@sjcrh/proteinpaint-types 2.86.0 → 2.87.1

package/src/routes/termdb.categories.ts

@@ -0,0 +1,73 @@
+import type { RoutePayload } from './routeApi.js'
+import type { Filter } from '../filter.ts'
+import type { TermWrapper } from '../terms/tw.ts'
+
+export type CategoriesRequest = {
+	genome: string
+	dslabel: string
+	embedder: string
+	/** termwrapper object */
+	tw: TermWrapper
+	filter?: Filter
+	/** quick fix only for gdc */
+	currentGeneNames?: string[]
+	/** optional property added by mds3 tk, to limit to cases mutated in this region */
+	rglst?: any
+}
+
+interface Entries {
+	samplecount: number
+	key: string
+	label: string
+}
+
+export type CategoriesResponse = {
+	lst: Entries[]
+	orderedLabels?: []
+}
+
+export const termdbCategoriesPayload: RoutePayload = {
+	request: {
+		typeId: 'CategoriesRequest'
+	},
+	response: {
+		typeId: 'CategoriesResponse'
+	},
+	examples: [
+		{
+			request: {
+				body: {
+					genome: 'hg38-test',
+					dslabel: 'TermdbTest',
+					embedder: 'localhost',
+					term: { id: 'diaggrp' },
+					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.cluster.ts

@@ -0,0 +1,103 @@
+import type { RoutePayload } from './routeApi.js'
+import { ErrorResponse } from './errorResponse.ts'
+import { Filter } from '../filter.ts'
+import { Term } from '../terms/term.ts'
+import { GeneExpressionTerm } from '../terms/geneExpression.ts'
+import { MetaboliteIntensityTerm } from '../terms/metaboliteIntensity.ts'
+import { NumericDictTerm } from '../terms/numeric.ts'
+
+export type Gene = {
+	/** gene symbol, required */
+	gene: string
+	/** optionally, client may supply chr/start/stop; if missing, backend code may add them when processing native dataset */
+	chr?: string
+	start?: number
+	stop?: number
+}
+
+type TermdbClusterRequestBase = {
+	/** Genome id */
+	genome: string
+	/** Dataset label */
+	dslabel: string
+	/** cluster method */
+	clusterMethod: string
+	/** distance method */
+	distanceMethod: string
+	/** pp filter */
+	filter?: Filter
+	/** todo gdc filter */
+	filter0?: any
+}
+
+export type TermdbClusterRequestGeneExpression = TermdbClusterRequestBase & {
+	/** Data type */
+	dataType: 'geneExpression'
+	/** List of terms */
+	terms: GeneExpressionTerm[]
+	/** perform z-score transformation on values */
+	zScoreTransformation?: string
+}
+
+export type TermdbClusterRequestMetabolite = TermdbClusterRequestBase & {
+	/** Data type */
+	dataType: 'metaboliteIntensity'
+	/** List of terms */
+	terms: MetaboliteIntensityTerm[]
+	/** perform z-score transformation on values */
+	zScoreTransformation?: string
+}
+
+export type TermdbClusterRequestNumericDictTerm = TermdbClusterRequestBase & {
+	/** Data type */
+	dataType: 'numericDictTerm'
+	/** List of terms */
+	terms: NumericDictTerm[]
+	/** perform z-score transformation on values */
+	zScoreTransformation?: string
+}
+
+export type TermdbClusterRequest =
+	| TermdbClusterRequestGeneExpression
+	| TermdbClusterRequestMetabolite
+	| TermdbClusterRequestNumericDictTerm
+
+export type Hclust = {
+	merge: { n1: number; n2: number }[]
+	height: { height: number }[]
+	order: { name: string }[]
+	inputOrder: string[]
+}
+export type Clustering = {
+	row: Hclust
+	col: Hclust
+	matrix: number[][]
+}
+
+// response with clustering result of multiple gene/rows
+export type ValidResponse = {
+	/**  */
+	clustering: Clustering
+	/**  */
+	byTermId: { [index: string]: any }
+	/**  */
+	bySampleId: { [index: string]: any }
+}
+
+//response of just 1 gene, thus unable to do clustering
+export type SingletermResponse = {
+	term: Term
+	data: any
+}
+
+export type TermdbClusterResponse = ErrorResponse | ValidResponse | SingletermResponse
+
+export const termdbClusterPayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbClusterRequest'
+	},
+	response: {
+		typeId: 'TermdbClusterResponse'
+	}
+	//examples: []
+}

package/src/routes/termdb.cohort.summary.ts

@@ -0,0 +1,14 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type TermdbCohortSummaryRequest = any
+export type TermdbCohortSummaryResponse = any
+
+export const termdbCohortSummaryPayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbCohortSummaryRequest'
+	},
+	response: {
+		typeId: 'TermdbCohortSummaryResponse'
+	}
+	// examples: []
+}

package/src/routes/termdb.cohorts.ts

@@ -0,0 +1,14 @@
+import { RoutePayload } from './routeApi.js'
+
+export type TermdbCohortsRequest = any
+export type TermdbCohortsResponse = any
+
+export const termdbCohortsPayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbCohortsRequest'
+	},
+	response: {
+		typeId: 'TermdbCohortsResponse'
+	}
+	//examples: []
+}

package/src/routes/termdb.descrstats.ts

@@ -0,0 +1,78 @@
+import type { RoutePayload } from './routeApi.js'
+import type { Filter } from '../filter.ts'
+import type { TermWrapper } from '../terms/tw.ts'
+import type { ErrorResponse } from './errorResponse.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
+}
+
+interface entries {
+	id: string
+	label: string
+	value: number
+}
+
+type ValidResponse = {
+	values: entries[]
+}
+
+export type DescrStatsResponse = ValidResponse | ErrorResponse
+
+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.numericcategories.ts

@@ -0,0 +1,32 @@
+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

@@ -0,0 +1,65 @@
+import type { RoutePayload } from './routeApi.js'
+import type { Filter } from '../filter.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 */
+	tid: string
+	filter: Filter
+}
+
+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],
+					tid: '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.rootterm.ts

@@ -0,0 +1,49 @@
+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.sampleImages.ts

@@ -0,0 +1,26 @@
+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: []
+}

package/src/routes/termdb.singleSampleMutation.ts

@@ -0,0 +1,29 @@
+import type { RoutePayload } from './routeApi.js'
+import type { ErrorResponse } from './errorResponse.ts'
+
+export type TermdbSingleSampleMutationRequest = {
+	/** Genome id */
+	genome: string
+	/** Dataset label */
+	dslabel: string
+	/** sample id */
+	sample: string
+}
+type ValidResponse = {
+	/** List of mutation data points from this sample TODO change to type of M elements */
+	mlst: object[]
+	/** */
+	dt2total?: { dt: number; total: number }[]
+}
+
+export type TermdbSingleSampleMutationResponse = ErrorResponse | ValidResponse
+
+export const termdbSingleSampleMutationPayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbSingleSampleMutationRequest'
+	},
+	response: {
+		typeId: 'TermdbSingleSampleMutationResponse'
+	}
+	// examples: []
+}

package/src/routes/termdb.singlecellDEgenes.ts

@@ -0,0 +1,41 @@
+import type { RoutePayload } from './routeApi.js'
+import type { ErrorResponse } from './errorResponse.ts'
+
+export type TermdbSingleCellDEgenesRequest = {
+	/** Genome id */
+	genome: string
+	/** Dataset label */
+	dslabel: string
+	/** Sample name
+	for GDC the value is "seurat.analysis.tsv" file UUID rather than sample name. the file contains the analysis results for an experiment
+	*/
+	sample: string
+	/** column name to provide cell groups/clustering, for which DE genes are precomputed.  */
+	columnName: string
+	/** User selected cell group/cluster, corresponds to columnName, for which DE genes will be returned to client */
+	categoryName: string
+}
+
+export type HasDataResponse = {
+	/** list of significant DE genes for the given category in the sample */
+	genes: {
+		/** gene name */
+		name: string
+		/** adjusted p-value */
+		p_val_adj: number
+		/** log foldchange */
+		avg_log2FC: number
+	}[]
+}
+
+export type TermdbSingleCellDEgenesResponse = ErrorResponse | HasDataResponse
+
+export const termdbSingleCellDEgenesPayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbSingleCellDEgenesRequest'
+	},
+	response: {
+		typeId: 'TermdbSingleCellDEgenesResponse'
+	}
+	// examples: []
+}

package/src/routes/termdb.singlecellData.ts

@@ -0,0 +1,69 @@
+import type { RoutePayload } from './routeApi.js'
+import { ErrorResponse } from './errorResponse.ts'
+
+export type Cell = {
+	/** Cell id or barcode */
+	cellId: string
+	/** X coord of the cell */
+	x: number
+	/** Y coord of the cell */
+	y: number
+	/** Z coord of the cell, should be present for all cells and trigger 3d plot   */
+	z?: number
+	/** The cell may have different classifications, e.g. by cell type, CNV, FUSION, etc. */
+	category: string
+	/** Gene expression data for this cell */
+	geneExp?: number
+}
+
+export type Plot = {
+	/** name of the plot */
+	name: string
+	/** List of cells with gene expression */
+	expCells?: Cell[]
+	/** List of cells with no gene expression, if no gene provided all cells will be here */
+	noExpCells?: Cell[]
+	/** Column name to color by, e.g Cell type, CNV, Fusion */
+	colorBy: string
+	colorColumns: string[]
+	colorMap?: { [key: string]: string }
+}
+
+export type TermdbSingleCellDataRequest = {
+	/** Genome id */
+	genome: string
+	/** Dataset label */
+	dslabel: string
+	/** Sample name for which the sc results will be shown.
+	for GDC the value is "seurat.analysis.tsv" file UUID rather than any sample name. the file contains the analysis results for an experiment */
+	sample: { eID?: string; sID: string }
+	/** List of plot names from this sample to request data for */
+	plots: string[]
+	/** Gene name to retrieve expression data for all cells of the given sample, and to overlay on maps */
+	gene?: string
+}
+
+export type HasdataResponse = {
+	/** List of plots from singlecell experiment of this sample */
+	plots: Plot[]
+
+	/** Terms used to annotate cells */
+	//terms: Term[]
+}
+
+export type NodataResponse = {
+	/** Flag to indicate no sc data for this sample */
+	nodata: boolean
+}
+
+export type TermdbSingleCellDataResponse = NodataResponse | ErrorResponse | HasdataResponse
+
+export const termdbSingleCellDataPayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbSingleCellDataRequest'
+	},
+	response: {
+		typeId: 'TermdbSingleCellDataResponse'
+	}
+	// examples: []
+}

package/src/routes/termdb.singlecellSamples.ts

@@ -0,0 +1,46 @@
+import type { RoutePayload } from './routeApi.js'
+import type { ErrorResponse } from './errorResponse.ts'
+
+export type Sample = {
+	/** Sample name, required */
+	sample: string
+	/** optional list of sc data files available for this sample, gdc-specific
+	if available:
+		each row of sample table will infact be one experiment.
+		selecting one will use its experimentID as "sample" value in request parameter
+		each experiment may have additional fields that may be displayed in table. see singleCell.samples.experimentColumns[]
+
+	if no exp, then each sample will just have one experiment identifiable by its sample name, and this name is used in request
+	*/
+	[key: string]: any //sample column/term value
+	experiments?: { experimentID: string }[]
+
+	// a sample may have additional fields that will be displayed in table, see singleCell.samples.sampleColumns[]
+}
+
+export type TermdbSingleCellSamplesRequest = {
+	/** Genome id */
+	genome: string
+	/** Dataset label */
+	dslabel: string
+	//filter0?: Filter0 // for gdc
+}
+type ValidResponse = {
+	/** List of sample names with singlecell data */
+	samples: Sample[]
+	fields: string[]
+	columnNames: string[]
+	sameLegend?: boolean
+}
+
+export type TermdbSingleCellSamplesResponse = ErrorResponse | ValidResponse
+
+export const termdbSingleCellSamplesPayload: RoutePayload = {
+	request: {
+		typeId: 'TermdbSingleCellSamplesRequest'
+	},
+	response: {
+		typeId: 'TermdbSingleCellSamplesResponse'
+	}
+	// examples: []
+}

package/src/routes/termdb.termchildren.ts

@@ -0,0 +1,49 @@
+import type { RoutePayload } from './routeApi.js'
+
+export type TermChildrenRequest = {
+	/** 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
+	get_children: number
+	tid: string
+}
+
+interface Entries {
+	name: string
+	id: string
+	isleaf: boolean
+	included_types: string[]
+	child_types: string[]
+}
+
+export type TermChildrenResponse = {
+	lst: Entries[]
+}
+
+export const termChildrenPayload: RoutePayload = {
+	request: {
+		typeId: 'TermChildrenRequest'
+	},
+	response: {
+		typeId: 'TermChildrenResponse'
+	},
+	examples: [
+		{
+			request: {
+				body: {
+					genome: 'hg38-test',
+					dslabel: 'TermdbTest',
+					embedder: 'localhost',
+					get_children: 1,
+					cohortValues: 'ABC',
+					tid: 'GO:0000001'
+				}
+			},
+			response: {
+				header: { status: 200 }
+			}
+		}
+	]
+}