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* The lab's own store: the demo workspaces published on the lab's bucket, and
* the data files they are made of.
*
* They used to ship inside the bundle, in `public/demo/`, which put 250 MB of
* Hi-C into every Pages artifact and every desktop checkout — and made the
* deployed site read them through the *whole-object fallback*, because Pages
* gzips `application/octet-stream` and a gzipped body cannot be range-read
* (docs/hosting.md). Moving them to S3 fixes both at once: the app is a few MB
* again, and the demos are now read the way §11 says a published dataset is
* read — a `HEAD`, then bounded range `GET`s — which means the landing page
* exercises the same path a reader's own bucket will.
*
* The price is the half of the hosting requirements that same-origin hosting
* used to waive: the bucket must answer a CORS preflight and expose
* `Content-Length` and `Content-Range`. That is bucket configuration, not code,
* and `scripts/publish-demo.sh` applies it alongside the upload.
*
* **Every figure in the store is a workspace file, not a data file.** A `.cool`
* in the list could only ever offer what dropping that file offers: a map at
* its landing view, with nothing beside it. What a first-time reader should
* meet is the application doing its job — a window worth looking at, tracks on
* both edges of the map, three maps of one locus side by side — and all of that
* is exactly what `state/workspace.ts` writes down. So the figures are
* `.chromosomix.json` files that live next to the data they name, and choosing
* one is the same gesture as dropping a workspace somebody sent you. The data
* files are listed too, under each figure's fold, for the reader who wants the
* `.mcool` alone — as rows, with the two verbs every store row has.
*
* The figures are filed under two headings (§24.2). **Demo** is what the viewer
* does, ordered as an argument rather than by dataset: one map with its tracks,
* then the same tracks with no map at all and close enough to read the reading
* frames, then three maps of one locus side by side, then a human chromosome's
* splicing in the 1D browser, then a time course in decks — the simplest
* complete thing first. **Papers** is the figures of the lab's papers, each a
* session over the data the paper published.
*
* A note on the format, because it is what made every one of these stop
* opening once: `App.openWorkspaceFile` reads `kind: "chromosomix.workspace"`
* and refuses anything else, so a published file still written in the older
* single-session shape is a card that fails on click with "not a workspace".
* The files in `demo/store/` are written by `scripts/make_rsg_store.py`, in the
* current shape; the copies on the bucket are only as current as the last run
* of `scripts/publish-store.sh`, which is the step that makes the store true.
*
* Each workspace sits in the bucket folder holding the files it names, and the
* names *inside* it stay relative — resolved against the file's own URL on the
* way in (`resolveConfig`). That is what keeps a card's folder a self-contained
* thing: `demo/store/` can be copied to another bucket, or served off a laptop,
* and every one of its workspaces still opens.
*/
import { splitUri } from './labels'
import type { StoreEntry, StoreFile } from '../state/store'
import { STORE_KIND, STORE_VERSION } from '../state/store'
import { devFeature, type DevFeature } from '../state/devFeatures'
declare const __DEMO_BASE__: string
/**
* The published root, with its trailing slash: one folder per dataset under it.
*
* The repository's own `demo/` directory mirrors this — it is what
* `scripts/publish-demo.sh` uploads and what `demo-examples.test.ts` checks —
* with one exception: the store's folder, `demo/store/`, holds files of several
* gigabytes that are copied into it on the bucket rather than kept in git, so
* the repository carries its workspaces and `demo/store/MANIFEST.tsv`, which
* names every file in it and where it comes from. The test reads the manifest
* where it cannot read the file, so a name a workspace uses that the bucket
* will not have is still a red CI run.
*/
export const DEMO_BUCKET = 'https://rsglab-data.s3.eu-west-3.amazonaws.com/demo/'
/**
* Where to read the demos from, when it is not {@link DEMO_BUCKET}.
*
* Empty in both shipped builds, which is what makes the web target and the
* desktop target read the identical URLs. The override survives as a
* build-time escape hatch (`DEMO_BASE=… vite build`) for the two cases that
* want it: a fork publishing its own bucket, and `python3 -m http.server` over
* a local copy of `demo/` when the network is not available.
*
* `typeof` because `vitest` applies no `define` block (see `version.ts`).
*/
const DEMO_BASE: string = typeof __DEMO_BASE__ === 'string' ? __DEMO_BASE__ : ''
/**
* The headings the store's figures are filed under, in the order they stand.
*
* *Demo* is what the viewer does; *Papers* is the figures of the lab's papers,
* each card a session over the data the paper published (§24.2).
*/
export type DemoSection = 'Demo' | 'Papers'
/**
* The paper's GM12878 files (Figs. 1a and 2): the folder's path, its label, its kind, its format and its
* assembly — 4DN's map, ENCODE's ChIA-PET map and tracks, UCSC's sequence and genes, and what the app
* computed on them.
*/
const PAPER_HUMAN = [
['human/4DNFIXP4QG5B.mcool', 'GM12878 Hi-C, 4.0 billion contacts (Rao et al. 2014, 4DN)', 'map', 'mcool', 'hg38'],
['human/ENCFF379AWZ.hic', 'GM12878 CTCF ChIA-PET, Ruan lab (ENCODE ENCSR184YZV)', 'map', 'hic', 'hg38'],
['human/hg38.2bit', 'Human sequence, UCSC hg38', 'genome', '2bit', 'hg38'],
['human/hg38.refGene.txt.gz', 'RefSeq genes, UCSC hg38', 'genome', 'genepred', 'hg38'],
['human/ENCFF734CUT.bigWig', 'CTCF ChIP-seq, Broad (ENCODE ENCSR000AKB)', 'genome', 'bigwig', 'hg38'],
['human/ENCFF644EEX.bigWig', 'CTCF ChIP-seq, UW (ENCODE ENCSR000DRZ)', 'genome', 'bigwig', 'hg38'],
['human/ENCFF156URE.bigBed', 'CTCF peaks, conservative IDR (ENCODE)', 'genome', 'bigbed', 'hg38'],
['human/ENCFF487LOB.bigWig', 'ATAC-seq (ENCODE ENCSR095QNB)', 'genome', 'bigwig', 'hg38'],
['human/ENCFF928SQL.bigBed', 'ATAC-seq peaks (ENCODE)', 'genome', 'bigbed', 'hg38'],
['human/ENCFF990PUN.bigWig', 'Total RNA-seq, plus strand (ENCODE ENCSR000AEC)', 'genome', 'bigwig', 'hg38'],
['human/ENCFF005BFP.bigWig', 'Total RNA-seq, minus strand (ENCODE ENCSR000AEC)', 'genome', 'bigwig', 'hg38'],
...([5, 10, 20, 40] as const).map(
(w) =>
[`human/4DNFIXP4QG5B_10000.insulation-w${w}.bw`, `Diamond insulation, 10 kb, ${w * 10}-kb window`, 'genome', 'bigwig', 'hg38'] as const,
),
['human/4DNFIXP4QG5B_10000.borders.bed', 'Borders on the insulation, 10 kb', 'genome', 'bed', 'hg38'],
['human/GM12878_CTCF.peaks.bed', 'CTCF peaks called on both labs’ ChIP-seq, IDR ≤ 0.05', 'genome', 'bed', 'hg38'],
['human/GM12878_CTCF.consecutive.bedpe', 'Consecutive CTCF peaks, paired', 'genome', 'bedpe', 'hg38'],
['human/4DNFIXP4QG5B_2000.chr14.insulation-w50.bw', 'Diamond insulation of chr14, 2 kb', 'genome', 'bigwig', 'hg38'],
['human/4DNFIXP4QG5B_2000.chr14.borders.bed', 'Borders on chr14’s insulation, 2 kb', 'genome', 'bed', 'hg38'],
['human/4DNFIXP4QG5B_250000.compartments-e1.bw', 'Compartments (E1), 250 kb', 'genome', 'bigwig', 'hg38'],
['human/4DNFIXP4QG5B_250000.compartments-ab.bed', 'A and B compartments, 250 kb', 'genome', 'bed', 'hg38'],
['human/4DNFIXP4QG5B_5000.4c-chr14-89150001-89180000.bw', '4C from chr14:89,150,001-89,180,000, O/E', 'genome', 'bigwig', 'hg38'],
['human/4DNFIXP4QG5B_2000.chr14-88.55-90.10Mb.bed3d', '3D model of chr14:88.55–90.10 Mb, 2 kb', 'genome', 'bed3d', 'hg38'],
['human/hg38.CTCF-motifs.bed', 'CTCF motif sites, hg38', 'genome', 'bed', 'hg38'],
] as const
/** The paper's *B. subtilis* time course, a map a condition: the store's name, and the condition as Fig. S3b says it. */
const PAPER_SUBTILIS = [
['WT', 'WT'],
['dparAB', 'ΔparAB'],
['induction_0min', '+parB 0 min'],
['induction_15min', '+parB 15 min'],
['induction_20min', '+parB 20 min'],
['induction_30min', '+parB 30 min'],
['induction_35min', '+parB 35 min'],
['induction_45min', '+parB 45 min'],
] as const
/** The paper's *P. aeruginosa* maps, a strain each: the lab's sample, and the genotype as Fig. S3c says it. */
const PAPER_AERUGINOSA = [
['PAO1_v3_MM38', 'WT'],
['PAO1_v3_FG0235', 'SMC-ScpAB–'],
['PAO1_v3_FG0238', 'MksBEF–'],
] as const
/**
* The figures, in the order they are offered.
*
* Each card says enough to choose and no more: a `title`, one `line` on what
* is on screen, the `assembly`, and where the data came from (`provenance`,
* the accession or the DOI, because a demo with no provenance is a screenshot).
* The paragraph that used to be the whole row is `detail`, behind a fold on the
* card: it says what the *session* adds on top of the file, which is the part a
* reader cannot see from the name.
*
* `folder` is the card's own directory under {@link DEMO_BUCKET}, and its
* `files` are named from there: entries sharing a folder — as the three yeast
* figures do — are that many figures over one copy of the data, not that many
* copies of it, and a `../` reaches a file another card's folder holds.
*/
const DEMO: Array<{
section: DemoSection
folder: string
file: string
title: string
line: string
assembly: string
provenance: string
detail: string
/** The data files the session is made of, from its folder — its card's *N files* fold. */
files: string[]
/** The dev feature this figure belongs to, if it is one (§29): absent from the store while it is off. */
dev?: DevFeature
}> = [
{
section: 'Demo',
folder: 'store/yeast',
file: 'Yeast_microC.chromosomix.json',
title: 'Yeast micro-C',
line: 'One map at 1.6 kb, with the sequence, genes, RNA-seq, ATAC, MNase, shotgun, SNPs and its loops.',
assembly: 'S288C (R64)',
provenance: 'GEO GSE151553 · DOI 10.7554/eLife.59889',
detail:
'Micro-C XL of strain A364A (Costantino et al. 2020), balanced, opened on 400 kb of chromosome XIV ' +
'at 1.6 kb — a window with a weight for every bin. The sequence and the gene model run along both ' +
'edges; under the map, RNA-seq of a wild type and a mutant, two replicates each, drawn as one chart ' +
'per gene; ATAC, MNase and shotgun coverage; and SNPs in sixteen samples of wine, ale, lager, bioethanol ' +
'and other strains. The 636 loops drawn on it were called on this map by the app’s own Chromosight.',
files: [
'GSE151553_A364_merged.mcool',
'S288c.fa',
'S288c.gtf',
'Yeast_RNAseq.barChart',
'Yeast_ATAC.bw',
'Yeast_MNase.bw',
'Yeast_shotgun.bw',
'Yeast_snps.vcf.gz',
'Yeast_microC_loops.bedpe',
],
},
{
section: 'Demo',
folder: 'store/yeast',
file: 'Yeast_landscape.chromosomix.json',
title: 'Yeast chromatin landscape',
line: 'No map, and close: 5.5 kb of chromosome XIV with its six reading frames, the genes, RNA-seq by sample, ATAC, MNase, shotgun and SNPs.',
assembly: 'S288C (R64)',
provenance: 'Ensembl R64-1-1 · GEO GSE151553 (the map’s tracks)',
detail:
'The same tracks with no contact map, opened from the FASTA alone at RHO5, RPS3 and MRPL22. Close ' +
'enough for the sequence lane to draw the six reading frames under it — starts in green, stops in ' +
'red — so an open reading frame reads as a run of grey between two red marks, and lines up with the ' +
'gene above it. RNA-seq is one chart per gene, wild type against mutant on a 0–400 CPM axis; ATAC ' +
'and MNase share a group and each keep their own axis, so the nucleosome-free promoter and the ' +
'array beside it are read together.',
files: [
'S288c.fa',
'S288c.gtf',
'Yeast_RNAseq.barChart',
'Yeast_ATAC.bw',
'Yeast_MNase.bw',
'Yeast_shotgun.bw',
'Yeast_snps.vcf.gz',
],
},
{
section: 'Demo',
folder: 'store/yeast',
file: 'Yeast_HiC_microC_PCP.chromosomix.json',
title: 'Hi-C, micro-C and PCP',
line: 'One locus by three methods, side by side, each map with MNase and the genes under it.',
assembly: 'S288C (R64); W303 for the Hi-C',
provenance: 'GEO GSE151553 · GSE217022 · GSM8476641',
detail:
'Three maps of chrXV:200–400 kb in one deck: Hi-C of G1 cells carrying the M. mycoides chromosome at ' +
'1 kb (Meneu et al. 2025), micro-C XL of A364A at 1.6 kb (Costantino et al. 2020) and PCP — proximity ' +
'copy paste — of G1 cells at 1 kb (Delamarre et al.), drawn as counts since the file carries no ' +
'weights. The files share no resolution, so each is read at the one nearest the others. The Hi-C ' +
'strain is W303, whose chromosome XV lies within 26 bp of S288C’s here, so one window is one place ' +
'in all three; MNase and the S288C genes are under every map.',
files: [
'GSE151553_A364_merged.mcool',
'../meneu2025/HiC/HiC_Mmyco_G1.mcool',
'Yeast_PCP_GSM8476641_G1_rep1.mcool',
'Yeast_MNase.bw',
'S288c.gtf',
],
},
{
section: 'Demo',
folder: 'store/human',
file: 'Human_chrX_splicing.chromosomix.json',
title: 'Splicing on human chrX',
line: 'The 1D browser over hg19’s karyotype: a sashimi plot from reads, and two samples’ junctions on one axis.',
assembly: 'hg19 (GRCh37)',
provenance: 'Geuvadis · DOI 10.1038/nature12531 · nf-core/test-datasets rnasplice',
detail:
'The browser opened from UCSC’s hg19 cytoBand alone — its bands tile each chromosome, so it ' +
'declares the genome — at RPL10 in Xq28. Under the ideogram, the Ensembl gene model; one ' +
'lymphoblastoid sample’s reads as depth, with the introns they skip drawn over it as arcs ' +
'and counted; and STAR’s junction tables for a GBR and a YRI sample, both read against one ' +
'typed axis of 1 to 500 reads so their arcs compare. Pan out to FLNA to see the reverse ' +
'strand’s arcs hang below the line, or type a band — Xq13 — in the locus box.',
files: [
'hg19_cytoBand.txt',
'Homo_sapiens.GRCh37.chrX.gtf.gz',
'Geuvadis_chrX_GBR_ERR188428.bam',
'Geuvadis_chrX_GBR_ERR188428.SJ.out.tab',
'Geuvadis_chrX_YRI_ERR188454.SJ.out.tab',
],
},
{
section: 'Demo',
folder: 'store/gibcus2018',
file: 'Gibcus2018_mitosis.chromosomix.json',
title: 'Mitotic chromosome formation',
line: 'Chicken DT40 cells from G2 into prometaphase: six Hi-C maps of the time course, in three decks.',
assembly: 'galGal5',
provenance: '4DN · Gibcus et al. 2018 · DOI 10.1126/science.aao6135',
detail:
'One synchronous release from a G2 block, at G2, 5, 10, 15, 30 and 60 min (Gibcus et al. 2018, from ' +
'the 4DN Data Portal), in three tabs: chromosome 7 whole at 250 kb, where the checkerboard of ' +
'compartments is gone by 10 min and a broad mitotic band takes the diagonal; 40 Mb of chromosome 1 ' +
'at 100 kb with each time point’s first eigenvector under its map; and 4 Mb of it at 25 kb, at G2, ' +
'5 and 60 min, with their insulation on one axis as the domains disappear.',
files: [
'G2_4DNFIT479GDR.mcool',
'5m_4DNFINSJ2GYV.mcool',
'10m_4DNFIYOEGHHV.mcool',
'15m_4DNFILKIISAU.mcool',
'30m_4DNFI165SFJU.mcool',
'60m_4DNFIWHQLZTL.mcool',
'G2_4DNFILLAMSTE_compartments.bw',
'5m_4DNFI9HASBHH_compartments.bw',
'10m_4DNFIG48YRMT_compartments.bw',
'15m_4DNFIY1KBU1S_compartments.bw',
'30m_4DNFIOCFXWMD_compartments.bw',
'60m_4DNFIX92O41_compartments.bw',
'G2_4DNFI1PRBI5L_diamond.bw',
'5m_4DNFIIAPL9WO_insulation.bw',
'60m_4DNFI12IF3LX_diamond.bw',
],
},
{
section: 'Demo',
folder: 'metagenomics/mock-community',
file: 'Mock_microbial_community.chromosomix.json',
title: 'Mock microbial community',
line: '49 MAGs over 20,566 contigs in one .metacool — the multi-genome file this viewer exists for.',
assembly: 'mock community',
provenance: 'SRA SRR32680160 · DOI 10.1038/s41564-025-02108-2',
detail:
'A MetaTOR binning of a mock community profiled by metaHiC: 49 genomes over 20,566 ' +
'contigs in one 1 kb .metacool (14 MB). Lands on the genomes table, largest MAG first.',
files: ['Mock_microbial_community.metacool', 'Mock_microbial_community.mmetacool'],
dev: 'metacool',
},
{
section: 'Papers',
folder: 'store/chromosomix_paper',
file: 'Chromosomix_paper.chromosomix.json',
title: 'The Chromosomix paper',
line: 'Seven tabs, a panel each: GM12878 Hi-C with its tracks and model (Fig. 1a) and at CTCF’s sites (Fig. 2), mouse ES-cell Hi-C from the whole genome down to Sox2 (Fig. 1c, d), and three bacteria read along their arms (Fig. S3a–c).',
assembly: 'hg38 · mm10 · C. necator N-1 · B. subtilis PY79 · P. aeruginosa',
provenance: '4DN 4DNFIXP4QG5B · Rao et al. 2014 · ENCODE · 4DN 4DNFI5QJNFAT · Kubo et al. 2021 · Huang et al. 2021 · GEO GSE76513',
detail:
'The data of the paper’s figures, a tab a panel. Fig. 1a: in situ Hi-C of GM12878 (Rao et al. 2014, a 27-GB ' +
'.mcool of 4.0 billion contacts, from 4DN) at 5 kb over chr14:88.55–90.10 Mb, three cells across: the map, ' +
'with ENCODE’s CTCF ChIA-PET of GM12878 (a .hic) in its lower triangle and both as observed over expected, ' +
'its insulation and borders above it, its compartments and E1 at its left and the 4C profile from ' +
'chr14:89,150,001-89,180,000 under it, and the TAD and its borders marked; a tracks cell with ENCODE’s CTCF, ' +
'ATAC-seq and RNA-seq, CTCF’s motif, ATAC peaks, UCSC’s refGene and hg38 sequence; and the model the app ' +
'inferred from the map, its TAD borders as beads and every bead coloured by its distance to one pinned in the ' +
'central sub-TAD. Fig. 2: the same map ' +
'on chr19 at 10 kb with two labs’ CTCF ChIP-seq and ATAC-seq, and nothing computed: the Analysis column opens ' +
'each task of the figure’s chain on its recipe — insulation at four scales, the peaks on the two CTCF tracks, ' +
'the APA between each peak and the next at 2 kb, and the metaplots. Fig. 1c: in situ Hi-C of F123 mouse embryonic stem ' +
'cells (a 7-GB .mcool of 1.07 billion contacts) at five scales side by side — the genome at 2.5 Mb, chromosome 3 ' +
'as the correlation of its observed/expected at 250 kb, chr3:27–37 Mb at 10 kb, the Sox2 locus as ' +
'observed/expected at 5 kb with its loops, and Sox2 with its control region at 2 kb — each with the tracks the ' +
'panel draws under it, and under each the model the app inferred at that scale. Fig. 1d: chr3:32–36 Mb at 10 kb ' +
'with its insulation, borders and CTCF, beside chromosome 3’s model coloured by CTCF. Fig. S3a: C. necator’s ' +
'first chromosome, its origin in the middle, over the decay along the diagonal and then along both arms. ' +
'Fig. S3b: B. subtilis wild type, ΔparAB, and six times after ParB is induced. Fig. S3c: P. aeruginosa wild type, ' +
'SMC-ScpAB– and MksBEF–, as the correlation along both arms, with each strain’s E1 under its map and the ' +
'wild type’s RNA-seq (PAK, GEO GSE76513) under its own. A deck keeps ' +
'one look a map, so a panel reading one map several ways opens on one of them; each map’s score picker has the ' +
'others.',
files: [
...PAPER_HUMAN.map(([file]) => file),
'mouse/4DNFI5QJNFAT.mcool',
'mouse/mm10_genes.gtf.gz',
'mouse/4DNFIFFXFV82.bw',
'mouse/4DNFIXE23VC7.bw',
'mouse/4DNFIQYJLKKH.bw',
'mouse/4DNFI5QJNFAT_250000.compartments-e1.bw',
'mouse/4DNFI5QJNFAT_250000.compartments-ab.bed',
'mouse/4DNFI5QJNFAT_10000.insulation-w10.bw',
'mouse/4DNFI5QJNFAT_10000.borders.bed',
'mouse/4DNFI5QJNFAT_10000.domains.bed',
'mouse/4DNFI5QJNFAT_5000.loops.bedpe',
'mouse/4DNFI5QJNFAT_2500000.genome.bed3d',
'mouse/4DNFI5QJNFAT_250000.chr3.bed3d',
'mouse/4DNFI5QJNFAT_10000.chr3-27-37Mb.bed3d',
'mouse/4DNFI5QJNFAT_5000.chr3-34-35Mb.bed3d',
'mouse/4DNFI5QJNFAT_2000.Sox2-SCR.bed3d',
'C_necator/C_necator_N1_VJ_MM260.mcool',
'C_necator/C_necator_N1_VJ.fa',
'C_necator/C_necator_N1_VJ_MM260_4000.oriter-loci.bed',
'C_necator/C_necator_N1_VJ_MM260_4000.gc-skew-cumulative.bw',
...PAPER_SUBTILIS.map(([name]) => `B_subtilis/Bsubtilis_${name}.mcool`),
'B_subtilis/PY79.fa',
'B_subtilis/PY79.gff3',
...PAPER_AERUGINOSA.map(([sample]) => `P_aeruginosa/${sample}.mcool`),
'P_aeruginosa/PAO1_v3.fa',
'P_aeruginosa/GSE76513_PAK_T0_pooled.unstranded.CPM.bw',
...PAPER_AERUGINOSA.map(([sample]) => `P_aeruginosa/${sample}_8000.e1-arms.bw`),
],
},
{
section: 'Papers',
folder: 'store/meneu2025',
file: 'Meneu2025_bacterial_chromosomes.chromosomix.json',
title: 'Bacterial chromosomes in a yeast nucleus',
line: 'Yeast carrying an M. mycoides or an M. pneumoniae chromosome: each with its nucleosomes, transcription and cohesin, then both genomes whole.',
assembly: 'W303 + M. mycoides; S288C + M. pneumoniae',
provenance: 'GEO GSE217022 · DOI 10.1126/science.adm9466',
detail:
'Meneu et al. 2025, in two tabs. First the two bacterial chromosomes in G2/M, side by side at 4 kb ' +
'— M. mycoides’s 1.2 Mb and M. pneumoniae’s 818 kb, each cell on its own chromosome — with the ' +
'genes, MNase (130–200 bp fragments), RNA-seq on both strands, and Pol II and Scc1 ChIP over input ' +
'under each. Then the two strains in G1, whole genome at 16 kb, each bacterial chromosome beside ' +
'the sixteen of yeast.',
files: [
'HiC/HiC_Mmyco_G2M.mcool',
'HiC/HiC_Mpneumo_G2M.mcool',
'HiC/HiC_Mmyco_G1.mcool',
'HiC/HiC_Mpneumo_G1.mcool',
'genome_references/W303_Mmmyco.gff3',
'genome_references/S288c_Mpneumo.gtf',
'MNase/MNase_Mmyco_rep1.130-200.CPM.bw',
'MNase/MNase_Mpneumo_rep1.130-200.CPM.bw',
'RNA/RNAseq_Mmyco_rep1.fwd-CPM.bw',
'RNA/RNAseq_Mmyco_rep1.rev-CPM.bw',
'RNA/RNAseq_Mpneumo_rep1.fwd-CPM.bw',
'RNA/RNAseq_Mpneumo_rep1.rev-CPM.bw',
'ChIP/PolII_Mmyco_rep1.vs-input.bw',
'ChIP/PolII_Mpneumo_rep1.vs-input.bw',
'ChIP/Scc1_Mmyco_rep1.vs-input.bw',
'ChIP/Scc1_Mpneumo_rep1.vs-input.bw',
],
},
]
/**
* The data files under the figures, one row each.
*
* What the store lists *besides* the figures: every file the figures are made
* of, so a reader who wants the micro-C map alone, the MNase bigWig on their
* own map, or the metagenome as an `.mmetacool` ladder, has a row to press.
* Each figure's card lists its own rows under a fold (`ui/stores/GalleryView.ts`);
* a row shared by two figures — the yeast tracks, the Meneu paper's G1 Hi-C —
* is one row, under each.
*/
const DEMO_DATA: Array<{
folder: string
file: string
label: string
kind: 'map' | 'genome'
format: string
assembly: string
dataset: string
/** The dev feature this file belongs to, if it is one (§29). */
dev?: DevFeature
}> = [
...(
[
['GSE151553_A364_merged.mcool', 'Yeast micro-C, A364A', 'map', 'mcool'],
// The same counts as a Juicer .hic, which is the only contact map an
// assembly hub can name — the hub example in the paste box points at it.
['GSE151553_A364_merged.hic', 'Yeast micro-C, A364A, as a .hic', 'map', 'hic'],
['Yeast_PCP_GSM8476641_G1_rep1.mcool', 'Yeast PCP, G1', 'map', 'mcool'],
['S288c.fa', 'S288C sequence', 'genome', 'fasta'],
// The same sequence packed at two bits a base (§8.21). Beside the FASTA
// rather than instead of it, because the two are read by different roads:
// a FASTA under the whole-read limit is held whole, a `.2bit` is read by
// range and is what an assembly hub names.
['S288c.2bit', 'S288C sequence, as a .2bit', 'genome', '2bit'],
['S288c.gtf', 'Genes', 'genome', 'gtf'],
['Yeast_RNAseq.barChart', 'RNA-seq, wild type and mutant, CPM per gene', 'genome', 'barChart'],
['Yeast_ATAC.bw', 'ATAC-seq', 'genome', 'bigwig'],
['Yeast_MNase.bw', 'MNase-seq', 'genome', 'bigwig'],
['Yeast_shotgun.bw', 'Shotgun coverage', 'genome', 'bigwig'],
['Yeast_snps.vcf.gz', 'SNPs, 16 samples', 'genome', 'vcf'],
['Yeast_microC_loops.bedpe', 'Micro-C loop calls', 'genome', 'bedpe'],
] as const
).map(([file, label, kind, format]) => ({
folder: 'store/yeast',
file,
label,
kind,
format,
assembly: 'S288C (R64)',
dataset: 'Yeast',
})),
...(
[
['hg19_cytoBand.txt', 'Human karyotype, UCSC’s bands', 'cytoBand'],
['Homo_sapiens.GRCh37.chrX.gtf.gz', 'Genes, chromosome X', 'gtf'],
['Geuvadis_chrX_GBR_ERR188428.bam', 'RNA-seq reads, GBR ERR188428', 'bam'],
['Geuvadis_chrX_GBR_ERR188383.SJ.out.tab', 'Splice junctions, GBR ERR188383', 'SJ.out.tab'],
['Geuvadis_chrX_GBR_ERR188428.SJ.out.tab', 'Splice junctions, GBR ERR188428', 'SJ.out.tab'],
['Geuvadis_chrX_YRI_ERR188454.SJ.out.tab', 'Splice junctions, YRI ERR188454', 'SJ.out.tab'],
['Geuvadis_chrX_YRI_ERR204916.SJ.out.tab', 'Splice junctions, YRI ERR204916', 'SJ.out.tab'],
['Geuvadis_chrX_GBR_ERR188428.junctions.bed', 'Splice junctions as regtools writes them', 'junctions.bed'],
] as const
).map(([file, label, format]) => ({
folder: 'store/human',
file,
label,
kind: 'genome' as const,
format,
assembly: 'hg19 (GRCh37)',
dataset: 'Human, Geuvadis chrX',
})),
...(
[
['G2', 'G2_4DNFIT479GDR', 'G2_4DNFILLAMSTE', 'G2_4DNFI1PRBI5L_diamond'],
['5 min', '5m_4DNFINSJ2GYV', '5m_4DNFI9HASBHH', '5m_4DNFIIAPL9WO_insulation'],
['10 min', '10m_4DNFIYOEGHHV', '10m_4DNFIG48YRMT', null],
['15 min', '15m_4DNFILKIISAU', '15m_4DNFIY1KBU1S', null],
['30 min', '30m_4DNFI165SFJU', '30m_4DNFIOCFXWMD', null],
['60 min', '60m_4DNFIWHQLZTL', '60m_4DNFIX92O41', '60m_4DNFI12IF3LX_diamond'],
] as const
).flatMap(([when, map, e1, insulation]) => [
{ file: `${map}.mcool`, label: `DT40 Hi-C, ${when}`, kind: 'map' as const, format: 'mcool' },
{ file: `${e1}_compartments.bw`, label: `Compartments (E1), ${when}`, kind: 'genome' as const, format: 'bigwig' },
...(insulation === null
? []
: [{ file: `${insulation}.bw`, label: `Insulation, ${when}`, kind: 'genome' as const, format: 'bigwig' }]),
]).map((row) => ({ ...row, folder: 'store/gibcus2018', assembly: 'galGal5', dataset: 'Gibcus et al. 2018' })),
...(
[
['HiC/HiC_Mmyco_G2M.mcool', 'Hi-C, M. mycoides, G2/M', 'map', 'mcool', 'W303 + M. mycoides'],
['HiC/HiC_Mpneumo_G2M.mcool', 'Hi-C, M. pneumoniae, G2/M', 'map', 'mcool', 'S288C + M. pneumoniae'],
['HiC/HiC_Mmyco_G1.mcool', 'Hi-C, M. mycoides, G1', 'map', 'mcool', 'W303 + M. mycoides'],
['HiC/HiC_Mpneumo_G1.mcool', 'Hi-C, M. pneumoniae, G1', 'map', 'mcool', 'S288C + M. pneumoniae'],
['genome_references/W303_Mmmyco.gff3', 'Genes, W303 and M. mycoides', 'genome', 'gff3', 'W303 + M. mycoides'],
['genome_references/S288c_Mpneumo.gtf', 'Genes, S288C and M. pneumoniae', 'genome', 'gtf', 'S288C + M. pneumoniae'],
['MNase/MNase_Mmyco_rep1.130-200.CPM.bw', 'MNase-seq, M. mycoides', 'genome', 'bigwig', 'W303 + M. mycoides'],
['MNase/MNase_Mpneumo_rep1.130-200.CPM.bw', 'MNase-seq, M. pneumoniae', 'genome', 'bigwig', 'S288C + M. pneumoniae'],
['RNA/RNAseq_Mmyco_rep1.fwd-CPM.bw', 'RNA-seq +, M. mycoides', 'genome', 'bigwig', 'W303 + M. mycoides'],
['RNA/RNAseq_Mmyco_rep1.rev-CPM.bw', 'RNA-seq −, M. mycoides', 'genome', 'bigwig', 'W303 + M. mycoides'],
['RNA/RNAseq_Mpneumo_rep1.fwd-CPM.bw', 'RNA-seq +, M. pneumoniae', 'genome', 'bigwig', 'S288C + M. pneumoniae'],
['RNA/RNAseq_Mpneumo_rep1.rev-CPM.bw', 'RNA-seq −, M. pneumoniae', 'genome', 'bigwig', 'S288C + M. pneumoniae'],
['ChIP/PolII_Mmyco_rep1.vs-input.bw', 'Pol II over input, M. mycoides', 'genome', 'bigwig', 'W303 + M. mycoides'],
['ChIP/PolII_Mpneumo_rep1.vs-input.bw', 'Pol II over input, M. pneumoniae', 'genome', 'bigwig', 'S288C + M. pneumoniae'],
['ChIP/Scc1_Mmyco_rep1.vs-input.bw', 'Scc1 over input, M. mycoides', 'genome', 'bigwig', 'W303 + M. mycoides'],
['ChIP/Scc1_Mpneumo_rep1.vs-input.bw', 'Scc1 over input, M. pneumoniae', 'genome', 'bigwig', 'S288C + M. pneumoniae'],
] as const
).map(([file, label, kind, format, assembly]) => ({
folder: 'store/meneu2025',
file,
label,
kind,
format,
assembly,
dataset: 'Meneu et al. 2025',
})),
...(
[
...PAPER_HUMAN,
['mouse/4DNFI5QJNFAT.mcool', 'Mouse ES-cell Hi-C (4DN)', 'map', 'mcool', 'mm10'],
['mouse/mm10_genes.gtf.gz', 'Genes, UCSC mm10', 'genome', 'gtf', 'mm10'],
['mouse/4DNFIFFXFV82.bw', 'CTCF ChIP-seq', 'genome', 'bigwig', 'mm10'],
['mouse/4DNFIXE23VC7.bw', 'H3K27ac ChIP-seq', 'genome', 'bigwig', 'mm10'],
['mouse/4DNFIQYJLKKH.bw', 'H3K4me3 ChIP-seq', 'genome', 'bigwig', 'mm10'],
['mouse/4DNFI5QJNFAT_250000.compartments-e1.bw', 'Compartments (E1) of chromosome 3, 250 kb', 'genome', 'bigwig', 'mm10'],
['mouse/4DNFI5QJNFAT_250000.compartments-ab.bed', 'A and B compartments of chromosome 3, 250 kb', 'genome', 'bed', 'mm10'],
['mouse/4DNFI5QJNFAT_10000.insulation-w10.bw', 'Diamond insulation, 10 kb', 'genome', 'bigwig', 'mm10'],
['mouse/4DNFI5QJNFAT_10000.borders.bed', 'Borders on the insulation, 10 kb', 'genome', 'bed', 'mm10'],
['mouse/4DNFI5QJNFAT_10000.domains.bed', 'Domains between the borders, 10 kb', 'genome', 'bed', 'mm10'],
['mouse/4DNFI5QJNFAT_5000.loops.bedpe', 'Loops on chromosome 3, 5 kb', 'genome', 'bedpe', 'mm10'],
['mouse/4DNFI5QJNFAT_2500000.genome.bed3d', '3D model of the genome, 2.5 Mb', 'genome', 'bed3d', 'mm10'],
['mouse/4DNFI5QJNFAT_250000.chr3.bed3d', '3D model of chromosome 3, 250 kb', 'genome', 'bed3d', 'mm10'],
['mouse/4DNFI5QJNFAT_10000.chr3-27-37Mb.bed3d', '3D model of chr3:27–37 Mb, 10 kb', 'genome', 'bed3d', 'mm10'],
['mouse/4DNFI5QJNFAT_5000.chr3-34-35Mb.bed3d', '3D model of the Sox2 locus, 5 kb', 'genome', 'bed3d', 'mm10'],
['mouse/4DNFI5QJNFAT_2000.Sox2-SCR.bed3d', '3D model of Sox2 and its control region, 2 kb', 'genome', 'bed3d', 'mm10'],
['C_necator/C_necator_N1_VJ_MM260.mcool', 'C. necator N-1 Hi-C (MM260)', 'map', 'mcool', 'C. necator N-1'],
['C_necator/C_necator_N1_VJ.fa', 'C. necator N-1 sequence', 'genome', 'fasta', 'C. necator N-1'],
['C_necator/C_necator_N1_VJ_MM260_4000.oriter-loci.bed', 'Origins and termini', 'genome', 'bed', 'C. necator N-1'],
['C_necator/C_necator_N1_VJ_MM260_4000.gc-skew-cumulative.bw', 'Cumulative GC skew, 4 kb', 'genome', 'bigwig', 'C. necator N-1'],
...PAPER_SUBTILIS.map(
([name, label]) =>
[`B_subtilis/Bsubtilis_${name}.mcool`, `B. subtilis Hi-C, ${label}`, 'map', 'mcool', 'B. subtilis PY79'] as const,
),
['B_subtilis/PY79.fa', 'B. subtilis PY79 sequence', 'genome', 'fasta', 'B. subtilis PY79'],
['B_subtilis/PY79.gff3', 'Genes, B. subtilis PY79', 'genome', 'gff3', 'B. subtilis PY79'],
...PAPER_AERUGINOSA.map(
([sample, label]) =>
[`P_aeruginosa/${sample}.mcool`, `P. aeruginosa Hi-C, ${label}`, 'map', 'mcool', 'P. aeruginosa (PAO1_v3)'] as const,
),
['P_aeruginosa/PAO1_v3.fa', 'P. aeruginosa sequence (PAO1_v3)', 'genome', 'fasta', 'P. aeruginosa (PAO1_v3)'],
[
'P_aeruginosa/GSE76513_PAK_T0_pooled.unstranded.CPM.bw',
'RNA-seq, PAK, CPM (GEO GSE76513)',
'genome',
'bigwig',
'P. aeruginosa (PAO1_v3)',
],
...PAPER_AERUGINOSA.map(
([sample, label]) =>
[`P_aeruginosa/${sample}_8000.e1-arms.bw`, `E1 along both arms, ${label}, 8 kb`, 'genome', 'bigwig', 'P. aeruginosa (PAO1_v3)'] as const,
),
] as const
).map(([file, label, kind, format, assembly]) => ({
folder: 'store/chromosomix_paper',
file,
label,
kind,
format,
assembly,
dataset: 'The Chromosomix paper',
})),
{
folder: 'metagenomics/mock-community',
file: 'Mock_microbial_community.metacool',
label: 'Mock community, 49 MAGs, 1 kb',
kind: 'map',
format: 'metacool',
assembly: 'mock community',
dataset: 'Mock microbial community',
dev: 'metacool',
},
{
folder: 'metagenomics/mock-community',
file: 'Mock_microbial_community.mmetacool',
label: 'Mock community, resolution ladder',
kind: 'map',
format: 'mmetacool',
assembly: 'mock community',
dataset: 'Mock microbial community',
dev: 'metacool',
},
]
/**
* A file's path under `demo/`, from the folder that names it — `..` stepped up
* out of, so a card's `../meneu2025/…` and the row the Meneu card lists are one
* path and one row.
*/
function under(folder: string, file: string): string {
const out: string[] = []
for (const part of `${folder}/${file}`.split('/')) {
if (part === '..') out.pop()
else if (part !== '' && part !== '.') out.push(part)
}
return out.join('/')
}
/**
* The annotation files published beside a demo map, and where each belongs.
*
* Keyed by the map's file name rather than by its URL, because the URL depends
* on where the app is served from and the pairing does not. All seven are on the
* map's own assembly — Ensembl's R64-1-1, whose `I`…`XVI` the map spells
* `chrI`…`chrXVI`, which §8.2 reads as the same names — which is exactly what
* makes them worth offering as one click: a reader gets a complete, correct
* picture without hunting for seven URLs, and the overlap report has something
* to report success about.
*
* Not the same thing as the figures above, and both are worth having. A figure
* is a composed session — the tracks placed, coloured and grouped — and this is
* the whole shelf, offered to a reader who opened the map on its own (its row
* under the yeast cards, or its URL) and wants the rest of it.
*/
interface DemoAnnotation {
file: string
/** A short name, since the file's own is a sentence about the experiment. */
label: string
}
/**
* The shelf beside one map: the dataset folder it lives in, and what is in it.
*
* The folder is recorded even though {@link demoAnnotationsFor} never reads it
* — that function resolves against the *map's own URL*, which is the only thing
* that also works for a copy of the folder served from somewhere else. It is
* here for the test, which has to find these files on disk or in the manifest.
*/
const DEMO_ANNOTATIONS: Record<string, { folder: string; entries: DemoAnnotation[] }> = {
'GSE151553_A364_merged.mcool': {
folder: 'store/yeast',
entries: [
{ file: 'S288c.gtf', label: 'genes' },
{ file: 'Yeast_RNAseq.barChart', label: 'RNA-seq' },
{ file: 'Yeast_ATAC.bw', label: 'ATAC' },
{ file: 'Yeast_MNase.bw', label: 'MNase' },
{ file: 'Yeast_shotgun.bw', label: 'shotgun' },
{ file: 'Yeast_snps.vcf.gz', label: 'SNPs' },
{ file: 'Yeast_microC_loops.bedpe', label: 'loops' },
],
},
}
/** One loadable annotation, with the URL resolved for wherever this is served. */
export interface DemoAnnotationLink extends DemoAnnotation {
url: string
}
/**
* The annotations published beside the map at `uri`, or `[]`.
*
* Two sources, asked in this order, and the order is the argument. A store row
* that carried `tracks` said so **about this exact file** — the catalogue's
* publisher named them beside the URI the reader just clicked — where the table
* below matches on a *file name*, which is a guess that happens to be a good
* one. A specific answer beats a general one, so a registered shelf wins
* outright rather than being concatenated.
*
* The table itself is matched on the file name at the end of the URI, so it
* works for the bucket, for a local copy of `demo/store/yeast/` served from
* anywhere else, and for a fork publishing the same folder under its own name — and not
* for a *local* file of the same name, which would be someone else's data under
* a familiar name.
*/
export function demoAnnotationsFor(uri: string): DemoAnnotationLink[] {
const registered = shelves.get(splitUri(uri).path)
if (registered !== undefined) return registered.map((link) => ({ ...link }))
if (!/^https?:\/\//i.test(uri)) return []
// The file half: an `.mcool` is opened at one of its entries, and the name
// the table is keyed by is the file's, not `1600`.
const file = splitUri(uri).path.split('?')[0].split('#')[0]
const name = file.split('/').pop() ?? ''
const shelf = DEMO_ANNOTATIONS[name]
if (shelf === undefined) return []
const base = file.slice(0, file.length - name.length)
return shelf.entries.map((entry) => ({ ...entry, url: `${base}${entry.file}` }))
}
/**
* The published tracks to *offer*, which is none once a session has its own.
*
* A **restored session already names the tracks it wants** and is a moment away
* from putting them on screen. Offered anyway, the button appeared under rows
* that were already appearing and proposed seven more, most of them the same files
* a second time. `restoring` covers an imported workspace, a `?config=` link and
* a plain reload alike, because all three arrive the same way.
*/
export function demoAnnotationsToOffer(
uri: string,
options: { restoring: boolean },
): DemoAnnotationLink[] {
return options.restoring ? [] : demoAnnotationsFor(uri)
}
/**
* Every published annotation, as its path under `demo/`, for the test that
* checks they are on disk — and so for the sync that puts them on the bucket.
*/
export const DEMO_ANNOTATION_FILES: readonly string[] = Object.values(DEMO_ANNOTATIONS).flatMap(
(shelf) => shelf.entries.map((entry) => under(shelf.folder, entry.file)),
)
/**
* The workspace files this module offers, as their paths under `demo/`, for the
* test that reads every one of them off disk and opens what it names.
*/
export const DEMO_FILES: readonly string[] = DEMO.map((entry) => under(entry.folder, entry.file))
/** The data files the store lists, as their paths under `demo/`, for the same test. */
export const DEMO_DATA_FILES: readonly string[] = DEMO_DATA.map((entry) =>
under(entry.folder, entry.file),
)
/**
* Where the demos are read from, absolute, wherever this is running.
*
* Resolved against the page when there is one, even though both candidates are
* already absolute: it costs nothing, and it is what lets the escape hatch be a
* *relative* base — `DEMO_BASE=/demo/ npm run build` for a copy served beside
* the app. The `typeof` guard is for the node test runtime, which has no
* `window` and in which this is still worth calling.
*/
function demoBase(): string {
const base = DEMO_BASE !== '' ? DEMO_BASE : DEMO_BUCKET
if (typeof window === 'undefined') return base
try {
return new URL(base, window.location.href).href
} catch {
return base
}
}
/**
* The columns the lab's store declares.
*
* Every card and every file row is drawn from these, so what a column is
* called here is what the gallery reads: `section` is the heading a card stands
* under, `provenance` and `detail` are the card's chip and its fold, `format`
* and `dataset` are the file rows' chip and their grouping. A store somebody
* else writes may call its columns anything; this one is read by a front that
* knows it.
*/
const DEMO_COLUMNS = [
{ key: 'section', label: 'Section' },
{ key: 'assembly', label: 'Assembly' },
{ key: 'dataset', label: 'Dataset' },
{ key: 'format', label: 'Format' },
{ key: 'provenance', label: 'Provenance' },
{ key: 'detail', label: 'What is on screen' },
]
/**
* The lab's store, inline: the figures, under their sections, then the data files.
*
* Inline rather than fetched because it is the one store that costs no request
* and the only one that is certainly there (§24.2). Every URI is absolute
* already, so `resolveStore` has nothing left to do to them: an inline store
* has no URL of its own to be relative to.
*/
export function demosStore(): StoreFile {
const base = demoBase()
return {
kind: STORE_KIND,
version: STORE_VERSION,
name: 'RSG lab data',
description:
'Composed figures over the lab’s published data, and the files they are made of. Every ' +
'one is read over the network exactly as a file on your own bucket would be.',
base,
columns: DEMO_COLUMNS,
entries: [
// A figure or a file that belongs to a dev feature is not listed while
// the switch is off (§29): the store is on the landing page, which is
// the first place a reader would learn of it.
...DEMO.filter(shown).map(
(entry): StoreEntry => ({
label: entry.title,
uri: `${base}${under(entry.folder, entry.file)}`,
kind: 'workspace',
note: entry.line,
fields: {
section: entry.section,
assembly: entry.assembly,
provenance: entry.provenance,
detail: entry.detail,
// The files the figure is made of, as the URIs of the rows below,
// so the card lists them under its fold without a second lookup.
// `|`-joined because a field is one string; no URI carries a bar.
files: entry.files.map((file) => `${base}${under(entry.folder, file)}`).join('|'),
},
}),
),
...DEMO_DATA.filter(shown).map(
(entry): StoreEntry => ({
label: entry.label,
uri: `${base}${under(entry.folder, entry.file)}`,
kind: entry.kind,
fields: { assembly: entry.assembly, dataset: entry.dataset, format: entry.format },
}),
),
],
}
}
/**
* One of the store's figures, by its file: what the card calls it, its one line
* and its provenance, and the address it is read from — for the landing page's
* example sessions (§24.11), which open two of these figures by name rather than
* through the drawer. Read from the same list the store's cards are, so a
* figure renamed, moved to another folder or served from `DEMO_BASE` is renamed,
* moved and served for both.
*/
export function demoFigure(file: string): { uri: string; title: string; line: string; provenance: string } {
const entry = DEMO.find((figure) => figure.file === file)
if (entry === undefined) throw new Error(`The lab's store has no figure ${file}.`)
return {
uri: `${demoBase()}${under(entry.folder, entry.file)}`,
title: entry.title,
line: entry.line,
provenance: entry.provenance,
}
}
/** Whether a figure or a file of the lab's store is listed: always, unless its dev feature is off. */
function shown(entry: { dev?: DevFeature }): boolean {
return entry.dev === undefined || devFeature(entry.dev)
}
// ---------------------------------------------------------------------------
// Shelves a store brought with it
// ---------------------------------------------------------------------------
/**
* The tracks a store row named, held until the file it belongs to is opened.
*
* A store entry may carry `tracks` — the bigWigs the same experiment published
* beside the map (§24.1) — and they are the same *offer* the demo map's ten
* annotations are: here is a set of tracks to look at, for a reader who has
* none. So they are answered through the same question rather than a second
* one, and `Session` needs no idea that a store exists.
*
* In memory and never in storage, deliberately. The offer is about the file
* being opened right now; a shelf that outlived the tab would be a promise to
* fetch URLs out of a catalogue the reader has since forgotten.
*/
const shelves = new Map<string, DemoAnnotationLink[]>()
/**
* The shelves that were **asked for** rather than merely brought along.
*
* *Open with its tracks* says what it does, so it has to do it: a reader who
* presses those words and gets a genome and a button has been given the thing
* they pressed past. Every other road to the same file — the row's own open
* verb, a `?store=` link, a dropped copy — keeps the offer, because opening a
* genome is not a request for eight more files.
*
* A set beside the map rather than a field on the link, because it is a fact
* about the *gesture* and not about the tracks: the same shelf is asked for
* through one door and offered through another, and a flag on each link would
* have to be rewritten on every registration to say so.
*/
const asked = new Set<string>()
/**
* Remember the tracks published beside `uri`, so the Tracks card can offer them.
*
* Keyed on the **absolute URI's file half**, so it answers for the same file
* opened at an entry (`file.mcool::resolutions/1000`) as for the file itself —
* which is the common case rather than the exotic one, since a collection
* opened at its root lands on one of its entries and the URI the session ends
* up on is not the one the store row carried.
*
* Last registration wins: two stores naming the same map is not a conflict worth
* a policy, and the one the reader has just clicked is the one they mean.
*/
export function registerShelf(
uri: string,
tracks: ReadonlyArray<{ label: string; url: string }>,
options: { asked?: boolean } = {},
): void {
const key = splitUri(uri).path
if (key === '') return
if (tracks.length === 0) {
shelves.delete(key)
asked.delete(key)
return
}
if (options.asked === true) asked.add(key)
else asked.delete(key)
shelves.set(
key,
tracks.map((track) => ({
// The file name is what a track row falls back to when it has no label,
// and what `demo-examples.test.ts` checks the published set against;
// derived here rather than asked for, since a store carries a label and a
// URL and nothing in between.
file: track.url.split('?')[0].split('#')[0].split('/').pop() ?? track.url,
label: track.label,
url: track.url,
})),
)
}
/**
* Whether this file's shelf was asked for, and should be loaded rather than
* offered.
*
* Read once, by the session building its cards, and **cleared as it is read**:
* the gesture is spent. Without that, closing the tracks and reopening the same
* genome would bring all eight back, which is the one reading of *open with its
* tracks* nobody wants — the reader has just said no to them.
*/
export function shelfWasAsked(uri: string): boolean {
const key = splitUri(uri).path
if (!asked.has(key)) return false
asked.delete(key)
return true
}
/** Forget every registered shelf. Tests only — the map is otherwise per page. */
export function clearShelves(): void {
shelves.clear()
asked.clear()
}
// ---------------------------------------------------------------------------
// Worked examples for the paste boxes
// ---------------------------------------------------------------------------
/**
* A hub and a store, ready to paste — and **ready to open**.
*
* The point of an example beside a paste box is not to show syntax, which the
* specification does better. It is to be something a reader can press *open*
* on and then edit into their own: the two below name the published demo files,
* so each of them draws a shelf on the first press wherever this build is
* served from, and the reader's first edit is to a thing that already worked
* rather than to a template they cannot tell the state of.
*
* Which means they are held to the same bar as any other demo: every URL is one
* of {@link DEMO_DATA_FILES} or {@link DEMO_ANNOTATION_FILES}, so the test that
* checks those covers these too, and neither example can come to name a file
* the bucket does not have.
*
* The hub is an **assembly hub**: it names the store's own `.2bit` through
* `twoBitPath`, which is the only way a hub carries its own sequence and the
* rung of §24.10's ladder worth demonstrating. It is the text a reader wrote and
* checked against the bucket, rather than one composed here and argued about,
* moved onto the store's R64 files with the rest of the yeast demo — the same
* genome line, the same composite of two, the same map — and the URLs are built from
* {@link DEMO_BUCKET} rather than from {@link demoBase} for a reason that only
* shows up under `DEMO_BASE`: a local copy of `demo/` has these files, but the
* example is a thing to *press*, and a base that pointed it at a directory
* somebody is still filling would break the one promise it makes.
*/
export function exampleHubText(): string {
return [
'# A UCSC track hub, in one file: the hub line, its genome, and its tracks.',
'# Three separate files (hub.txt, genomes.txt, trackDb.txt) can be pasted',
'# one after another in the same text box. ',
'',
'hub exampleHub',
'shortLabel Example hub',
'longLabel Yeast demo data from RSG lab',
'useOneFile on',
'',
'genome R64-1-1',
'organism Saccharomyces cerevisiae',
` twoBitPath ${DEMO_BUCKET}store/yeast/S288c.2bit`,
'',
'track signal',
'compositeTrack on',
'shortLabel Signal',
'longLabel Two tracks, grouped as their hub groups them',
'type bigWig',
'',
' track mnase',
' parent signal on',
' shortLabel MNase',
' longLabel Nucleosome occupancy',
` bigDataUrl ${DEMO_BUCKET}store/yeast/Yeast_MNase.bw`,
' type bigWig',
'',
' track atac',
' parent signal on',
' shortLabel ATAC',
' longLabel ATAC-seq accessibility',
` bigDataUrl ${DEMO_BUCKET}store/yeast/Yeast_ATAC.bw`,
' type bigWig',
'',
'track contacts',
'shortLabel Micro-C map',
'longLabel A contact map, which opens through the map door',
`bigDataUrl ${DEMO_BUCKET}store/yeast/GSE151553_A364_merged.hic`,
'type hic',
'',
].join('\n')
}
/**
* The store-file counterpart: the same two demo files, as a shelf.
*
* Deliberately small. A store's whole shape is `kind`, `columns` and `entries`,
* and an example with twenty rows would bury that under nineteen copies of the
* one line worth reading.
*/
export function exampleStoreText(): string {
const at = `${demoBase()}store/yeast/`
return `${JSON.stringify(
{
kind: STORE_KIND,
version: STORE_VERSION,
name: 'Example shelf',
description: 'Two of the demo files, as a store you can edit',
columns: [
{ key: 'assay', label: 'Assay' },
{ key: 'assembly', label: 'Assembly' },
],
entries: [
{
label: 'Yeast micro-C, A364A',
uri: `${at}GSE151553_A364_merged.mcool`,
kind: 'map',
note: 'A contact map, which opens through the map door',
fields: { assay: 'Micro-C', assembly: 'R64-1-1' },
tracks: [{ label: 'MNase', url: `${at}Yeast_MNase.bw` }],
},
{
label: 'MNase',
uri: `${at}Yeast_MNase.bw`,
kind: 'genome',
note: 'A bigWig, which opens as a browser over its own genome',
fields: { assay: 'MNase-seq', assembly: 'R64-1-1' },
},
],
},
null,
2,
)}\n`
}
/**
* Every URL the two examples name, as their paths under `demo/`.
*
* For the test that reads the published demo files off disk, or off the store's
* manifest: an example that names a file the bucket does not have is an example
* that fails on its first press, which is the one thing worse than no example at all.
*/
export const EXAMPLE_FILES: readonly string[] = [
'store/yeast/S288c.2bit',
'store/yeast/Yeast_MNase.bw',
'store/yeast/Yeast_ATAC.bw',
'store/yeast/GSE151553_A364_merged.hic',
'store/yeast/GSE151553_A364_merged.mcool',
]
|