@sjcrh/proteinpaint-types 2.130.0 → 2.132.0

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-Y5BVEGR2.js";
+} from "./chunk-7RY7HC24.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-WHO7HCNU.js";
+} from "./chunk-UL54XEPY.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-6C4DMGK3.js";
+} from "./chunk-J7ODYX6N.js";
 import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.130.0",
+  "version": "2.132.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -1508,6 +1508,13 @@ type DtAssayAvailability = DtAssayAvailabilityGetter | DtAssayAvailabilityTerm
 
 /** using ds-supplied getter */
 type DtAssayAvailabilityGetter = {
+	/** define q
+	returns:
+	{
+		yesSamples: Set() of sample ids
+		noSamples: Set() of sample ids
+	}
+	*/
 	get: (q: any) => any
 }
 /** using dictionary term */

package/src/routes/gdc.grin2.ts

@@ -37,8 +37,11 @@ export type GdcGRIN2listRequest = {
 		experimentalStrategy: ExperimentalStrategy
 	}
 
-	/** Options for CNV file retrieval. Presence indicates CNV files should be returned (for future use) */
-	cnvOptions?: any
+	/** 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
@@ -48,39 +51,38 @@ export type GdcGRIN2listRequest = {
  * Response for GRIN2 file listing
  */
 export type GdcGRIN2listResponse = {
-	/** List of file objects passing filter and to be displayed on 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 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[]
-		/** to add additional stats on cnv file listing */
+		/** Maximum total size of files allowed, for indicating on UI while selecting files */
+		maxTotalSizeCompressed: number
 	}
 }
 
@@ -93,6 +95,7 @@ export type RunGRIN2Request = {
 	caseFiles: {
 		[caseId: string]: {
 			maf?: string
+			cnv?: string
 		}
 	}
 	/**  Options for filtering MAF file content */
@@ -101,14 +104,20 @@ export type RunGRIN2Request = {
 		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
 	}
-	/**  Options for CNV file retrieval (will be added later)
-	 cnvOptions?: {
-	 * lossThreshold?: number // Default: -0.5
-	 * gainThreshold?: number // Default: 0.5
-	 * segLength?: number // Default: 2000000
-	 *}
-	 */
 }
 
 /** Error entry from failed file downloads */

package/src/routes/termdb.singleSampleMutation.ts

@@ -6,8 +6,8 @@ export type TermdbSingleSampleMutationRequest = {
 	genome: string
 	/** Dataset label */
 	dslabel: string
-	/** sample id */
-	sample: string
+	/** sample id, allow string or number; for native ds, sample name in number will be cast into string */
+	sample: string | number
 }
 type ValidResponse = {
 	/** List of mutation data points from this sample TODO change to type of M elements */

package/src/termdb.matrix.ts

@@ -17,6 +17,12 @@ type SampleEntry = {
 	}
 }
 
+type CategoryEntry = {
+	key: string
+	label: string
+	samplecount: number
+}
+
 export type ValidGetDataResponse = {
 	samples: {
 		[index: string | number]: SampleEntry
@@ -33,6 +39,9 @@ export type ValidGetDataResponse = {
 				bins?: any
 				/** CTE.events. These info are not available in term object and is computed during run time. */
 				events?: any
+				/** Categories of term. Only computed for categorical terms that
+				have an empty term.values{}. */
+				categories?: CategoryEntry[]
 			}
 		>
 		/** metadata about samples (e.g. print names). avoid duplicating such in sample data elements (e.g. mutations)

package/src/terms/term.ts

@@ -105,6 +105,9 @@ export type BaseTerm = {
 	included_types?: string[]
 	isleaf?: boolean
 	values?: TermValues
+	/** Do not build .values{} when building termdb. Used for 
+	making categorical term with empty .values{} in TermdbTest */
+	skipValuesBuild?: boolean
 }
 
 export type Term = BaseTerm & (NumericTerm | CategoricalTerm | ConditionTerm | SampleLstTerm | SnpsTerm | GvTerm)