@sjcrh/proteinpaint-types 2.188.1 → 2.190.0

package/src/routes/clearwsisessions.ts

@@ -1,19 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type ClearWSImagesSessionsRequest = {
-	sessions: Array<any>
-}
-
-export type ClearWSImagesSessionsResponse = {
-	message: string
-}
-
-export const clearWSImagesSessionsPayload: RoutePayload = {
-	request: {
-		typeId: 'ClearWSImagesSessionsRequest'
-	},
-	response: {
-		typeId: 'ClearWSImagesSessionsResponse'
-	}
-	// examples: []
-}

package/src/routes/correlationVolcano.ts

@@ -1,51 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { TermWrapper } from '../terms/tw.ts'
-import type { Filter } from '../filter.ts'
-
-/** */
-export type CorrelationVolcanoRequest = {
-	genome: string
-	dslabel: string
-	filter?: Filter
-	filter0?: any // gdc
-	/** feature tw */
-	featureTw: TermWrapper
-	/** variables */
-	variableTwLst: TermWrapper[]
-	/** correlation method */
-	correlationMethod: 'pearson' | 'spearman'
-	__protected__: any
-}
-
-export type CorrelationVolcanoResponse = {
-	/** Terms with not enough vectors to calculate correlation to be shown in legend */
-	skippedVariables: {
-		/** matching tw $id */
-		tw$id: string
-	}[]
-	/** each element is test result of one variable corresponding to variableTwLst */
-	variableItems: VariableItemEntry[]
-}
-
-export type VariableItemEntry = {
-	/** correlation coefficient, -1 to 1 */
-	correlation: number
-	/** pvalue */
-	original_pvalue: number
-	/** pvalue */
-	adjusted_pvalue: number
-	/** tw.$id, for client to match the item with variableTwLst */
-	tw$id: string
-	/** number of samples analyzed. samples not having complete data for all terms will be excluded, thus size may be lower than current cohort */
-	sampleSize: number
-}
-
-export const CorrelationVolcanoPayload: RoutePayload = {
-	request: {
-		typeId: 'CorrelationVolcanoRequest'
-	},
-	response: {
-		typeId: 'CorrelationVolcanoResponse'
-	}
-	//examples: []
-}

package/src/routes/dataset.ts

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

package/src/routes/deleteWSITileSelection.ts

@@ -1,25 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-import type { TileSelection } from './aiProjectSelectedWSImages.ts'
-
-export type DeleteWSITileSelectionRequest = {
-	genome: string
-	dslabel: string
-	projectId: number
-	tileSelection: TileSelection
-	classID: number
-	wsimage: string
-}
-
-export type DeleteWSITileSelectionResponse = {
-	status: string
-	error?: string
-}
-
-export const deleteWSITileSelectionPayload: RoutePayload = {
-	request: {
-		typeId: 'DeleteWSITileSelectionRequest'
-	},
-	response: {
-		typeId: 'DeleteWSITileSelectionResponse'
-	}
-}

package/src/routes/dsdata.ts

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

package/src/routes/dzimages.ts

@@ -1,25 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type DZImagesRequest = {
-	genome: string
-	dslabel: string
-	file: string
-
-	// params: {
-	// 	[key: string]: any
-	// }
-	sampleId?: string
-	sample_id?: string
-}
-
-export type DZImagesResponse = string
-
-export const dzImagesPayload: RoutePayload = {
-	request: {
-		typeId: 'DZImagesRequest'
-	},
-	response: {
-		typeId: 'DZImagesResponse'
-	}
-	// examples: []
-}

package/src/routes/errorResponse.ts

@@ -1,6 +0,0 @@
-export type ErrorResponse = {
-	/* Status code. https://developer.mozilla.org/en-US/docs/Web/HTTP/Status */
-	status: number
-	/* Msg */
-	error: string
-}

package/src/routes/filter.gdc.ts

@@ -1,15 +0,0 @@
-/* the gdc cohort filter object
-is invisible on pp ui
-always used as "filter0" property in pp client code and in request to pp back
-pp does not compute on it, on pp backend, it's passed to gdc api queries
-
-FIXME type is not properly defined yet
-*/
-export type GdcFilter0 = {
-	op: string
-	// TODO: this should allow an array of objects, and/or nesting ???
-	content: {
-		field: string
-		value: string
-	}
-}

package/src/routes/gdc.grin2.ts

@@ -1,246 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-/**
- * Represents a file from GDC API (MAF)
- */
-export type GdcGRIN2File = {
-	/** A string representing the file's UUID, can be accessed via https://api.gdc.cancer.gov/data/<uuid> */
-	id: string
-	/** A string representing a submitter ID for the case associated with this file */
-	case_submitter_id: string
-	/** Case UUID */
-	case_uuid: string
-	/** An integer as the byte size of this file, compressed */
-	file_size: number
-	/** Array of strings, each is 'tumor descriptor+tissue type', for all samples involved in generating the file */
-	sample_types: string[]
-	/** A string as the project id of the case */
-	project_id: string
-	/** The format of the file (MAF) */
-	file_format?: 'MAF'
-}
-
-type ExperimentalStrategy = {
-	wxs: 'WXS'
-}
-
-/**
- * Request parameters for GRIN2 file listing
- */
-export type GdcGRIN2listRequest = {
-	/** JSON, optional GDC cohort filter to restrict cases */
-	filter0?: any
-
-	/** Options for MAF file retrieval. Presence indicates MAF files should be returned */
-	mafOptions?: {
-		/** Name of experimental strategy to get files for */
-		experimentalStrategy: ExperimentalStrategy
-	}
-
-	/** Options for CNV file retrieval. Presence indicates CNV files should be returned */
-	cnvOptions?: {
-		/** Data type for CNV analysis */
-		dataType?: string
-	}
-
-	/** Options for fusion file retrieval. Presence indicates fusion files should be returned (for future use) */
-	fusionOptions?: any
-}
-
-/**
- * Response for GRIN2 file listing
- */
-export type GdcGRIN2listResponse = {
-	/** all maf-related results when mafOptions is supplied */
-	mafFiles?: {
-		// TODO suggest to move above maf-related results under mafFiles{}
-		/** list of maf files returned to client */
-		files: GdcGRIN2File[]
-		/** Total number of files found by API (in case bigger than files.length) */
-		filesTotal: number
-		/** Maximum total size of files allowed, for indicating on UI while selecting files */
-		maxTotalSizeCompressed: number
-		/** File counts by type */
-		fileCounts?: {
-			maf: number
-		}
-		/** Applied filters (for UI reference) */
-		appliedFilters?: {
-			experimentalStrategy?: ExperimentalStrategy
-		}
-		/** Deduplication stats */
-		deduplicationStats?: {
-			originalFileCount: number
-			deduplicatedFileCount: number
-			duplicatesRemoved: number
-			caseDetails?: Array<{ caseName: string; fileCount: number; keptFileSize: number }>
-			filteredFiles: Array<{ fileId: string; fileSize: number; reason: string }>
-		}
-	}
-	/** all cnv-related results when cnvOptions is supplied */
-	cnvFiles?: {
-		/** list of cnv files returned to client */
-		files: GdcGRIN2File[]
-		/** Maximum total size of files allowed, for indicating on UI while selecting files */
-		maxTotalSizeCompressed: number
-	}
-}
-
-/**
- * Parameters for running GRIN2 analysis
- */
-
-export type RunGRIN2Request = {
-	/**  Case files to analyze - maps case ID to file information */
-	caseFiles: {
-		[caseId: string]: {
-			maf?: string
-			cnv?: string
-		}
-	}
-	/**  Options for filtering MAF file content */
-	mafOptions?: {
-		/** Minimum total depth of returned MAF files */
-		minTotalDepth?: number // Default: 10
-		/** Minimum alternate allele count of returned MAF files */
-		minAltAlleleCount?: number // Default: 2
-		/** String array of consequence types */
-		consequences?: string[]
-		/** Maximum mutation count cutoff for highly mutated scenarios */
-		hyperMutator?: number
-	}
-	/**  Options for filtering CNV file content*/
-	cnvOptions?: {
-		/** Threshold for copy number loss detection */
-		lossThreshold?: number // Default: -0.4
-		/** Threshold for copy number gain detection */
-		gainThreshold?: number // Default: 0.3
-		/** Maximum segment length to include (0 = no filter) */
-		segLength?: number // Default: 0
-		/** Hypermutator max cut off for CNVs per case */
-		hyperMutator?: number // Default: 500
-	}
-	/** Device pixel ratio for rendering */
-	devicePixelRatio?: number // 2
-	/** Plot dimensions */
-	plot_width?: number // 1000
-	plot_height?: number // 400
-	/** Radius of the PNG rendered dots */
-	pngDotRadius?: number // 2
-}
-
-/** Error entry from failed file downloads */
-export type RustErrorEntry = {
-	case_id: string
-	data_type: string
-	error_type: string
-	error_details: string
-	attempts_made: number
-}
-
-/** Summary information from Rust processing */
-export type RustSummary = {
-	type: 'summary'
-	total_files: number
-	successful_files: number
-	failed_files: number
-	errors: RustErrorEntry[]
-	filtered_records: number
-	filtered_maf_records: number
-	filtered_cnv_records: number
-	included_maf_records: number
-	included_cnv_records: number
-
-	/** The complex nested structure of the per case object
-	 *  Records filtered by case, with MAF and CNV statistics
-	 */
-	filtered_records_by_case: Record<
-		string,
-		{
-			maf: {
-				matched_consequences: Record<string, any>
-				rejected_consequences: Record<string, any>
-				t_alt_count: number
-				t_depth: number
-				invalid_rows: number
-				excluded_by_min_depth: number
-				excluded_by_min_alt_count: number
-				excluded_by_consequence_type: number
-				total_processed: number
-				total_included: number
-				skipped_chromosomes: Record<string, number>
-			}
-			cnv: {
-				segment_mean: number
-				seg_length: number
-				invalid_rows: number
-				excluded_by_loss_threshold: number
-				excluded_by_gain_threshold: number
-				excluded_by_segment_length: number
-				total_processed: number
-				total_included: number
-				skipped_chromosomes: Record<string, number>
-			}
-		}
-	>
-
-	hyper_mutator_records: Record<string, string[]>
-	excluded_by_max_record: Record<string, string[]>
-}
-
-/** Structured output from Rust GRIN2 processing */
-export type RustGRIN2Result = {
-	/** String of successful file data */
-	successful_data: string
-	/** Array of failed file information */
-	failed_files: RustErrorEntry[]
-	/** Summary statistics */
-	summary: RustSummary
-}
-
-/**
- * Response for GRIN2 analysis run
- */
-export type RunGRIN2Response = {
-	/** Status of the analysis */
-	status: 'success' | 'error'
-	/** Error message if status is 'error' */
-	error?: string
-	/** Path to the generated image if status is 'success' */
-	pngImg?: string
-	/** Download status */
-	download?: any
-	/** Table of top genes indentified by analysis */
-	topGeneTable?: any
-	/** Data from Rust for making the analysis summary div */
-	rustResult?: RustGRIN2Result
-	/** Timing info from nodejs */
-	timing?: {
-		/** Time taken to run Rust processing */
-		rustProcessingTime: number
-		/** Time taken to run GRIN2 processing */
-		grin2Time: number
-		/** Total time taken for the entire run */
-		totalTime: number
-	}
-}
-/**
- * Route payload definitions for type checking
- */
-export const gdcGRIN2listPayload: RoutePayload = {
-	request: {
-		typeId: 'GdcGRIN2listRequest'
-	},
-	response: {
-		typeId: 'GdcGRIN2listResponse'
-	}
-}
-
-export const runGRIN2Payload: RoutePayload = {
-	request: {
-		typeId: 'RunGRIN2Request'
-	},
-	response: {
-		typeId: 'RunGRIN2Response'
-	}
-}

package/src/routes/gdc.maf.ts

@@ -1,52 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-//import GdcFilter0 from './filter.gdc'
-
-// an object representing gdc maf file, to be shown on client table
-
-export type GdcMafFile = {
-	/** A string representing the file's UUID (Universally Unique Identifier) , can be accessed via https://api.gdc.cancer.gov/data/<uuid>*/
-	id: string
-	/** A string representing a submitter ID for the case associated with this file */
-	case_submitter_id: string
-	// case uuid
-	case_uuid: string
-	/** An integer as the byte size of this file, compressed */
-	file_size: number
-	/** Array of strings, each is 'tumor descriptor+tissue type', for all samples involved in generating the maf file */
-	sample_types: string[]
-	/** A string representing the type of workflow used to generate or process this file */
-	//workflow_type: string
-	/** A string as the project id of the case */
-	project_id: string
-}
-
-export type ExperimentalStrategy = {
-	targeted: 'Targeted Sequencing'
-	wxs: 'WXS'
-}
-
-export type GdcMafRequest = {
-	/** Name of exp strategy to get maf files for */
-	experimentalStrategy: ExperimentalStrategy
-	/** JSON, optional GDC cohort filter to restrict cases; if supplied, will only get maf files for these cases. the filter is readonly and pass to GDC API query */
-	filter0?: any
-}
-
-export type GdcMafResponse = {
-	/** List of file objects passing filter and to be displayed on client */
-	files: GdcMafFile[]
-	/** Total number of files found by API (in case bigger than files.length) */
-	filesTotal: number
-	/** Maximum total size of maf files allowed, for indicating on ui while selecting files */
-	maxTotalSizeCompressed: number
-}
-
-export const gdcMafPayload: RoutePayload = {
-	request: {
-		typeId: 'GdcMafRequest'
-	},
-	response: {
-		typeId: 'GdcMafResponse'
-	}
-	//examples: []
-}

package/src/routes/gdc.mafBuild.ts

@@ -1,20 +0,0 @@
-import type { RoutePayload } from './routeApi.ts'
-
-export type GdcMafBuildRequest = {
-	/** List of input file uuids in gdc */
-	fileIdLst: string[]
-	/** List of columns in output MAF file */
-	columns: string[]
-}
-
-export type GdcMafBuildResponse = any
-
-export const GdcMafPayload: RoutePayload = {
-	request: {
-		typeId: 'GdcMafBuildRequest'
-	},
-	response: {
-		typeId: 'GdcMafBuildResponse'
-	}
-	//examples: []
-}

package/src/routes/genelookup.ts

@@ -1,22 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type GeneLookupRequest = {
-	input: string
-	genome: string
-	deep: boolean
-}
-
-export type GeneLookupResponse = {
-	error?: string
-	hits: string[]
-}
-
-export const geneLookupPayload: RoutePayload = {
-	request: {
-		typeId: 'GeneLookupRequest'
-	},
-	response: {
-		typeId: 'GeneLookupResponse'
-	}
-	//examples: []
-}

package/src/routes/genesetEnrichment.ts

@@ -1,116 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-import type { DERequest } from './termdb.DE.js'
-
-export type GenesetEnrichmentRequest = {
-	/** Sample genes to be queried. Optional when `cacheId` is given — the
-	 * server loads genes from the DE cache file in that case. */
-	genes?: string[]
-	/** Fold changes aligned to `genes`. Optional when `cacheId` is given. */
-	fold_change?: number[]
-	/** DE cache ID (returned by the volcano/DE route). Deterministic hash
-	 * of the DE inputs. If set, the server reads genes + fold_change from
-	 * the cache file and ignores any `genes`/`fold_change` fields sent in
-	 * this request. */
-	cacheId?: string
-	/** Snapshot of the original DE request that produced `cacheId`. When
-	 * the cache file is missing (TTL eviction or farm node that has never
-	 * seen this request), the server uses this to recompute and rewrite
-	 * the cache. Without this field, a cache miss is unrecoverable. */
-	/** Dataset label forwarded for auth middleware / dataset scoping. */
-	dslabel?: string
-	/** Snapshot of the original DE request that produced `cacheId`. When
-	 * the cache file is missing (TTL eviction or farm node that has never
-	 * seen this request), the server uses this to recompute and rewrite
-	 * the cache. Without this field, a cache miss is unrecoverable.
-	 * This mirrors the partial DE payload shape sent by clients. */
-	daRequest?: Partial<DERequest>
-	fetchDE?: boolean
-	/** Filter non-coding genes */
-	filter_non_coding_genes: boolean
-	/** Genome build */
-	genome: string
-	/** Type of GO to be queried e.g MF, CC, BP */
-	geneSetGroup: string
-	/** Gene set name whose enrichment score is to be profiled */
-	geneset_name?: string
-	/** Number of permutations to be carried out for GSEA analysis.
-	 * Only read by the blitzgsea path; cerno and fetchDE requests omit it. */
-	num_permutations?: number
-	/** Method used for GSEA blitzgsea/cerno */
-	method: 'blitzgsea' | 'cerno'
-	/** DAP-specific parameters: organism/assay/cohort identify the DAP file */
-	dapParams?: { organism: string; assay: string; cohort: string }
-}
-
-type blitzgsea_geneset_attributes = {
-	/** Absolute enrichment score */
-	es: number
-	/** Normalized enrichment score */
-	nes: number
-	/** Size of gene set */
-	geneset_size: number
-	/** Leading edge genes */
-	leading_edge: string
-	/** pvalue */
-	pvalue: number
-	/** sidak (multiple testing correction) */
-	sidak: number
-	/** false discovery rate */
-	fdr: number
-}
-
-// Key value pair of geneset name and blitzgsea geneset attributes
-type blitzgsea_map = {
-	[geneset_name: string]: blitzgsea_geneset_attributes
-}
-
-type cerno_geneset_attributes = {
-	/** Absolute enrichment score */
-	es: number
-	/** Area under curve score */
-	auc: number
-	/** Size of gene set */
-	geneset_size: number
-	/** Leading edge genes */
-	leading_edge: string
-	/** pvalue */
-	pvalue: number
-	/** false discovery rate */
-	fdr: number
-}
-
-type blitzgsea_json = {
-	/** array of pathway_attributes */
-	data: blitzgsea_map[]
-}
-
-// Key value pair of geneset name and cerno geneset attributes
-type cerno_map = {
-	[geneset_name: string]: cerno_geneset_attributes
-}
-
-/** Pass gsea image to client side */
-type blitzgsea_image_name = string
-
-type blitzgseaResult = {
-	pathway: blitzgsea_json | blitzgsea_image_name
-}
-
-type cernoResult = {
-	data: cerno_map[]
-}
-
-export type GenesetEnrichmentResponse = {
-	/** gsea result or an image (for plotting) is sent to client side */
-	data: blitzgseaResult | cernoResult
-}
-
-export const genesetEnrichmentPayload: RoutePayload = {
-	request: {
-		typeId: 'GenesetEnrichmentRequest'
-	},
-	response: {
-		typeId: 'GenesetEnrichmentResponse'
-	}
-	//examples: []
-}

package/src/routes/genesetOverrepresentation.ts

@@ -1,48 +0,0 @@
-import type { RoutePayload } from './routeApi.js'
-
-export type GenesetOverrepresentationRequest = {
-	/**  Sample genes to be queried */
-	sample_genes: string
-	/** Background genes against which the sample genes will be queried. if missing will use all protein-coding genes, available in gene db */
-	background_genes?: string
-	/** Genome build */
-	genome: string
-	/** msigdb branch term name. all genesets under this branch will be analyzed */
-	geneSetGroup: string
-	/** Boolean variable describing if non-coding genes should be filtered */
-	filter_non_coding_genes: boolean
-}
-
-export type GenesetOverrepresentationResponse = {
-	/** Name of pathway */
-	pathway_name: string
-	/** Original p-value */
-	p_value_original: number
-	/** Adjusted p-value */
-	p_value_adjusted: number
-}
-
-export type gene_overrepresentation_input = {
-	/** Input sample genes */
-	sample_genes: string
-	/** Input background genes */
-	background_genes?: string
-	/** Path to msigdb */
-	msigdb: string
-	/** Name of Gene Set Group */
-	gene_set_group: string
-	/** Path to gene db */
-	genedb: string
-	/** Boolean variable describing if non-coding genes should be filtered */
-	filter_non_coding_genes: boolean
-}
-
-export const genesetOverrepresentationPayload: RoutePayload = {
-	request: {
-		typeId: 'GenesetOverrepresentationRequest'
-	},
-	response: {
-		typeId: 'GenesetOverrepresentationResponse'
-	}
-	// examples: []
-}