets:
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- label: pramuscleskeletal2018
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- label: prarn_muscleskeletal2018
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node_files: ["sources.txt", "targets.txt"]
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# DataLoader.py can currently only load a single edge file, which is the primary network
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edge_files: ["interactome.tsv"]

‎web/.prettierrc‎

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{
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"printWidth": 120,
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"plugins": ["prettier-plugin-astro"],
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"overrides": [
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{
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"files": "*.astro",
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"options": {
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"parser": "astro"
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}
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}
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]
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}

‎web/astro.config.mts‎

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// @ts-check
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import { defineConfig } from 'astro/config';
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import { defineConfig } from "astro/config";
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// https://astro.build/config
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export default defineConfig({
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base: '/spras-benchmarking',
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trailingSlash: 'always'
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base: "/spras-benchmarking",
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trailingSlash: "always",
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});

‎web/package.json‎

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"type": "module",
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"version": "0.0.1",
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"scripts": {
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"prepare-output": "mkdir -p public/data && cp -r ../output/ public/data",
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"prepare-output": "mkdir -p public/data && cp -r ../output/ public/data && cp -r ../configs/ public/data",
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"dev": "pnpm prepare-output && astro dev",
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"build": "pnpm prepare-output && astro build",
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"preview": "astro preview",
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"astro": "astro"
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"astro": "astro",
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"format": "pnpm exec prettier . --write"
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},
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"dependencies": {
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"@fontsource-variable/noto-sans": "^5.2.10",
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"astro": "^5.16.6",
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"dayjs": "^1.11.19",
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"medium-zoom": "^1.1.0",
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"sass": "^1.97.1"
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"sass": "^1.97.1",
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"yaml": "^2.8.2"
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},
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"devDependencies": {
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"prettier": "3.7.4",
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"prettier-plugin-astro": "0.14.1",
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"vis-data": "^8.0.3",
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"vis-network": "^10.0.2"
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}
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}
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}

‎web/pnpm-lock.yaml‎

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‎web/src/components/Colors.astro‎

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<style is:global lang="scss">
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@use 'sass:color';
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@use "sass:color";
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$color-1: oklch(0.6744 0.1426 151.9);
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$color-2: oklch(0.6376 0.2299 24.84);
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$color-3: oklch(0.8002 0.1669 74.36);
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$color-4: oklch(0.6465 0.1022 212.93);
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$color-1: oklch(0.6744 0.1426 151.9);
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$color-2: oklch(50.908% 0.1675 306.81);
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$color-3: oklch(0.6376 0.2299 24.84);
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$color-4: oklch(0.8002 0.1669 74.36);
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$color-5: oklch(0.6465 0.1022 212.93);
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.color-1 { color: color.adjust($color-1, $lightness: -20%); }
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.color-2 { color: color.adjust($color-2, $lightness: -20%); }
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.color-3 { color: color.adjust($color-3, $lightness: -20%); }
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.color-4 { color: color.adjust($color-4, $lightness: -20%); }
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.color-1 {
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color: color.adjust($color-1, $lightness: -20%);
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}
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.color-2 {
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color: color.adjust($color-2, $lightness: -20%);
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}
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.color-3 {
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color: color.adjust($color-3, $lightness: -20%);
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}
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.color-4 {
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color: color.adjust($color-4, $lightness: -20%);
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}
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.color-5 {
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color: color.adjust($color-5, $lightness: -20%);
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}
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.color-1-dark { color: color.adjust($color-1, $lightness: -40%); }
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.color-2-dark { color: color.adjust($color-2, $lightness: -40%); }
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.color-3-dark { color: color.adjust($color-3, $lightness: -40%); }
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.color-4-dark { color: color.adjust($color-4, $lightness: -40%); }
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.color-1-dark {
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color: color.adjust($color-1, $lightness: -40%);
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}
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.color-2-dark {
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color: color.adjust($color-2, $lightness: -40%);
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}
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.color-3-dark {
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color: color.adjust($color-3, $lightness: -40%);
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}
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.color-4-dark {
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color: color.adjust($color-4, $lightness: -40%);
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}
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.color-5-dark {
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color: color.adjust($color-5, $lightness: -40%);
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}
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</style>

‎web/src/components/MediumZoom.astro‎

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<script>
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import mediumZoom from 'medium-zoom';
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import mediumZoom from "medium-zoom";
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mediumZoom('[data-zoomable]')
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mediumZoom("[data-zoomable]");
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</script>

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