@sjcrh/proteinpaint-types 2.129.2 → 2.129.6

package/dist/{chunk-UWNYHMCA.js → chunk-5VCMJ7QL.js}

@@ -70,13 +70,15 @@ var validGdcGRIN2listRequest = (input) => {
 var validGdcGRIN2listResponse = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && "number" === typeof input3.filesTotal && "number" === typeof input3.maxTotalSizeCompressed && (void 0 === input3.fileCounts || "object" === typeof input3.fileCounts && null !== input3.fileCounts && $io2(input3.fileCounts)) && (void 0 === input3.appliedFilters || "object" === typeof input3.appliedFilters && null !== input3.appliedFilters && false === Array.isArray(input3.appliedFilters) && $io3(input3.appliedFilters)) && (void 0 === input3.deduplicationStats || "object" === typeof input3.deduplicationStats && null !== input3.deduplicationStats && $io4(input3.deduplicationStats));
+    const $io0 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && "number" === typeof input3.filesTotal && "number" === typeof input3.maxTotalSizeCompressed && (void 0 === input3.fileCounts || "object" === typeof input3.fileCounts && null !== input3.fileCounts && $io2(input3.fileCounts)) && (void 0 === input3.appliedFilters || "object" === typeof input3.appliedFilters && null !== input3.appliedFilters && false === Array.isArray(input3.appliedFilters) && $io3(input3.appliedFilters)) && (void 0 === input3.deduplicationStats || "object" === typeof input3.deduplicationStats && null !== input3.deduplicationStats && $io4(input3.deduplicationStats)) && (void 0 === input3.mafFiles || "object" === typeof input3.mafFiles && null !== input3.mafFiles && $io7(input3.mafFiles)) && (void 0 === input3.cnvFiles || "object" === typeof input3.cnvFiles && null !== input3.cnvFiles && $io8(input3.cnvFiles));
     const $io1 = (input3) => "string" === typeof input3.id && "string" === typeof input3.case_submitter_id && "string" === typeof input3.case_uuid && "number" === typeof input3.file_size && (Array.isArray(input3.sample_types) && input3.sample_types.every((elem) => "string" === typeof elem)) && "string" === typeof input3.project_id && (void 0 === input3.file_format || "MAF" === input3.file_format);
     const $io2 = (input3) => "number" === typeof input3.maf;
     const $io3 = (input3) => void 0 === input3.experimentalStrategy || "WXS" === input3.experimentalStrategy;
     const $io4 = (input3) => "number" === typeof input3.originalFileCount && "number" === typeof input3.deduplicatedFileCount && "number" === typeof input3.duplicatesRemoved && (void 0 === input3.caseDetails || Array.isArray(input3.caseDetails) && input3.caseDetails.every((elem) => "object" === typeof elem && null !== elem && $io5(elem))) && (Array.isArray(input3.filteredFiles) && input3.filteredFiles.every((elem) => "object" === typeof elem && null !== elem && $io6(elem)));
     const $io5 = (input3) => "string" === typeof input3.caseName && "number" === typeof input3.fileCount && "number" === typeof input3.keptFileSize;
     const $io6 = (input3) => "string" === typeof input3.fileId && "number" === typeof input3.fileSize && "string" === typeof input3.reason;
+    const $io7 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io1(elem));
+    const $io8 = (input3) => Array.isArray(input3.files) && input3.files.every((elem) => "object" === typeof elem && null !== elem && $io1(elem));
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -130,6 +132,22 @@ var validGdcGRIN2listResponse = (input) => {
         path: _path2 + ".deduplicationStats",
         expected: "(__type.o2 | undefined)",
         value: input3.deduplicationStats
+      }), void 0 === input3.mafFiles || ("object" === typeof input3.mafFiles && null !== input3.mafFiles || $report(_exceptionable2, {
+        path: _path2 + ".mafFiles",
+        expected: "(__type.o5 | undefined)",
+        value: input3.mafFiles
+      })) && $vo7(input3.mafFiles, _path2 + ".mafFiles", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".mafFiles",
+        expected: "(__type.o5 | undefined)",
+        value: input3.mafFiles
+      }), void 0 === input3.cnvFiles || ("object" === typeof input3.cnvFiles && null !== input3.cnvFiles || $report(_exceptionable2, {
+        path: _path2 + ".cnvFiles",
+        expected: "(__type.o6 | undefined)",
+        value: input3.cnvFiles
+      })) && $vo8(input3.cnvFiles, _path2 + ".cnvFiles", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".cnvFiles",
+        expected: "(__type.o6 | undefined)",
+        value: input3.cnvFiles
       })].every((flag) => flag);
       const $vo1 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
         path: _path2 + ".id",
@@ -249,6 +267,40 @@ var validGdcGRIN2listResponse = (input) => {
         expected: "string",
         value: input3.reason
       })].every((flag) => flag);
+      const $vo7 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
+        path: _path2 + ".files",
+        expected: "Array<GdcGRIN2File>",
+        value: input3.files
+      })) && input3.files.map((elem, _index5) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
+        path: _path2 + ".files[" + _index5 + "]",
+        expected: "GdcGRIN2File",
+        value: elem
+      })) && $vo1(elem, _path2 + ".files[" + _index5 + "]", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".files[" + _index5 + "]",
+        expected: "GdcGRIN2File",
+        value: elem
+      })).every((flag) => flag) || $report(_exceptionable2, {
+        path: _path2 + ".files",
+        expected: "Array<GdcGRIN2File>",
+        value: input3.files
+      })].every((flag) => flag);
+      const $vo8 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.files) || $report(_exceptionable2, {
+        path: _path2 + ".files",
+        expected: "Array<GdcGRIN2File>",
+        value: input3.files
+      })) && input3.files.map((elem, _index6) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
+        path: _path2 + ".files[" + _index6 + "]",
+        expected: "GdcGRIN2File",
+        value: elem
+      })) && $vo1(elem, _path2 + ".files[" + _index6 + "]", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".files[" + _index6 + "]",
+        expected: "GdcGRIN2File",
+        value: elem
+      })).every((flag) => flag) || $report(_exceptionable2, {
+        path: _path2 + ".files",
+        expected: "Array<GdcGRIN2File>",
+        value: input3.files
+      })].every((flag) => flag);
       return ("object" === typeof input2 && null !== input2 || $report(true, {
         path: _path + "",
         expected: "GdcGRIN2listResponse",

package/dist/gdc.grin2.js

@@ -5,7 +5,7 @@ import {
   validGdcGRIN2listResponse,
   validRunGRIN2Request,
   validRunGRIN2Response
-} from "./chunk-UWNYHMCA.js";
+} from "./chunk-5VCMJ7QL.js";
 import "./chunk-CNSSF43V.js";
 export {
   gdcGRIN2listPayload,

package/dist/index.js

@@ -175,7 +175,7 @@ import {
   validGdcGRIN2listResponse,
   validRunGRIN2Request,
   validRunGRIN2Response
-} from "./chunk-UWNYHMCA.js";
+} from "./chunk-5VCMJ7QL.js";
 import {
   gdcMafPayload,
   validGdcMafRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.129.2",
+  "version": "2.129.6",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -78,12 +78,6 @@ type GenomicPositionEntry = {
 }
 */
 
-type Chr2bcffile = {
-	/** index is the chr (e.g. 'chr1', 'chr2', etc.)
-	 * value is the bcf file path */
-	[index: string]: string
-}
-
 type bcfMafFile = {
 	/** bcf file for only variants, no samples and FORMAT */
 	bcffile: string
@@ -113,8 +107,14 @@ type SnvindelByRange = {
 	//local ds can have following different setup
 	/** one single bcf file */
 	bcffile?: string
-	/** one bcf file per chr */
-	chr2bcffile?: Chr2bcffile
+	/** one bcf file per chr
+	after loading, this is transformed into byrange._tk.chr2files{}, and deleted!
+	*/
+	chr2bcffile?: {
+		/** index is the chr (e.g. 'chr1', 'chr2', etc.)
+		 * value is the bcf file path */
+		[index: string]: string
+	}
 	/** bcf+maf combined */
 	bcfMafFile?: bcfMafFile
 	/** allow to apply special configurations to certain INFO fields of the bcf file */
@@ -1495,41 +1495,51 @@ type MutationSet = {
 	fusion: string
 }
 
-type BaseDtEntry = {
+/** different methods to return samples with assay availability info */
+type DtAssayAvailability = DtAssayAvailabilityGetter | DtAssayAvailabilityTerm
+
+/** using ds-supplied getter */
+type DtAssayAvailabilityGetter = {
+	get: (q: any) => any
+}
+/** using dictionary term */
+type DtAssayAvailabilityTerm = {
+	/** id of this assay term for this dt */
 	term_id: string
+	/** optional label */
+	label?: string
+	/** categories meaning the sample has this assay */
 	yes: { value: string[] }
+	/** categories meaning the sample doesn't have this assay */
 	no: { value: string[] }
-	label?: string
-}
-
-type SNVByOrigin = {
-	[index: string]: BaseDtEntry
-}
-
-type DtEntrySNV = {
-	byOrigin: SNVByOrigin
 }
 
-type ByDt = {
-	/** SNVs differentiate by sample origin. Non-SNV, no differentiation*/
-	[index: number]: DtEntrySNV | BaseDtEntry
-}
-
-type AssayValuesEntry = {
-	[index: string]: { label: string; color: string }
+type DtAssayAvailabilityByOrigin = {
+	byOrigin: {
+		/** each key is an origin value or category */
+		[index: string]: DtAssayAvailability
+	}
 }
 
-type AssaysEntry = {
-	id: string
-	name: string
-	type: string
-	values?: AssayValuesEntry
+type Mds3AssayAvailability = {
+	/** object of key-value pairs. keys are dt values */
+	byDt: {
+		/** each index is a dt value */
+		[index: number]: DtAssayAvailabilityByOrigin | DtAssayAvailability
+	}
 }
 
-type AssayAvailability = {
-	byDt?: ByDt
+// mds legacy; delete when all are migrated to mds3
+type LegacyAssayAvailability = {
 	file?: string
-	assays?: AssaysEntry[]
+	assays?: {
+		id: string
+		name: string
+		type: string
+		values?: {
+			[index: string]: { label: string; color: string }
+		}
+	}[]
 }
 
 export type CumBurdenData = {
@@ -1887,7 +1897,7 @@ type ViewMode = {
 /*** types supporting Mds Dataset types ***/
 type BaseMds = {
 	genome?: string //Not declared in TermdbTest
-	assayAvailability?: AssayAvailability
+	assayAvailability?: Mds3AssayAvailability | LegacyAssayAvailability
 }
 
 export type Mds = BaseMds & {
@@ -1965,6 +1975,14 @@ export type isSupportedChartCallbacks = {
 }
 
 export type Mds3 = BaseMds & {
+	/** set in initGenomesDs.js during launch, should use .genomename instead of .genome */
+	genomename?: string // use this
+	genome?: string // avoid using it
+	/** server-side genome obj to which this ds belongs to is attached here in initGenomesDs.js during launch, 
+	so this obj can be conveniently available to server side functions without having to introduce extra param
+	TODO apply Genome type
+	*/
+	genomeObj?: any
 	label?: Title
 	isMds3: boolean
 	loadWithoutBlocking?: boolean

package/src/routes/gdc.grin2.ts

@@ -70,6 +70,18 @@ export type GdcGRIN2listResponse = {
 		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[]
+	}
+	/** 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 */
+	}
 }
 
 /**