@sjcrh/proteinpaint-types 2.124.0 → 2.126.0

package/dist/clearwsisession.js

@@ -1,3 +1,6 @@
+import {
+  clearWSImagesSessionsPayload
+} from "./chunk-RPX4TVMD.js";
 import {
   __toESM,
   require_lib
@@ -5,19 +8,6 @@ import {
 
 // dist/clearwsisession.ts
 var import_typia = __toESM(require_lib(), 1);
-
-// src/routes/clearwsisessions.ts
-var clearWSImagesSessionsPayload = {
-  request: {
-    typeId: "ClearWSImagesSessionsRequest"
-  },
-  response: {
-    typeId: "ClearWSImagesSessionsResponse"
-  }
-  // examples: []
-};
-
-// dist/clearwsisession.ts
 var validClearWSImagesSessionsRequest = (input) => {
   const errors = [];
   const __is = (input2) => {

package/dist/clearwsisessions.js

@@ -0,0 +1,13 @@
+import {
+  validClearWSImagesSessionsRequest,
+  validClearWSImagesSessionsResponse
+} from "./chunk-SMS3Y2XZ.js";
+import {
+  clearWSImagesSessionsPayload
+} from "./chunk-RPX4TVMD.js";
+import "./chunk-CNSSF43V.js";
+export {
+  clearWSImagesSessionsPayload,
+  validClearWSImagesSessionsRequest,
+  validClearWSImagesSessionsResponse
+};

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-K7P6C6KU.js";
+} from "./chunk-LVXO4MLR.js";
 import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,

package/dist/gdc.grin2.js

@@ -0,0 +1,17 @@
+import {
+  gdcGRIN2Payload,
+  runGRIN2Payload,
+  validGdcGRIN2listRequest,
+  validGdcGRIN2listResponse,
+  validRunGRIN2Request,
+  validRunGRIN2Response
+} from "./chunk-NWEXA2YB.js";
+import "./chunk-CNSSF43V.js";
+export {
+  gdcGRIN2Payload,
+  runGRIN2Payload,
+  validGdcGRIN2listRequest,
+  validGdcGRIN2listResponse,
+  validRunGRIN2Request,
+  validRunGRIN2Response
+};

package/dist/genesetEnrichment.js

@@ -2,7 +2,7 @@ import {
   genesetEnrichmentPayload,
   validGenesetEnrichmentRequest,
   validGenesetEnrichmentResponse
-} from "./chunk-XZAH6P4D.js";
+} from "./chunk-A3XJW6BZ.js";
 import "./chunk-CNSSF43V.js";
 export {
   genesetEnrichmentPayload,

package/dist/healthcheck.js

@@ -2,7 +2,7 @@ import {
   healthcheckPayload,
   validHealthCheckRequest,
   validHealthCheckResponse
-} from "./chunk-KRYTJ2SL.js";
+} from "./chunk-RWMZSRX7.js";
 import "./chunk-CNSSF43V.js";
 export {
   healthcheckPayload,

package/dist/index.js

@@ -1,48 +1,68 @@
+import {
+  validWSImagesRequest,
+  validWSImagesResponse,
+  wsImagesPayload
+} from "./chunk-UZH5HOBP.js";
+import {
+  validWSISamplesRequest,
+  validWSISamplesResponse,
+  wsiSamplesPayload
+} from "./chunk-W6NLM363.js";
+import {
+  termdbSingleCellSamplesPayload,
+  validTermdbSingleCellSamplesRequest,
+  validTermdbSingleCellSamplesResponse
+} from "./chunk-LPBYQJG4.js";
+import {
+  termChildrenPayload,
+  validTermChildrenRequest,
+  validTermChildrenResponse
+} from "./chunk-HKGWC7OO.js";
 import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-AGSW7G4T.js";
+} from "./chunk-O4RAE6UJ.js";
 import {
   topMutatedGenePayload,
-  validTopMutatedGeneRequest,
-  validTopMutatedGeneResponse
-} from "./chunk-WQGLAGSY.js";
+  validtopMutatedGeneRequest,
+  validtopMutatedGeneResponse
+} from "./chunk-YGX6BZZY.js";
 import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-NCFUZ5VV.js";
+} from "./chunk-2S4T3WUF.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-SQBZAOWB.js";
+} from "./chunk-7IRM7OKB.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-RX5EB2HL.js";
+} from "./chunk-VSNV3MLV.js";
 import {
   tilePayload,
   validTileRequest,
   validTileResponse
 } from "./chunk-KFVYRW7D.js";
 import {
-  validWSImagesRequest,
-  validWSImagesResponse,
-  wsImagesPayload
-} from "./chunk-UZH5HOBP.js";
+  descrStatsPayload,
+  validDescrStatsRequest,
+  validDescrStatsResponse
+} from "./chunk-YOS2YTCE.js";
 import {
-  validWSISamplesRequest,
-  validWSSamplesResponse,
-  wsiSamplesPayload
-} from "./chunk-5HL5BPE5.js";
+  numericCategoriesPayload,
+  validNumericCategoriesRequest,
+  validNumericCategoriesResponse
+} from "./chunk-5O422YU6.js";
 import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-3ZT4UCFM.js";
+} from "./chunk-BXPSDGWG.js";
 import {
   rootTermPayload,
   validRootTermRequest,
@@ -69,15 +89,15 @@ import {
   validTermdbSingleCellDataResponse
 } from "./chunk-ZAMCS7PC.js";
 import {
-  termdbSingleCellSamplesPayload,
-  validTermdbSingleCellSamplesRequest,
-  validTermdbSingleCellSamplesResponse
-} from "./chunk-LPBYQJG4.js";
+  sampleWSImagesPayload,
+  validSampleWSImagesRequest,
+  validSampleWSImagesResponse
+} from "./chunk-D5OG676D.js";
 import {
-  termChildrenPayload,
-  validTermChildrenRequest,
-  validTermChildrenResponse
-} from "./chunk-HKGWC7OO.js";
+  snpPayload,
+  validSnpRequest,
+  validSnpResponse
+} from "./chunk-J4QAF4EU.js";
 import {
   diffExpPayload,
   validDERequest,
@@ -87,17 +107,17 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-XPOHYEAY.js";
+} from "./chunk-537XOM43.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-ZMOSABYP.js";
+} from "./chunk-GZCIY2WK.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-F64WJMRL.js";
+} from "./chunk-DJCPG2RT.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -109,15 +129,15 @@ import {
   validTermdbCohortsResponse
 } from "./chunk-EH7VAE5S.js";
 import {
-  descrStatsPayload,
-  validDescrStatsRequest,
-  validDescrStatsResponse
-} from "./chunk-5XRJ5ATE.js";
+  hicdataPayload,
+  validHicdataRequest,
+  validHicdataResponse
+} from "./chunk-VKBTOKI2.js";
 import {
-  numericCategoriesPayload,
-  validNumericCategoriesRequest,
-  validNumericCategoriesResponse
-} from "./chunk-LBGUOJR3.js";
+  hicGenomePayload,
+  validHicGenomeRequest,
+  validHicGenomeResponse
+} from "./chunk-I2KWGMNM.js";
 import {
   hicstatPayload,
   validHicstatRequest,
@@ -144,15 +164,18 @@ import {
   validPdomainResponse
 } from "./chunk-L5DFYFWX.js";
 import {
-  sampleWSImagesPayload,
-  validSampleWSImagesRequest,
-  validSampleWSImagesResponse
-} from "./chunk-D5OG676D.js";
+  dzImagesPayload,
+  validDZImagesRequest,
+  validDZImagesResponse
+} from "./chunk-XT2IWGYK.js";
 import {
-  snpPayload,
-  validSnpRequest,
-  validSnpResponse
-} from "./chunk-J4QAF4EU.js";
+  gdcGRIN2Payload,
+  runGRIN2Payload,
+  validGdcGRIN2listRequest,
+  validGdcGRIN2listResponse,
+  validRunGRIN2Request,
+  validRunGRIN2Response
+} from "./chunk-NWEXA2YB.js";
 import {
   gdcMafPayload,
   validGdcMafRequest,
@@ -172,7 +195,7 @@ import {
   genesetEnrichmentPayload,
   validGenesetEnrichmentRequest,
   validGenesetEnrichmentResponse
-} from "./chunk-XZAH6P4D.js";
+} from "./chunk-A3XJW6BZ.js";
 import {
   genesetOverrepresentationPayload,
   validGenesetOverrepresentationRequest,
@@ -182,22 +205,12 @@ import {
   healthcheckPayload,
   validHealthCheckRequest,
   validHealthCheckResponse
-} from "./chunk-KRYTJ2SL.js";
-import {
-  hicdataPayload,
-  validHicdataRequest,
-  validHicdataResponse
-} from "./chunk-VKBTOKI2.js";
-import {
-  hicGenomePayload,
-  validHicGenomeRequest,
-  validHicGenomeResponse
-} from "./chunk-I2KWGMNM.js";
+} from "./chunk-RWMZSRX7.js";
 import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-QMWUUGEK.js";
+} from "./chunk-CJC7ZHSZ.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,
@@ -208,11 +221,18 @@ import {
   validBurdenRequest,
   validBurdenResponse
 } from "./chunk-ZVTZJRGS.js";
+import {
+  validClearWSImagesSessionsRequest,
+  validClearWSImagesSessionsResponse
+} from "./chunk-SMS3Y2XZ.js";
+import {
+  clearWSImagesSessionsPayload
+} from "./chunk-RPX4TVMD.js";
 import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-K7P6C6KU.js";
+} from "./chunk-LVXO4MLR.js";
 import {
   datasetPayload,
   validDatasetRequest,
@@ -223,11 +243,6 @@ import {
   validDsDataRequest,
   validDsDataResponse
 } from "./chunk-4GCROGGK.js";
-import {
-  dzImagesPayload,
-  validDZImagesRequest,
-  validDZImagesResponse
-} from "./chunk-XT2IWGYK.js";
 import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,
@@ -236,11 +251,13 @@ export {
   brainImagingPayload,
   brainImagingSamplesPayload,
   burdenPayload,
+  clearWSImagesSessionsPayload,
   datasetPayload,
   descrStatsPayload,
   diffExpPayload,
   dsDataPayload,
   dzImagesPayload,
+  gdcGRIN2Payload,
   gdcMafPayload,
   geneLookupPayload,
   genesetEnrichmentPayload,
@@ -256,6 +273,7 @@ export {
   pdomainPayload,
   percentilePayload,
   rootTermPayload,
+  runGRIN2Payload,
   sampleWSImagesPayload,
   snpPayload,
   termChildrenPayload,
@@ -283,6 +301,8 @@ export {
   validBurdenResponse,
   validCategoriesRequest,
   validCategoriesResponse,
+  validClearWSImagesSessionsRequest,
+  validClearWSImagesSessionsResponse,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse,
   validDERequest,
@@ -295,6 +315,8 @@ export {
   validDescrStatsResponse,
   validDsDataRequest,
   validDsDataResponse,
+  validGdcGRIN2listRequest,
+  validGdcGRIN2listResponse,
   validGdcMafBuildRequest,
   validGdcMafBuildResponse,
   validGdcMafRequest,
@@ -325,6 +347,8 @@ export {
   validPercentileResponse,
   validRootTermRequest,
   validRootTermResponse,
+  validRunGRIN2Request,
+  validRunGRIN2Response,
   validSampleWSImagesRequest,
   validSampleWSImagesResponse,
   validSnpRequest,
@@ -355,16 +379,16 @@ export {
   validTermsByIdsResponse,
   validTileRequest,
   validTileResponse,
-  validTopMutatedGeneRequest,
-  validTopMutatedGeneResponse,
   validViolinRequest,
   validViolinResponse,
   validWSISamplesRequest,
+  validWSISamplesResponse,
   validWSImagesRequest,
   validWSImagesResponse,
-  validWSSamplesResponse,
   validimgRequest,
   validimgResponse,
+  validtopMutatedGeneRequest,
+  validtopMutatedGeneResponse,
   violinPayload,
   wsImagesPayload,
   wsiSamplesPayload

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-XPOHYEAY.js";
+} from "./chunk-537XOM43.js";
 import "./chunk-CNSSF43V.js";
 export {
   boxplotPayload,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-ZMOSABYP.js";
+} from "./chunk-GZCIY2WK.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-F64WJMRL.js";
+} from "./chunk-DJCPG2RT.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-5XRJ5ATE.js";
+} from "./chunk-YOS2YTCE.js";
 import "./chunk-CNSSF43V.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-LBGUOJR3.js";
+} from "./chunk-5O422YU6.js";
 import "./chunk-CNSSF43V.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-3ZT4UCFM.js";
+} from "./chunk-BXPSDGWG.js";
 import "./chunk-CNSSF43V.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-AGSW7G4T.js";
+} from "./chunk-O4RAE6UJ.js";
 import "./chunk-CNSSF43V.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topMutatedGenes.js

@@ -1,11 +1,11 @@
 import {
   topMutatedGenePayload,
-  validTopMutatedGeneRequest,
-  validTopMutatedGeneResponse
-} from "./chunk-WQGLAGSY.js";
+  validtopMutatedGeneRequest,
+  validtopMutatedGeneResponse
+} from "./chunk-YGX6BZZY.js";
 import "./chunk-CNSSF43V.js";
 export {
   topMutatedGenePayload,
-  validTopMutatedGeneRequest,
-  validTopMutatedGeneResponse
+  validtopMutatedGeneRequest,
+  validtopMutatedGeneResponse
 };

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-NCFUZ5VV.js";
+} from "./chunk-2S4T3WUF.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-SQBZAOWB.js";
+} from "./chunk-7IRM7OKB.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-RX5EB2HL.js";
+} from "./chunk-VSNV3MLV.js";
 import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,

package/dist/wsisamples.js

@@ -1,11 +1,11 @@
 import {
   validWSISamplesRequest,
-  validWSSamplesResponse,
+  validWSISamplesResponse,
   wsiSamplesPayload
-} from "./chunk-5HL5BPE5.js";
+} from "./chunk-W6NLM363.js";
 import "./chunk-CNSSF43V.js";
 export {
   validWSISamplesRequest,
-  validWSSamplesResponse,
+  validWSISamplesResponse,
   wsiSamplesPayload
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.124.0",
+  "version": "2.126.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -1966,6 +1966,12 @@ export type Mds3 = BaseMds & {
 	isMds3: boolean
 	loadWithoutBlocking?: boolean
 	preInit?: PreInit
+	init?: {
+		/** number of milliseconds to wait before calling th preInit.getStatus() again */
+		retryDelay?: number
+		/** maximum number of times to call preInit.getStatus() before giving up */
+		retryMax?: number
+	}
 	initErrorCallback?: (a: any) => void
 	viewModes?: ViewMode[]
 	dsinfo?: KeyVal[]

package/src/index.ts

@@ -17,6 +17,7 @@ export * from './routes/errorResponse.ts'
 export * from './routes/filter.gdc.ts'
 export * from './routes/gdc.maf.ts'
 export * from './routes/gdc.mafBuild.ts'
+export * from './routes/gdc.grin2.ts'
 export * from './routes/termdb.topMutatedGenes.ts'
 export * from './routes/genelookup.ts'
 export * from './routes/genesetEnrichment.ts'

package/src/routes/gdc.grin2.ts

@@ -0,0 +1,101 @@
+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'
+}
+
+enum ExperimentalStrategy {
+	wxs = 'WXS'
+}
+
+/**
+ * Request parameters for GRIN2 file listing
+ */
+export type GdcGRIN2listRequest = {
+	/** Name of experimental strategy to get files for */
+	experimentalStrategy: ExperimentalStrategy
+	/** JSON, optional GDC cohort filter to restrict cases */
+	filter0?: any
+	/** Optional array of file types to include ('MAF') */
+	fileTypes?: Array<'MAF'>
+}
+
+/**
+ * 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?: {
+		fileTypes?: Array<'MAF'>
+		experimentalStrategy?: ExperimentalStrategy
+	}
+}
+
+/**
+ * Parameters for running GRIN2 analysis
+ */
+export type RunGRIN2Request = {
+	[caseId: string]: { maf?: string }
+}
+
+/**
+ * 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' */
+	imagestring?: string
+	/** Download status */
+	download?: any
+	/** Table of top genes indentified by analysis */
+	topgenetable?: any
+}
+/**
+ * Route payload definitions for type checking
+ */
+export const gdcGRIN2Payload: RoutePayload = {
+	request: {
+		typeId: 'GdcGRIN2listRequest'
+	},
+	response: {
+		typeId: 'GdcGRIN2listResponse'
+	}
+}
+
+export const runGRIN2Payload: RoutePayload = {
+	request: {
+		typeId: 'RunGRIN2Request'
+	},
+	response: {
+		typeId: 'RunGRIN2Response'
+	}
+}

package/src/routes/genesetEnrichment.ts

@@ -17,6 +17,8 @@ export type GenesetEnrichmentRequest = {
 	pickle_file?: string
 	/** Number of permutations to be carried out for GSEA analysis */
 	num_permutations: number
+	/** Method used for GSEA blitzgsea/cerno */
+	method: 'blitzgsea' | 'cerno'
 }
 
 type pathway_attributes = {