@sjcrh/proteinpaint-types 2.188.1 → 2.190.0

package/src/routes/termdb.descrstats.ts

@@ -1,75 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { Filter } from '../filter.ts'
-import type { TermWrapper } from '../terms/tw.ts'
-
-export type DescrStatsRequest = {
-	/** genome label in the serverconfig.json */
-	genome: string
-	/** dataset label for the given genome */
-	dslabel: string
-	embedder: string
-	/** wrapper of a numeric term, q.mode can be any as getData() will always pull sample-level values for summarizing */
-	tw: TermWrapper
-	/** if true, the (violin) plot is in log scale and must exclude 0-values from the stat */
-	logScale?: boolean
-	/** optional pp filter */
-	filter?: Filter
-	/** optional gdc filter */
-	filter0?: any
-}
-
-export type DescrStats = {
-	[key: string]: {
-		key: string
-		label: string
-		value: number
-	}
-}
-
-export type DescrStatsResponse = DescrStats
-
-export const descrStatsPayload: RoutePayload = {
-	request: {
-		typeId: 'DescrStatsRequest'
-	},
-	response: {
-		typeId: 'DescrStatsResponse'
-	},
-	examples: [
-		{
-			request: {
-				body: {
-					genome: 'hg38-test',
-					dslabel: 'TermdbTest',
-					embedder: 'localhost',
-					tw: { term: { id: 'hrtavg' }, q: { mode: 'continuous' } },
-					filter: {
-						type: 'tvslst',
-						in: true,
-						join: '',
-						lst: [
-							{
-								tag: 'cohortFilter',
-								type: 'tvs',
-								tvs: {
-									term: {
-										name: 'Cohort',
-										type: 'categorical',
-										values: { ABC: { label: 'ABC' }, XYZ: { label: 'XYZ' } },
-										id: 'subcohort',
-										isleaf: false,
-										groupsetting: { disabled: true }
-									},
-									values: [{ key: 'ABC', label: 'ABC' }]
-								}
-							}
-						]
-					}
-				}
-			},
-			response: {
-				header: { status: 200 }
-			}
-		}
-	]
-}

package/src/routes/termdb.diffMeth.ts

@@ -1,63 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { DataEntry, VolcanoData, VolcanoRenderRequest } from './termdb.DE.js'
-
-export type DiffMethRequest = {
-	/** Genome build name */
-	genome: string
-	/** Dataset label */
-	dslabel: string
-	/** Object containing two arrays of samples for differential methylation analysis */
-	samplelst: any
-	/** Minimum non-NA samples required per group (default 3) */
-	min_samples_per_group?: number
-	/** Term for confounding variable 1 (if present) */
-	tw?: any
-	/** Term for confounding variable 2 (if present) */
-	tw2?: any
-	/** Option to return early with actual number of samples with methylation values */
-	preAnalysis?: boolean
-	/** Parameters for the server-side `da` Rust renderer. Always required — the
-	 * server always returns a rendered PNG plus the threshold-passing rows. */
-	volcanoRender: VolcanoRenderRequest
-}
-
-/** Response when DiffMethRequest.preAnalysis === true. Returns per-group
- * sample counts (keyed by group name) plus an optional validation alert. */
-export type DiffMethPreAnalysisResponse = {
-	data: Record<string, number | string>
-}
-
-/** Response for a full differential methylation run (preAnalysis absent/false). */
-export type DiffMethFullResponse = {
-	/** The volcano payload — per-promoter interactive dots + PNG + extents +
-	 * totals. See VolcanoData for details. */
-	data: VolcanoData<DiffMethEntry>
-	/** Effective sample size for group 1 */
-	sample_size1: number
-	/** Effective sample size for group 2 */
-	sample_size2: number
-}
-
-export type DiffMethResponse = DiffMethPreAnalysisResponse | DiffMethFullResponse
-
-export type DiffMethEntry = DataEntry & {
-	/** ENCODE CRE promoter ID (e.g. EH38E3756858) */
-	promoter_id: string
-	/** Gene symbol(s) associated with the promoter (comma-separated if multiple) */
-	gene_name: string
-	/** Chromosome (e.g. "chr1") */
-	chr: string
-	/** Promoter start coordinate (0-based) */
-	start: number
-	/** Promoter end coordinate (exclusive) */
-	stop: number
-}
-
-export const diffMethPayload: RoutePayload = {
-	request: {
-		typeId: 'DiffMethRequest'
-	},
-	response: {
-		typeId: 'DiffMethResponse'
-	}
-}

package/src/routes/termdb.dmr.ts

@@ -1,121 +0,0 @@
-import type { Filter } from '../filter.ts'
-import type { RoutePayload } from './routeApi.ts'
-
-export type TermdbDmrRequest = {
-	genome: string
-	dslabel: string
-	/** list of samples from each group */
-	group1: Sample[]
-	group2: Sample[]
-	/** query region */
-	chr: string
-	start: number
-	stop: number
-	/** DMRCate lambda parameter: Gaussian kernel bandwidth in nucleotides (default 1000) */
-	lambda?: number
-	/** DMRCate C parameter: scaling factor for kernel width (default 2) */
-	C?: number
-	/** FDR cutoff for CpG significance (default 0.05) */
-	fdr_cutoff?: number
-	/** display name for group1 (e.g. from volcano plot) */
-	group1Name?: string
-	/** display name for group2 (e.g. from volcano plot) */
-	group2Name?: string
-	/** Block width in CSS pixels for server-side track rendering (default 800) */
-	blockWidth?: number
-	/** Device pixel ratio for server-side track rendering (default 1) */
-	devicePixelRatio?: number
-	/** Maximum region size (bp) to show LOESS curves (default 50000) */
-	maxLoessRegion?: number
-	/** Group/DMR colors for server-side track rendering */
-	colors?: { group1: string; group2: string; hyper: string; hypo: string }
-	/** Backend engine: 'rust' (genome-wide eBayes, default) or 'r' (DMRCate via cached limma) */
-	backend?: 'rust' | 'r'
-	filter?: Filter
-	__protected__?: any
-}
-
-type Sample = {
-	sampleId: number | string
-	sample: string
-}
-
-export type DmrLoessCurves = {
-	/** Evenly spaced genomic positions where LOESS was evaluated */
-	positions: number[]
-	/** LOESS fitted values for group 1 (control) */
-	group1_fitted: number[]
-	/** Lower 95% CI bound for group 1 */
-	group1_ci_lower: number[]
-	/** Upper 95% CI bound for group 1 */
-	group1_ci_upper: number[]
-	/** LOESS fitted values for group 2 (case) */
-	group2_fitted: number[]
-	/** Lower 95% CI bound for group 2 */
-	group2_ci_lower: number[]
-	/** Upper 95% CI bound for group 2 */
-	group2_ci_upper: number[]
-}
-
-export type DmrDiagnostic = {
-	probes: {
-		positions: number[]
-		mean_group1: (number | null)[]
-		mean_group2: (number | null)[]
-		fdr: number[]
-		logFC: (number | null)[]
-	}
-	probe_spacings: number[]
-	/** LOESS smoothed curves with 95% CI for both groups */
-	loess?: DmrLoessCurves
-	/** Total probes analyzed genome-wide for eBayes */
-	total_probes_analyzed?: number
-	/** Peak RSS memory in MB */
-	peak_memory_mb?: number
-	/** Starting RSS memory in MB */
-	start_memory_mb?: number
-	/** Total elapsed time in milliseconds */
-	elapsed_ms?: number
-	/** Server-rendered track PNG as data URI (Rust backend only) */
-	track_png?: string | null
-}
-
-export type TermdbDmrSuccessResponse = {
-	status: 'ok'
-	dmrs: {
-		chr: string
-		start: number
-		stop: number
-		/** Number of CpG sites in this DMR */
-		no_cpgs: number
-		/** Minimum FDR from the kernel-smoothed estimate across the region */
-		min_smoothed_fdr: number
-		/** Harmonic mean of individual CpG FDR-corrected p-values */
-		HMFDR: number
-		/** Maximum methylation difference (beta-scale) within the DMR */
-		maxdiff: number
-		/** Mean methylation difference across the DMR */
-		meandiff: number
-		/** hyper = case hypermethylated relative to control; hypo = opposite */
-		direction: 'hyper' | 'hypo'
-		/** Comma-separated gene symbols overlapping the DMR */
-		overlapping_genes?: string | null
-	}[]
-	/** Diagnostic data: per-CpG probe means and statistics */
-	diagnostic?: DmrDiagnostic
-}
-
-export type TermdbDmrErrorResponse = {
-	error: string
-}
-
-export type TermdbDmrResponse = TermdbDmrSuccessResponse | TermdbDmrErrorResponse
-
-export const TermdbDmrPayload: RoutePayload = {
-	request: {
-		typeId: 'TermdbDmrRequest'
-	},
-	response: {
-		typeId: 'TermdbDmrResponse'
-	}
-}

package/src/routes/termdb.filterTermValues.ts

@@ -1,23 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type FilterTermValuesRequest = {
-	terms: any[]
-	filters: { [termid: string]: any[] }
-}
-
-export type FilterTermValuesResponse = {
-	[termId: string]: {
-		label: string
-		value: string
-		disabled?: boolean
-	}[]
-}
-
-export const FilterTermValuesPayload: RoutePayload = {
-	request: {
-		typeId: 'FilterTermValuesRequest'
-	},
-	response: {
-		typeId: 'FilterTermValuesResponse'
-	}
-}

package/src/routes/termdb.isoformAvailability.ts

@@ -1,22 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type TermdbIsoformAvailabilityRequest = {
-	genome: string
-	dslabel: string
-	/** candidate ENST IDs to check */
-	isoforms: string[]
-}
-
-export type TermdbIsoformAvailabilityResponse = {
-	/** subset of input isoforms that have data in the HDF5 */
-	available: string[]
-}
-
-export const TermdbIsoformAvailabilityPayload: RoutePayload = {
-	request: {
-		typeId: 'TermdbIsoformAvailabilityRequest'
-	},
-	response: {
-		typeId: 'TermdbIsoformAvailabilityResponse'
-	}
-}

package/src/routes/termdb.numericcategories.ts

@@ -1,32 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { Filter } from '../filter.ts'
-
-export type NumericCategoriesRequest = {
-	/** a user-defined genome label in the serverconfig.json, hg38, hg19, mm10, etc */
-	genome: string
-	/** a user-defined dataset label in the serverconfig.json, such as ClinVar, SJLife, GDC, etc */
-	dslabel: string
-	embedder: string
-	/** term id string */
-	tid: string
-	filter?: Filter
-}
-
-interface entries {
-	value: number
-	samplecount: number
-}
-
-export type NumericCategoriesResponse = {
-	lst: entries[]
-}
-
-export const numericCategoriesPayload: RoutePayload = {
-	request: {
-		typeId: 'NumericCategoriesRequest'
-	},
-	response: {
-		typeId: 'NumericCategoriesResponse'
-	},
-	// examples: []
-}

package/src/routes/termdb.percentile.ts

@@ -1,67 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { Filter } from '../filter.ts'
-import type { Term } from '../terms/term.ts'
-
-export type PercentileRequest = {
-	/** a user-defined genome label in the serverconfig.json, hg38, hg19, mm10, etc */
-	genome: string
-	/** a user-defined dataset label in the serverconfig.json, such as ClinVar, SJLife, GDC, etc */
-	dslabel: string
-	embedder: string
-	getpercentile: number[]
-	/** term id string */
-	term: Term
-	filter?: Filter
-	filter0?: any
-}
-
-export type PercentileResponse = {
-	values: number[]
-}
-
-export const percentilePayload: RoutePayload = {
-	request: {
-		typeId: 'PercentileRequest'
-	},
-	response: {
-		typeId: 'PercentileResponse'
-	},
-	examples: [
-		{
-			request: {
-				body: {
-					genome: 'hg38-test',
-					dslabel: 'TermdbTest',
-					embedder: 'localhost',
-					getpercentile: [50],
-					term: { id: 'agedx' },
-					filter: {
-						type: 'tvslst',
-						in: true,
-						join: '',
-						lst: [
-							{
-								tag: 'cohortFilter',
-								type: 'tvs',
-								tvs: {
-									term: {
-										name: 'Cohort',
-										type: 'categorical',
-										values: { ABC: { label: 'ABC' }, XYZ: { label: 'XYZ' } },
-										id: 'subcohort',
-										isleaf: false,
-										groupsetting: { disabled: true }
-									},
-									values: [{ key: 'ABC', label: 'ABC' }]
-								}
-							}
-						]
-					}
-				}
-			},
-			response: {
-				header: { status: 200 }
-			}
-		}
-	]
-}

package/src/routes/termdb.profileFormScores.ts

@@ -1,26 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type ProfileFormScoresRequest = {
-	scoreTerms: any[]
-	scScoreTerms?: any[]
-	filter?: any
-	userSites?: string[]
-	site?: string
-	isAggregate?: boolean
-}
-
-export type ProfileFormScoresResponse = {
-	term2Score: { [termId: string]: { [key: string]: number } }
-	sites: { label: string; value: string }[]
-	hospital?: string
-	n: number
-}
-
-export const ProfileFormScoresPayload: RoutePayload = {
-	request: {
-		typeId: 'ProfileFormScoresRequest'
-	},
-	response: {
-		typeId: 'ProfileFormScoresResponse'
-	}
-}

package/src/routes/termdb.profileForms2Scores.ts

@@ -1,25 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type ProfileForms2ScoresRequest = {
-	// q is optional: term wrappers from getMultivalueTWs() carry no q field,
-	// and JSON.stringify drops `q: undefined`, so the field may be absent on the wire.
-	scoreTerms: { term: { id: string }; q?: any }[]
-	scScoreTerms?: { term: { id: string }; q?: any }[]
-	filter?: any
-	filterByUserSites?: boolean
-}
-
-export type ProfileForms2ScoresResponse = {
-	term2Score: { [termId: string]: { [category: string]: number } }
-	sites: { label: string; value: string }[]
-	n: number
-}
-
-export const ProfileForms2ScoresPayload: RoutePayload = {
-	request: {
-		typeId: 'ProfileForms2ScoresRequest'
-	},
-	response: {
-		typeId: 'ProfileForms2ScoresResponse'
-	}
-}

package/src/routes/termdb.profileScores.ts

@@ -1,27 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type ProfileScoresRequest = {
-	scoreTerms: { score: any; maxScore?: any }[]
-	filter?: any
-	isRadarFacility?: boolean
-	userSites?: string[]
-	sites?: string[]
-	isAggregate?: boolean
-	facilityTW?: any
-}
-
-export type ProfileScoresResponse = {
-	term2Score: { [termId: string]: number }
-	sites: { label: string; value: string }[]
-	hospital?: string
-	n: number
-}
-
-export const ProfileScoresPayload: RoutePayload = {
-	request: {
-		typeId: 'ProfileScoresRequest'
-	},
-	response: {
-		typeId: 'ProfileScoresResponse'
-	}
-}

package/src/routes/termdb.proteome.ts

@@ -1,13 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type TermdbProteomeRequest = any
-export type TermdbProteomeResponse = any
-
-export const termdbProteomePayload: RoutePayload = {
-	request: {
-		typeId: 'TermdbProteomeRequest'
-	},
-	response: {
-		typeId: 'TermdbProteomeResponse'
-	}
-}

package/src/routes/termdb.rootterm.ts

@@ -1,49 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type RootTermRequest = {
-	/** a user-defined genome label in the serverconfig.json, hg38, hg19, mm10, etc */
-	genome: string
-	/** a user-defined dataset label in the serverconfig.json, such as ClinVar, SJLife, GDC, etc */
-	dslabel: string
-	embedder: string
-	default_rootterm: number
-	cohortValues: string
-	treeFilter: string
-}
-
-interface Entries {
-	name: string
-	id: string
-	isleaf: boolean
-	included_types: string[]
-	child_types: string[]
-}
-
-export type RootTermResponse = {
-	lst: Entries[]
-}
-
-export const rootTermPayload: RoutePayload = {
-	request: {
-		typeId: 'RootTermRequest'
-	},
-	response: {
-		typeId: 'RootTermResponse'
-	},
-	examples: [
-		{
-			request: {
-				body: {
-					genome: 'hg38-test',
-					dslabel: 'TermdbTest',
-					embedder: 'localhost',
-					default_rootterm: 1,
-					cohortValues: 'ABC'
-				}
-			},
-			response: {
-				header: { status: 200 }
-			}
-		}
-	]
-}

package/src/routes/termdb.runChart.ts

@@ -1,66 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type RunChartRequest = {
-	genome: string
-	dslabel: string
-	/**
-	 * term wrapper for x axis: { term, q }.
-	 * runChart2: q.mode='continuous' → 1 series.
-	 * runChart2Period: q.mode='discrete' (with bins) → multiple series by period.
-	 */
-	xtw: { term: { id: string }; q?: { mode?: 'continuous' | 'discrete' }; $id?: string }
-	/** term wrapper for y axis: { term, q }. When omitted, chart renders as frequency (count per time bucket). */
-	ytw?: { term: { id: string }; q?: { mode?: string }; $id?: string }
-	aggregation?: 'median'
-	/** When true (frequency mode only), series Y values are cumulative counts. */
-	showCumulativeFrequency?: boolean
-	filter?: any
-	__protected__?: any // auth token for accessing protected data
-}
-
-export type RunChartSeries = {
-	/** period/series identifier */
-	seriesId?: string
-	/** calculated Y median value for this curve */
-	median: number
-	points: Point[]
-}
-
-export type RunChartSuccessResponse = {
-	status: 'ok'
-	/** each series is one curve, with a median. a runchart may show 1 or multiple curves */
-	series: RunChartSeries[]
-}
-
-export type RunChartErrorResponse = {
-	error: string
-	/** Always empty on error; present so response shape is consistent for clients/checkers. */
-	series: RunChartSeries[]
-}
-
-/** Discriminated union: server returns success shape on 200 or error shape with series: []. */
-export type RunChartResponse = RunChartSuccessResponse | RunChartErrorResponse
-
-export function isRunChartSuccess(r: RunChartResponse): r is RunChartSuccessResponse {
-	return 'status' in r && r.status === 'ok'
-}
-
-type Point = {
-	/** decimal year, e.g. 2024.21321321 */
-	x: number
-	/** text of human-readable x value, e.g. "Jan 2024" which may be by the months, depends on dataset customization */
-	xName: string
-	/** timeline, e.g. number of days */
-	y: number
-	/** number of samples with this timeline at this time point */
-	sampleCount: number
-}
-
-export const runChartPayload: RoutePayload = {
-	request: {
-		typeId: 'RunChartRequest'
-	},
-	response: {
-		typeId: 'RunChartResponse'
-	}
-}

package/src/routes/termdb.sampleImages.ts

@@ -1,26 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type TermdbSampleImagesRequest = {
-	genome: string
-	/** Ds label */
-	dslabel: string
-	sampleId: number
-}
-
-export type Image = {
-	src: any
-}
-
-export type TermdbSampleImagesResponse = {
-	images: Image[]
-}
-
-export const termdbSampleImagesPayload: RoutePayload = {
-	request: {
-		typeId: 'TermdbSampleImagesRequest'
-	},
-	response: {
-		typeId: 'TermdbSampleImagesResponse'
-	}
-	//examples: []
-}