@sjcrh/proteinpaint-types 2.116.1-0 → 2.116.1-2

package/dist/{chunk-MDBZCBM2.js → chunk-CNR46KGX.js}

@@ -3450,19 +3450,19 @@ var validCorrelationVolcanoResponse = (input) => {
         value: input3.skippedVariables
       }), (Array.isArray(input3.variableItems) || $report(_exceptionable2, {
         path: _path2 + ".variableItems",
-        expected: "Array<__type>.o1",
+        expected: "Array<VariableItemEntry>",
         value: input3.variableItems
       })) && input3.variableItems.map((elem, _index2) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
         path: _path2 + ".variableItems[" + _index2 + "]",
-        expected: "__type.o1",
+        expected: "VariableItemEntry",
         value: elem
       })) && $vo2(elem, _path2 + ".variableItems[" + _index2 + "]", _exceptionable2) || $report(_exceptionable2, {
         path: _path2 + ".variableItems[" + _index2 + "]",
-        expected: "__type.o1",
+        expected: "VariableItemEntry",
         value: elem
       })).every((flag) => flag) || $report(_exceptionable2, {
         path: _path2 + ".variableItems",
-        expected: "Array<__type>.o1",
+        expected: "Array<VariableItemEntry>",
         value: input3.variableItems
       })].every((flag) => flag);
       const $vo1 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.tw$id || $report(_exceptionable2, {

package/dist/{chunk-IJHMCHUT.js → chunk-WQGLAGSY.js}

@@ -21,8 +21,10 @@ var topMutatedGenePayload = {
 var validTopMutatedGeneRequest = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && (void 0 === input3.geneFilter || "CGC" === input3.geneFilter) && (void 0 === input3.maxGenes || "number" === typeof input3.maxGenes) && (void 0 === input3.filter0 || "object" === typeof input3.filter0 && null !== input3.filter0 && false === Array.isArray(input3.filter0) && $io1(input3.filter0));
+    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && (void 0 === input3.geneFilter || "CGC" === input3.geneFilter) && (void 0 === input3.maxGenes || "number" === typeof input3.maxGenes) && (void 0 === input3.filter || "object" === typeof input3.filter && null !== input3.filter && false === Array.isArray(input3.filter) && $io1(input3.filter)) && (void 0 === input3.filter0 || "object" === typeof input3.filter0 && null !== input3.filter0 && false === Array.isArray(input3.filter0) && $io1(input3.filter0)) && (void 0 === input3.snv_mfndi || "number" === typeof input3.snv_mfndi) && (void 0 === input3.snv_splice || "number" === typeof input3.snv_splice) && (void 0 === input3.snv_utr || "number" === typeof input3.snv_utr) && (void 0 === input3.snv_s || "number" === typeof input3.snv_s) && (void 0 === input3.sv || "number" === typeof input3.sv) && (void 0 === input3.fusion || "number" === typeof input3.fusion) && (void 0 === input3.cnv || "number" === typeof input3.cnv) && (void 0 === input3.cnv_ms || "object" === typeof input3.cnv_ms && null !== input3.cnv_ms && $io2(input3.cnv_ms)) && (void 0 === input3.cnv_logratio || "object" === typeof input3.cnv_logratio && null !== input3.cnv_logratio && $io3(input3.cnv_logratio));
     const $io1 = (input3) => true;
+    const $io2 = (input3) => "string" === typeof input3.type && (void 0 !== input3.geneLst && null === input3.geneLst);
+    const $io3 = (input3) => "string" === typeof input3.type && (void 0 !== input3.geneLst && null === input3.geneLst);
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -44,6 +46,14 @@ var validTopMutatedGeneRequest = (input) => {
         path: _path2 + ".maxGenes",
         expected: "(number | undefined)",
         value: input3.maxGenes
+      }), void 0 === input3.filter || ("object" === typeof input3.filter && null !== input3.filter && false === Array.isArray(input3.filter) || $report(_exceptionable2, {
+        path: _path2 + ".filter",
+        expected: "(object | undefined)",
+        value: input3.filter
+      })) && $vo1(input3.filter, _path2 + ".filter", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".filter",
+        expected: "(object | undefined)",
+        value: input3.filter
       }), void 0 === input3.filter0 || ("object" === typeof input3.filter0 && null !== input3.filter0 && false === Array.isArray(input3.filter0) || $report(_exceptionable2, {
         path: _path2 + ".filter0",
         expected: "(object | undefined)",
@@ -52,8 +62,78 @@ var validTopMutatedGeneRequest = (input) => {
         path: _path2 + ".filter0",
         expected: "(object | undefined)",
         value: input3.filter0
+      }), void 0 === input3.snv_mfndi || "number" === typeof input3.snv_mfndi || $report(_exceptionable2, {
+        path: _path2 + ".snv_mfndi",
+        expected: "(number | undefined)",
+        value: input3.snv_mfndi
+      }), void 0 === input3.snv_splice || "number" === typeof input3.snv_splice || $report(_exceptionable2, {
+        path: _path2 + ".snv_splice",
+        expected: "(number | undefined)",
+        value: input3.snv_splice
+      }), void 0 === input3.snv_utr || "number" === typeof input3.snv_utr || $report(_exceptionable2, {
+        path: _path2 + ".snv_utr",
+        expected: "(number | undefined)",
+        value: input3.snv_utr
+      }), void 0 === input3.snv_s || "number" === typeof input3.snv_s || $report(_exceptionable2, {
+        path: _path2 + ".snv_s",
+        expected: "(number | undefined)",
+        value: input3.snv_s
+      }), void 0 === input3.sv || "number" === typeof input3.sv || $report(_exceptionable2, {
+        path: _path2 + ".sv",
+        expected: "(number | undefined)",
+        value: input3.sv
+      }), void 0 === input3.fusion || "number" === typeof input3.fusion || $report(_exceptionable2, {
+        path: _path2 + ".fusion",
+        expected: "(number | undefined)",
+        value: input3.fusion
+      }), void 0 === input3.cnv || "number" === typeof input3.cnv || $report(_exceptionable2, {
+        path: _path2 + ".cnv",
+        expected: "(number | undefined)",
+        value: input3.cnv
+      }), void 0 === input3.cnv_ms || ("object" === typeof input3.cnv_ms && null !== input3.cnv_ms || $report(_exceptionable2, {
+        path: _path2 + ".cnv_ms",
+        expected: "(__type | undefined)",
+        value: input3.cnv_ms
+      })) && $vo2(input3.cnv_ms, _path2 + ".cnv_ms", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".cnv_ms",
+        expected: "(__type | undefined)",
+        value: input3.cnv_ms
+      }), void 0 === input3.cnv_logratio || ("object" === typeof input3.cnv_logratio && null !== input3.cnv_logratio || $report(_exceptionable2, {
+        path: _path2 + ".cnv_logratio",
+        expected: "(__type.o1 | undefined)",
+        value: input3.cnv_logratio
+      })) && $vo3(input3.cnv_logratio, _path2 + ".cnv_logratio", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".cnv_logratio",
+        expected: "(__type.o1 | undefined)",
+        value: input3.cnv_logratio
       })].every((flag) => flag);
       const $vo1 = (input3, _path2, _exceptionable2 = true) => true;
+      const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.type || $report(_exceptionable2, {
+        path: _path2 + ".type",
+        expected: "string",
+        value: input3.type
+      }), (void 0 !== input3.geneLst || $report(_exceptionable2, {
+        path: _path2 + ".geneLst",
+        expected: "null",
+        value: input3.geneLst
+      })) && (null === input3.geneLst || $report(_exceptionable2, {
+        path: _path2 + ".geneLst",
+        expected: "null",
+        value: input3.geneLst
+      }))].every((flag) => flag);
+      const $vo3 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.type || $report(_exceptionable2, {
+        path: _path2 + ".type",
+        expected: "string",
+        value: input3.type
+      }), (void 0 !== input3.geneLst || $report(_exceptionable2, {
+        path: _path2 + ".geneLst",
+        expected: "null",
+        value: input3.geneLst
+      })) && (null === input3.geneLst || $report(_exceptionable2, {
+        path: _path2 + ".geneLst",
+        expected: "null",
+        value: input3.geneLst
+      }))].every((flag) => flag);
       return ("object" === typeof input2 && null !== input2 || $report(true, {
         path: _path + "",
         expected: "topMutatedGeneRequest",

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-MDBZCBM2.js";
+} from "./chunk-CNR46KGX.js";
 import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,

package/dist/index.js

@@ -7,7 +7,7 @@ import {
   topMutatedGenePayload,
   validTopMutatedGeneRequest,
   validTopMutatedGeneResponse
-} from "./chunk-IJHMCHUT.js";
+} from "./chunk-WQGLAGSY.js";
 import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
@@ -212,7 +212,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-MDBZCBM2.js";
+} from "./chunk-CNR46KGX.js";
 import {
   datasetPayload,
   validDatasetRequest,

package/dist/termdb.topMutatedGenes.js

@@ -2,7 +2,7 @@ import {
   topMutatedGenePayload,
   validTopMutatedGeneRequest,
   validTopMutatedGeneResponse
-} from "./chunk-IJHMCHUT.js";
+} from "./chunk-WQGLAGSY.js";
 import "./chunk-CNSSF43V.js";
 export {
   topMutatedGenePayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.116.1-0",
+  "version": "2.116.1-2",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -421,9 +421,14 @@ export type GeneArgumentEntry = {
 	label: string
 	/** Optional: Creates subtext below the main label */
 	sublabel?: string
-	/** boolean and string creates a checkbox
-	 * number creates a text input
-	 */
+	/** 'boolean' has two options.
+	 * 	- If .options[] is provided, it creates a 'submenu', a checkbox
+	 * 		that expands to show additional inputs when checked. .options[]
+	 * 		in this case is GeneArgumentEntry[]
+	 *  - If !.options[] is provided, it creates a checkbox
+	 * 'string' creates a checked checkbox if a .value is provided
+	 * 'number' creates a text number input
+	 * 'radio' creates a radio buttons, see options[] */
 	type: 'boolean' | 'string' | 'number' | 'radio'
 	/** value of the input or checkbox
 	 * required if type is string. Otherwise, optional
@@ -441,6 +446,8 @@ export type GeneArgumentEntry = {
 		 * 'text': creates a text area input
 		 * 'tree': launches termdb app and the tree
 		 * 'boolean': No element is created
+		 *
+		 * boolean is the default type
 		 */
 		type: 'text' | 'tree' | 'boolean' | string
 		/** value used to construct the server argument
@@ -799,7 +806,23 @@ type SingleSampleGbtk = {
 }
 
 type Mds3Queries = {
-	defaultBlock2GeneMode?: boolean
+	/** (gb=genomebrowser) controls gb chart button menu genesearchbox behavior, 
+	add some additional options after a gene is found, and mode of gb launched from the menu
+
+	- "protein":
+		genesearchbox only allow searching gene and not coord
+		launched gb goes into protein-mode
+		this is used for ds with only coding mutations over some protein-coding genes, and only want to show protein view for such
+	- "genomic":
+		searching either gene/coord will result in coord
+		gb will always be in genomic mode
+		this is used for ds with genome-wide variants only shown in genomic views, but not protein view
+	- none:
+		meaning gb can be shown in either protein or genomic mode
+		when searching coord, gb goes into genomic mode
+		when searching gene, show an option in chart btn menu to select protein or genomic view
+	*/
+	gbRestrictMode?: 'protein' | 'genomic'
 	snvindel?: SnvIndelQuery
 	svfusion?: SvFusion
 	cnv?: CnvSegment
@@ -1026,6 +1049,9 @@ type SurvivalSettings = {
 }
 
 type RegressionSettings = {
+	/** Disclaimer message shown under the cofficient table when
+	 * regression type is cox. */
+	coxDisclaimer?: string
 	/** disable interactions */
 	disableInteractions?: boolean
 	/** hide type III statistics table in results */
@@ -1198,7 +1224,6 @@ type Termdb = {
 	/** if true, backend is allowed to send sample names to client in charts */
 	displaySampleIds?: boolean
 	converSampleIds?: boolean
-	allowedTermTypes?: string[]
 	alwaysShowBranchTerms?: boolean
 	minimumSampleAllowed4filter?: number
 	minTimeSinceDx?: number
@@ -1243,8 +1268,38 @@ keep this setting here for reason of:
 		ssm?: UrlTemplateSsm | UrlTemplateSsm[]
 	}
 
-	/** ds-defined or dynamically created */
-	termtypeByCohort?: any
+	termtypeByCohort?: any // FIXME see below
+	/** TODO not declared due to tsc err
+	ds-defined or dynamically created. the array has an extra "nested" property
+	only describes dictionary terms,
+	non-dict terms are dynamically generated in getAllowedTermTypes() of termdb.config.ts based on query types
+	termtypeByCohort?: {
+		cohort: string
+		termType: string
+		termCount: number
+	}[] & {
+		nested: {
+			[cohort: string]: {
+				[termType: string]: number
+			}
+		}
+	}
+	*/
+
+	/** ds defined add on to termtypeByCohort; note that this is not cohort-specific!
+	this is combined with termtypeByCohort in getAllowedTermTypes()
+	for now is used to support following types which lacks good way to auto generate them:
+
+	- geneVariant
+		for somatic events. works for snvindel/svfusion/cnv.
+		since all these datatypes are optional, cannot define it in snvindel.termTypes which could be missing
+		** must be defined via allowedTermTypes[] **
+
+	- snp, snplst, snplocus
+		for germline markers
+	*/
+	allowedTermTypes?: string[]
+
 	/** ds-defined or dynamically created callbacks 
 	{
 		getSupportedChartTypes: (a: any) => any
@@ -1291,6 +1346,30 @@ keep this setting here for reason of:
 		/** allow color or shape changes in the lollipop */
 		allowSkewerChanges: boolean
 	}
+	//* specify color map per module/group of terms. Used in the profile dataset.
+	/** For example "National Context" is a profile module, that groups some multivalue terms for wich the category colors are the ones shown below: 
+	 colorMap: {
+				['*']: {
+					['Not applicable for my role']: '#aaa',
+					['Not Available/Do Not Know']: '#aaa',
+					["I don't know"]: '#aaa',
+					['Almost Never']: '#595959',
+					['Infrequently']: '#747474',
+					['No']: '#aaa'
+				},
+				['National Context']: {
+					['Almost Always']: '#15557C',
+					['Frequently']: '#1E77BB',
+					['Sometimes']: '#2FA9F4',
+					['Yes']: '#1E77BB'
+				},
+	}
+	If the colors are the same for all the categories, use the wildcard '*' to define the color for all the modules.
+	**/
+	colorMap?: {
+		/** colors for a category multivalues */
+		[index: string]: { [index: string]: string }
+	}
 }
 
 type SampleType = {

package/src/routes/correlationVolcano.ts

@@ -24,18 +24,20 @@ export type CorrelationVolcanoResponse = {
 		tw$id: string
 	}[]
 	/** each element is test result of one variable corresponding to variableTwLst */
-	variableItems: {
-		/** correlation coefficient, -1 to 1 */
-		correlation: number
-		/** pvalue */
-		original_pvalue: number
-		/** pvalue */
-		adjusted_pvalue: number
-		/** tw.$id, for client to match the item with variableTwLst */
-		tw$id: string
-		/** number of samples analyzed. samples not having complete data for all terms will be excluded, thus size may be lower than current cohort */
-		sampleSize: number
-	}[]
+	variableItems: VariableItemEntry[]
+}
+
+export type VariableItemEntry = {
+	/** correlation coefficient, -1 to 1 */
+	correlation: number
+	/** pvalue */
+	original_pvalue: number
+	/** pvalue */
+	adjusted_pvalue: number
+	/** tw.$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 = {

package/src/routes/termdb.topMutatedGenes.ts

@@ -7,8 +7,20 @@ export type topMutatedGeneRequest = {
 	geneFilter?: 'CGC'
 	/** max number of genes to return */
 	maxGenes?: number
+	/** pp filter */
+	filter?: object
 	/** gdc cohort filter */
 	filter0?: object
+	/** rest are arguments for built in query */
+	snv_mfndi?: number
+	snv_splice?: number
+	snv_utr?: number
+	snv_s?: number
+	sv?: number
+	fusion?: number
+	cnv?: number
+	cnv_ms?: { type: string; geneLst: null }
+	cnv_logratio?: { type: string; geneLst: null }
 }
 
 export type MutatedGene = {