@sjcrh/proteinpaint-types 2.128.0 → 2.128.3-bd2a3a1c9.0

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-LVXO4MLR.js";
+} from "./chunk-CI6OEJNH.js";
 import "./chunk-CNSSF43V.js";
 export {
   CorrelationVolcanoPayload,

package/dist/gdc.grin2.js

@@ -5,7 +5,7 @@ import {
   validGdcGRIN2listResponse,
   validRunGRIN2Request,
   validRunGRIN2Response
-} from "./chunk-B2DJ3H7H.js";
+} from "./chunk-DJ5QE625.js";
 import "./chunk-CNSSF43V.js";
 export {
   gdcGRIN2listPayload,

package/dist/genesetEnrichment.js

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

package/dist/index.js

@@ -22,7 +22,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-O4RAE6UJ.js";
+} from "./chunk-UXXLPWL2.js";
 import {
   topMutatedGenePayload,
   validtopMutatedGeneRequest,
@@ -32,17 +32,17 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-2S4T3WUF.js";
+} from "./chunk-Y5BVEGR2.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-7IRM7OKB.js";
+} from "./chunk-WHO7HCNU.js";
 import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-VSNV3MLV.js";
+} from "./chunk-6C4DMGK3.js";
 import {
   tilePayload,
   validTileRequest,
@@ -52,17 +52,17 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-YOS2YTCE.js";
+} from "./chunk-24RS7HFO.js";
 import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-5O422YU6.js";
+} from "./chunk-KHM52S5N.js";
 import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-BXPSDGWG.js";
+} from "./chunk-WK4CKVHY.js";
 import {
   rootTermPayload,
   validRootTermRequest,
@@ -107,17 +107,17 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-537XOM43.js";
+} from "./chunk-RP6RBKKL.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-GZCIY2WK.js";
+} from "./chunk-PX7P2A6A.js";
 import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-DJCPG2RT.js";
+} from "./chunk-BMHL5ZZJ.js";
 import {
   termdbCohortSummaryPayload,
   validTermdbCohortSummaryRequest,
@@ -175,7 +175,7 @@ import {
   validGdcGRIN2listResponse,
   validRunGRIN2Request,
   validRunGRIN2Response
-} from "./chunk-B2DJ3H7H.js";
+} from "./chunk-DJ5QE625.js";
 import {
   gdcMafPayload,
   validGdcMafRequest,
@@ -195,7 +195,7 @@ import {
   genesetEnrichmentPayload,
   validGenesetEnrichmentRequest,
   validGenesetEnrichmentResponse
-} from "./chunk-XZAH6P4D.js";
+} from "./chunk-HUMZDPUU.js";
 import {
   genesetOverrepresentationPayload,
   validGenesetOverrepresentationRequest,
@@ -210,7 +210,7 @@ import {
   brainImagingPayload,
   validBrainImagingRequest,
   validBrainImagingResponse
-} from "./chunk-CJC7ZHSZ.js";
+} from "./chunk-WSL4JPUP.js";
 import {
   brainImagingSamplesPayload,
   validBrainImagingSamplesRequest,
@@ -232,7 +232,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-LVXO4MLR.js";
+} from "./chunk-CI6OEJNH.js";
 import {
   datasetPayload,
   validDatasetRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-537XOM43.js";
+} from "./chunk-RP6RBKKL.js";
 import "./chunk-CNSSF43V.js";
 export {
   boxplotPayload,

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-GZCIY2WK.js";
+} from "./chunk-PX7P2A6A.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-DJCPG2RT.js";
+} from "./chunk-BMHL5ZZJ.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbClusterPayload,

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-YOS2YTCE.js";
+} from "./chunk-24RS7HFO.js";
 import "./chunk-CNSSF43V.js";
 export {
   descrStatsPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-5O422YU6.js";
+} from "./chunk-KHM52S5N.js";
 import "./chunk-CNSSF43V.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-BXPSDGWG.js";
+} from "./chunk-WK4CKVHY.js";
 import "./chunk-CNSSF43V.js";
 export {
   percentilePayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-O4RAE6UJ.js";
+} from "./chunk-UXXLPWL2.js";
 import "./chunk-CNSSF43V.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-2S4T3WUF.js";
+} from "./chunk-Y5BVEGR2.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-7IRM7OKB.js";
+} from "./chunk-WHO7HCNU.js";
 import "./chunk-CNSSF43V.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violin.js

@@ -2,7 +2,7 @@ import {
   validViolinRequest,
   validViolinResponse,
   violinPayload
-} from "./chunk-VSNV3MLV.js";
+} from "./chunk-6C4DMGK3.js";
 import "./chunk-CNSSF43V.js";
 export {
   validViolinRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.128.0",
+  "version": "2.128.3-bd2a3a1c9.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -614,6 +614,19 @@ type CnvSegment = {
 			[key: string]: any
 		}
 	}
+
+	/** in mds3 tk view and gdc cnv tool, when number of segments from view region exceeds this cutoff, it's piled up into density view to speed up
+	overrides default 1000
+	this cutoff does not apply to other uses beyond mds3 tk, including matrix and geneVariant
+	*/
+	densityViewCutoff?: number
+
+	/** this cutoff is applied in ds.queries.cnv.get(), in that up to this number of segments will be returned
+	overrides default 10k
+	this applies to matrix, geneVariant, and mds3 tk
+	todo there lacks a way for getter to message downstream code of exceeding limit
+	*/
+	maxReturnCutoff?: number
 }
 
 /*
@@ -1925,10 +1938,6 @@ export type PreInit = {
 		status 4xx are not considered recoverable (client-related request errors)
 	*/
 	getStatus: () => Promise<PreInitStatus>
-	/** 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
 	/**
 	 * dev only, used to test preInit handling by simulating different
 	 * responses in a known sequence of steps that may edit the preInit
@@ -1963,8 +1972,12 @@ export type Mds3 = BaseMds & {
 	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 */
+		/** maximum number of tries to complete initialization, including preInit.getStatus() before validation steps
+		 * and the nonblocking steps after validation. Before the retryMax is reached, errors are considered recoverable;
+		 * errors when retryMax is reached will be fatal. */
 		retryMax?: number
+		/** option to trigger mds3InitNonblocking() on this dataset */
+		hasNonblockingSteps?: boolean
 		/** server-computed cumulative count of the attempted init retries */
 		currentRetry?: number
 		/**

package/src/routes/gdc.grin2.ts

@@ -28,12 +28,20 @@ enum ExperimentalStrategy {
  * 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'>
+
+	/** 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 (for future use) */
+	cnvOptions?: any
+
+	/** Options for fusion file retrieval. Presence indicates fusion files should be returned (for future use) */
+	fusionOptions?: any
 }
 
 /**
@@ -52,7 +60,6 @@ export type GdcGRIN2listResponse = {
 	}
 	/** Applied filters (for UI reference) */
 	appliedFilters?: {
-		fileTypes?: Array<'MAF'>
 		experimentalStrategy?: ExperimentalStrategy
 	}
 }

package/src/routes/genesetEnrichment.ts

@@ -17,9 +17,11 @@ 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 = {
+type blitzgsea_geneset_attributes = {
 	/** Absolute enrichment score */
 	es: number
 	/** Normalized enrichment score */
@@ -36,19 +38,52 @@ type pathway_attributes = {
 	fdr: number
 }
 
-type gsea_result = {
+// 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: pathway_attributes[]
+	data: blitzgsea_map[]
 	/** file name of pickle file containing the stored gsea result in cache directory */
 	pickle_file: string
 }
 
+// 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 gsea_image = any
+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 */
-	pathway: gsea_result | gsea_image
+	data: blitzgseaResult | cernoResult
 }
 
 export const genesetEnrichmentPayload: RoutePayload = {

package/src/terms/geneVariant.ts

@@ -1,4 +1,4 @@
-import type { MinBaseQ, BaseTerm, TermGroupSetting, BaseTW, TermValues, BaseGroupSet, TermFilter } from '../index.ts'
+import type { MinBaseQ, BaseTerm, TermGroupSetting, BaseTW, TermValues, BaseGroupSet } from '../index.ts'
 import type { TermSettingInstance } from '../termsetting.ts'
 
 // q types
@@ -43,13 +43,13 @@ export type GvCoord = {
 export type RawGvTerm = GvBaseTerm &
 	(GvGene | GvCoord) & {
 		groupsetting?: TermGroupSetting
-		filter?: TermFilter
+		childTerms?: DtTerm[]
 	}
 
 export type GvTerm = GvBaseTerm &
 	(GvGene | GvCoord) & {
 		groupsetting: TermGroupSetting
-		filter: TermFilter
+		childTerms: DtTerm[]
 	}
 
 // tw types
@@ -94,7 +94,7 @@ export type DtTerm = {
 	query: string
 	name: string
 	name_noOrigin: string
-	geneVariantTerm?: RawGvTerm
+	parentTerm?: RawGvTerm
 	parent_id: any
 	isleaf: boolean
 	type: string

package/src/terms/term.ts

@@ -2,7 +2,7 @@ import type { Filter } from '../filter.js'
 import type { CategoricalTerm, CategoricalBaseQ } from './categorical.js'
 import type { ConditionTerm } from './condition.js'
 import type { NumericTerm } from './numeric.js'
-import type { GvTerm, DtTerm } from './geneVariant.js'
+import type { GvTerm } from './geneVariant.js'
 import type { SampleLstTerm } from './samplelst.js'
 import type { SnpsTerm } from './snps.js'
 
@@ -105,7 +105,6 @@ export type BaseTerm = {
 	included_types?: string[]
 	isleaf?: boolean
 	values?: TermValues
-	filter?: TermFilter
 }
 
 export type Term = BaseTerm & (NumericTerm | CategoricalTerm | ConditionTerm | SampleLstTerm | SnpsTerm | GvTerm)
@@ -120,18 +119,10 @@ export type ValuesGroup = {
 export type FilterGroup = {
 	name: string
 	type: 'filter'
-	filter: TermFilter & {
-		active: Filter // active filter
-		group: number // group index
-	}
+	filter: Filter
 	uncomputable: boolean
 }
 
-export type TermFilter = {
-	opts: { joinWith: string[] } // options for joining filters
-	terms: DtTerm[] // terms used to build a frontend vocab that will be used for filtering // TODO: generalize the term structure used here
-}
-
 export type GroupEntry = ValuesGroup | FilterGroup
 
 export type BaseGroupSet = {

package/dist/chunk-XZAH6P4D.js

@@ -1,130 +0,0 @@
-import {
-  __toESM,
-  require_lib
-} from "./chunk-CNSSF43V.js";
-
-// dist/genesetEnrichment.ts
-var import_typia = __toESM(require_lib(), 1);
-
-// src/routes/genesetEnrichment.ts
-var genesetEnrichmentPayload = {
-  request: {
-    typeId: "GenesetEnrichmentRequest"
-  },
-  response: {
-    typeId: "GenesetEnrichmentResponse"
-  }
-  //examples: []
-};
-
-// dist/genesetEnrichment.ts
-var validGenesetEnrichmentRequest = (input) => {
-  const errors = [];
-  const __is = (input2) => {
-    const $io0 = (input3) => Array.isArray(input3.genes) && input3.genes.every((elem) => "string" === typeof elem) && (Array.isArray(input3.fold_change) && input3.fold_change.every((elem) => "number" === typeof elem)) && "boolean" === typeof input3.filter_non_coding_genes && "string" === typeof input3.genome && "string" === typeof input3.geneSetGroup && (void 0 === input3.geneset_name || "string" === typeof input3.geneset_name) && (void 0 === input3.pickle_file || "string" === typeof input3.pickle_file) && "number" === typeof input3.num_permutations;
-    return "object" === typeof input2 && null !== input2 && $io0(input2);
-  };
-  if (false === __is(input)) {
-    const $report = import_typia.createValidate.report(errors);
-    ((input2, _path, _exceptionable = true) => {
-      const $vo0 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.genes) || $report(_exceptionable2, {
-        path: _path2 + ".genes",
-        expected: "Array<string>",
-        value: input3.genes
-      })) && input3.genes.map((elem, _index1) => "string" === typeof elem || $report(_exceptionable2, {
-        path: _path2 + ".genes[" + _index1 + "]",
-        expected: "string",
-        value: elem
-      })).every((flag) => flag) || $report(_exceptionable2, {
-        path: _path2 + ".genes",
-        expected: "Array<string>",
-        value: input3.genes
-      }), (Array.isArray(input3.fold_change) || $report(_exceptionable2, {
-        path: _path2 + ".fold_change",
-        expected: "Array<number>",
-        value: input3.fold_change
-      })) && input3.fold_change.map((elem, _index2) => "number" === typeof elem || $report(_exceptionable2, {
-        path: _path2 + ".fold_change[" + _index2 + "]",
-        expected: "number",
-        value: elem
-      })).every((flag) => flag) || $report(_exceptionable2, {
-        path: _path2 + ".fold_change",
-        expected: "Array<number>",
-        value: input3.fold_change
-      }), "boolean" === typeof input3.filter_non_coding_genes || $report(_exceptionable2, {
-        path: _path2 + ".filter_non_coding_genes",
-        expected: "boolean",
-        value: input3.filter_non_coding_genes
-      }), "string" === typeof input3.genome || $report(_exceptionable2, {
-        path: _path2 + ".genome",
-        expected: "string",
-        value: input3.genome
-      }), "string" === typeof input3.geneSetGroup || $report(_exceptionable2, {
-        path: _path2 + ".geneSetGroup",
-        expected: "string",
-        value: input3.geneSetGroup
-      }), void 0 === input3.geneset_name || "string" === typeof input3.geneset_name || $report(_exceptionable2, {
-        path: _path2 + ".geneset_name",
-        expected: "(string | undefined)",
-        value: input3.geneset_name
-      }), void 0 === input3.pickle_file || "string" === typeof input3.pickle_file || $report(_exceptionable2, {
-        path: _path2 + ".pickle_file",
-        expected: "(string | undefined)",
-        value: input3.pickle_file
-      }), "number" === typeof input3.num_permutations || $report(_exceptionable2, {
-        path: _path2 + ".num_permutations",
-        expected: "number",
-        value: input3.num_permutations
-      })].every((flag) => flag);
-      return ("object" === typeof input2 && null !== input2 || $report(true, {
-        path: _path + "",
-        expected: "GenesetEnrichmentRequest",
-        value: input2
-      })) && $vo0(input2, _path + "", true) || $report(true, {
-        path: _path + "",
-        expected: "GenesetEnrichmentRequest",
-        value: input2
-      });
-    })(input, "$input", true);
-  }
-  const success = 0 === errors.length;
-  return {
-    success,
-    errors,
-    data: success ? input : void 0
-  };
-};
-var validGenesetEnrichmentResponse = (input) => {
-  const errors = [];
-  const __is = (input2) => {
-    const $io0 = (input3) => true;
-    return "object" === typeof input2 && null !== input2 && $io0(input2);
-  };
-  if (false === __is(input)) {
-    const $report = import_typia.createValidate.report(errors);
-    ((input2, _path, _exceptionable = true) => {
-      const $vo0 = (input3, _path2, _exceptionable2 = true) => [true].every((flag) => flag);
-      return ("object" === typeof input2 && null !== input2 || $report(true, {
-        path: _path + "",
-        expected: "GenesetEnrichmentResponse",
-        value: input2
-      })) && $vo0(input2, _path + "", true) || $report(true, {
-        path: _path + "",
-        expected: "GenesetEnrichmentResponse",
-        value: input2
-      });
-    })(input, "$input", true);
-  }
-  const success = 0 === errors.length;
-  return {
-    success,
-    errors,
-    data: success ? input : void 0
-  };
-};
-
-export {
-  genesetEnrichmentPayload,
-  validGenesetEnrichmentRequest,
-  validGenesetEnrichmentResponse
-};