@sjcrh/proteinpaint-types 2.106.0 → 2.108.0

package/dist/burden.js

@@ -2,7 +2,7 @@ import {
   burdenPayload,
   validBurdenRequest,
   validBurdenResponse
-} from "./chunk-RLFGMVJZ.js";
+} from "./chunk-GHD26RNJ.js";
 import "./chunk-Z6B6IQIY.js";
 export {
   burdenPayload,

package/dist/{chunk-FUIYK4TP.js → chunk-2R2EFRAW.js}

@@ -3328,31 +3328,53 @@ var validCorrelationVolcanoRequest = (input) => {
 var validCorrelationVolcanoResponse = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => Array.isArray(input3.variableItems) && input3.variableItems.every((elem) => "object" === typeof elem && null !== elem && $io1(elem));
-    const $io1 = (input3) => "number" === typeof input3.correlation && "number" === typeof input3.original_pvalue && "number" === typeof input3.adjusted_pvalue && "string" === typeof input3.tw$id && "number" === typeof input3.sampleSize;
+    const $io0 = (input3) => Array.isArray(input3.skippedVariables) && input3.skippedVariables.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && (Array.isArray(input3.variableItems) && input3.variableItems.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)));
+    const $io1 = (input3) => "string" === typeof input3.tw$id;
+    const $io2 = (input3) => "number" === typeof input3.correlation && "number" === typeof input3.original_pvalue && "number" === typeof input3.adjusted_pvalue && "string" === typeof input3.tw$id && "number" === typeof input3.sampleSize;
     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.variableItems) || $report(_exceptionable2, {
-        path: _path2 + ".variableItems",
+      const $vo0 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.skippedVariables) || $report(_exceptionable2, {
+        path: _path2 + ".skippedVariables",
         expected: "Array<__type>",
-        value: input3.variableItems
-      })) && input3.variableItems.map((elem, _index1) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
-        path: _path2 + ".variableItems[" + _index1 + "]",
+        value: input3.skippedVariables
+      })) && input3.skippedVariables.map((elem, _index1) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
+        path: _path2 + ".skippedVariables[" + _index1 + "]",
         expected: "__type",
         value: elem
-      })) && $vo1(elem, _path2 + ".variableItems[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
-        path: _path2 + ".variableItems[" + _index1 + "]",
+      })) && $vo1(elem, _path2 + ".skippedVariables[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".skippedVariables[" + _index1 + "]",
         expected: "__type",
         value: elem
       })).every((flag) => flag) || $report(_exceptionable2, {
-        path: _path2 + ".variableItems",
+        path: _path2 + ".skippedVariables",
         expected: "Array<__type>",
+        value: input3.skippedVariables
+      }), (Array.isArray(input3.variableItems) || $report(_exceptionable2, {
+        path: _path2 + ".variableItems",
+        expected: "Array<__type>.o1",
         value: input3.variableItems
+      })) && input3.variableItems.map((elem, _index2) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
+        path: _path2 + ".variableItems[" + _index2 + "]",
+        expected: "__type.o1",
+        value: elem
+      })) && $vo2(elem, _path2 + ".variableItems[" + _index2 + "]", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".variableItems[" + _index2 + "]",
+        expected: "__type.o1",
+        value: elem
+      })).every((flag) => flag) || $report(_exceptionable2, {
+        path: _path2 + ".variableItems",
+        expected: "Array<__type>.o1",
+        value: input3.variableItems
+      })].every((flag) => flag);
+      const $vo1 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.tw$id || $report(_exceptionable2, {
+        path: _path2 + ".tw$id",
+        expected: "string",
+        value: input3.tw$id
       })].every((flag) => flag);
-      const $vo1 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.correlation || $report(_exceptionable2, {
+      const $vo2 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.correlation || $report(_exceptionable2, {
         path: _path2 + ".correlation",
         expected: "number",
         value: input3.correlation

package/dist/{chunk-XILU2DZ4.js → chunk-ERA5PPKH.js}

@@ -21,7 +21,7 @@ var genesetEnrichmentPayload = {
 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) && (void 0 === input3.num_permutations || "number" === typeof input3.num_permutations);
+    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)) {
@@ -71,9 +71,9 @@ var validGenesetEnrichmentRequest = (input) => {
         path: _path2 + ".pickle_file",
         expected: "(string | undefined)",
         value: input3.pickle_file
-      }), void 0 === input3.num_permutations || "number" === typeof input3.num_permutations || $report(_exceptionable2, {
+      }), "number" === typeof input3.num_permutations || $report(_exceptionable2, {
         path: _path2 + ".num_permutations",
-        expected: "(number | undefined)",
+        expected: "number",
         value: input3.num_permutations
       })].every((flag) => flag);
       return ("object" === typeof input2 && null !== input2 || $report(true, {

package/dist/{chunk-RLFGMVJZ.js → chunk-GHD26RNJ.js}

@@ -53,7 +53,7 @@ var burdenPayload = {
 var validBurdenRequest = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "number" === typeof input3.diaggrp && "number" === typeof input3.sex && "number" === typeof input3.white && "number" === typeof input3.agedx && "number" === typeof input3.bleo && "number" === typeof input3.etop && "number" === typeof input3.cisp && "number" === typeof input3.carbo && "number" === typeof input3.steriod && "number" === typeof input3.vcr && "number" === typeof input3.hdmtx && "number" === typeof input3.itmt && "number" === typeof input3.ced && "number" === typeof input3.dox && "number" === typeof input3.heart && "number" === typeof input3.brain && "number" === typeof input3.abd && "number" === typeof input3.pelvis && "number" === typeof input3.chest;
+    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "boolean" === typeof input3.showCI && "number" === typeof input3.diaggrp && "number" === typeof input3.sex && "number" === typeof input3.white && "number" === typeof input3.agedx && "number" === typeof input3.bleo && "number" === typeof input3.etop && "number" === typeof input3.cisp && "number" === typeof input3.carbo && "number" === typeof input3.steriod && "number" === typeof input3.vcr && "number" === typeof input3.hdmtx && "number" === typeof input3.itmt && "number" === typeof input3.ced && "number" === typeof input3.dox && "number" === typeof input3.heart && "number" === typeof input3.brain && "number" === typeof input3.abd && "number" === typeof input3.pelvis && "number" === typeof input3.chest;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -67,6 +67,10 @@ var validBurdenRequest = (input) => {
         path: _path2 + ".dslabel",
         expected: "string",
         value: input3.dslabel
+      }), "boolean" === typeof input3.showCI || $report(_exceptionable2, {
+        path: _path2 + ".showCI",
+        expected: "boolean",
+        value: input3.showCI
       }), "number" === typeof input3.diaggrp || $report(_exceptionable2, {
         path: _path2 + ".diaggrp",
         expected: "number",

package/dist/correlationVolcano.js

@@ -2,7 +2,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-FUIYK4TP.js";
+} from "./chunk-2R2EFRAW.js";
 import "./chunk-Z6B6IQIY.js";
 export {
   CorrelationVolcanoPayload,

package/dist/genesetEnrichment.js

@@ -2,7 +2,7 @@ import {
   genesetEnrichmentPayload,
   validGenesetEnrichmentRequest,
   validGenesetEnrichmentResponse
-} from "./chunk-XILU2DZ4.js";
+} from "./chunk-ERA5PPKH.js";
 import "./chunk-Z6B6IQIY.js";
 export {
   genesetEnrichmentPayload,

package/dist/index.js

@@ -172,7 +172,7 @@ import {
   genesetEnrichmentPayload,
   validGenesetEnrichmentRequest,
   validGenesetEnrichmentResponse
-} from "./chunk-XILU2DZ4.js";
+} from "./chunk-ERA5PPKH.js";
 import {
   genesetOverrepresentationPayload,
   validGenesetOverrepresentationRequest,
@@ -202,7 +202,7 @@ import {
   burdenPayload,
   validBurdenRequest,
   validBurdenResponse
-} from "./chunk-RLFGMVJZ.js";
+} from "./chunk-GHD26RNJ.js";
 import {
   clearWSImagesSessionsPayload,
   validClearWSImagesSessionsRequest,
@@ -212,7 +212,7 @@ import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse
-} from "./chunk-FUIYK4TP.js";
+} from "./chunk-2R2EFRAW.js";
 import {
   datasetPayload,
   validDatasetRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.106.0",
+  "version": "2.108.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -1318,17 +1318,29 @@ type AssayAvailability = {
 	assays?: AssaysEntry[]
 }
 
+export type CumBurdenData = {
+	/** directory containing cumulative burden data */
+	dir: string
+	files: {
+		fit: string
+		surv: string
+		sample: string
+	}
+	/** subdirectory containing bootstrap data */
+	bootsubdir: string
+	db: {
+		/** db file created by separate repo, pcb/utils/create.sql */
+		file: string
+		/** sqlite connection */
+		connection?: any
+	}
+}
+
 //Shared with genome.ts
 export type Cohort = {
 	/** if present, means correlation volcano plot analysis is enabled */
 	correlationVolcano?: CorrelationVolcano
-	cumburden?: {
-		files: {
-			fit: string
-			surv: string
-			sample: string
-		}
-	}
+	cumburden?: CumBurdenData
 	db: FileObj
 	/** customize the default chart to open on mass ui when there's no charts. if
 	 * missing it opens dictionary ui */

package/src/routes/burden.ts

@@ -5,6 +5,8 @@ export type BurdenRequest = {
 	genome: string
 	/** a user-defined dataset label in the serverconfig.json, such as ClinVar, SJLife, GDC, etc */
 	dslabel: string
+	/** boolean for whether to show 95% confidence interval */
+	showCI: boolean
 	/** the diagnosis group:
 	 * 1= "Acute lymphoblastic leukemia (ALL)"
 	 * 2= "Acute Myeloid Leukemia (AML)"

package/src/routes/correlationVolcano.ts

@@ -18,6 +18,11 @@ export type CorrelationVolcanoRequest = {
 }
 
 export type CorrelationVolcanoResponse = {
+	/** Terms with not enough vectors to calculate correlation to be shown in legend */
+	skippedVariables: {
+		/** matching tw $id */
+		tw$id: string
+	}[]
 	/** each element is test result of one variable corresponding to variableTwLst */
 	variableItems: {
 		/** correlation coefficient, -1 to 1 */

package/src/routes/genesetEnrichment.ts

@@ -15,8 +15,8 @@ export type GenesetEnrichmentRequest = {
 	geneset_name?: string
 	/** Pickle file to be queried for generating gsea image of a particular geneset */
 	pickle_file?: string
-	/** Number of permutations to be carried out for GSEA analysis, this variable will become compulsory once GSEA becomes stateless */
-	num_permutations?: number
+	/** Number of permutations to be carried out for GSEA analysis */
+	num_permutations: number
 }
 
 type pathway_attributes = {

package/src/routes/termdb.DE.ts

@@ -38,8 +38,8 @@ export type ExpressionInput = {
 	storage_type: 'HDF5' | 'text'
 	/** Confounding variable for DE analysis. Maybe array of string (Gender: Male/female) or number (Age). For now supporting 1 confounding variable. Later will add support for multiple confounding variables */
 	conf1?: any[]
-	/** Type of the confounding variable (categorical/float) */
-	conf1_type?: 'categorical' | 'float'
+	/** Type of the confounding variable (continuous/discrete) */
+	conf1_mode?: 'continuous' | 'discrete'
 	/** Number of variable genes to be included for DE analysis (optional) */
 	VarGenes?: number
 }