@sjcrh/proteinpaint-types 2.111.0 → 2.112.1-0

package/dist/{chunk-2OBKIEPJ.js → chunk-3QALQGW4.js}

@@ -74,15 +74,29 @@ var validDERequest = (input) => {
 var validDEResponse = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => "string" === typeof input3.data && "number" === typeof input3.sample_size1 && "number" === typeof input3.sample_size2 && "string" === typeof input3.method && true && true;
+    const $io0 = (input3) => Array.isArray(input3.data) && input3.data.every((elem) => "object" === typeof elem && null !== elem && $io1(elem)) && "number" === typeof input3.sample_size1 && "number" === typeof input3.sample_size2 && "string" === typeof input3.method && (void 0 === input3.images || Array.isArray(input3.images) && input3.images.every((elem) => "object" === typeof elem && null !== elem && $io2(elem)));
+    const $io1 = (input3) => "number" === typeof input3.adjusted_p_value && "number" === typeof input3.original_p_value && "number" === typeof input3.fold_change && "string" === typeof input3.gene_name && "string" === typeof input3.gene_symbol;
+    const $io2 = (input3) => "string" === typeof input3.src && "number" === typeof input3.size && "string" === typeof input3.key;
     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) => ["string" === typeof input3.data || $report(_exceptionable2, {
+      const $vo0 = (input3, _path2, _exceptionable2 = true) => [(Array.isArray(input3.data) || $report(_exceptionable2, {
         path: _path2 + ".data",
-        expected: "string",
+        expected: "Array<DataEntry>",
+        value: input3.data
+      })) && input3.data.map((elem, _index1) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
+        path: _path2 + ".data[" + _index1 + "]",
+        expected: "DataEntry",
+        value: elem
+      })) && $vo1(elem, _path2 + ".data[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".data[" + _index1 + "]",
+        expected: "DataEntry",
+        value: elem
+      })).every((flag) => flag) || $report(_exceptionable2, {
+        path: _path2 + ".data",
+        expected: "Array<DataEntry>",
         value: input3.data
       }), "number" === typeof input3.sample_size1 || $report(_exceptionable2, {
         path: _path2 + ".sample_size1",
@@ -96,7 +110,57 @@ var validDEResponse = (input) => {
         path: _path2 + ".method",
         expected: "string",
         value: input3.method
-      }), true, true].every((flag) => flag);
+      }), void 0 === input3.images || (Array.isArray(input3.images) || $report(_exceptionable2, {
+        path: _path2 + ".images",
+        expected: "(Array<DEImage> | undefined)",
+        value: input3.images
+      })) && input3.images.map((elem, _index2) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
+        path: _path2 + ".images[" + _index2 + "]",
+        expected: "DEImage",
+        value: elem
+      })) && $vo2(elem, _path2 + ".images[" + _index2 + "]", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".images[" + _index2 + "]",
+        expected: "DEImage",
+        value: elem
+      })).every((flag) => flag) || $report(_exceptionable2, {
+        path: _path2 + ".images",
+        expected: "(Array<DEImage> | undefined)",
+        value: input3.images
+      })].every((flag) => flag);
+      const $vo1 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.adjusted_p_value || $report(_exceptionable2, {
+        path: _path2 + ".adjusted_p_value",
+        expected: "number",
+        value: input3.adjusted_p_value
+      }), "number" === typeof input3.original_p_value || $report(_exceptionable2, {
+        path: _path2 + ".original_p_value",
+        expected: "number",
+        value: input3.original_p_value
+      }), "number" === typeof input3.fold_change || $report(_exceptionable2, {
+        path: _path2 + ".fold_change",
+        expected: "number",
+        value: input3.fold_change
+      }), "string" === typeof input3.gene_name || $report(_exceptionable2, {
+        path: _path2 + ".gene_name",
+        expected: "string",
+        value: input3.gene_name
+      }), "string" === typeof input3.gene_symbol || $report(_exceptionable2, {
+        path: _path2 + ".gene_symbol",
+        expected: "string",
+        value: input3.gene_symbol
+      })].every((flag) => flag);
+      const $vo2 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.src || $report(_exceptionable2, {
+        path: _path2 + ".src",
+        expected: "string",
+        value: input3.src
+      }), "number" === typeof input3.size || $report(_exceptionable2, {
+        path: _path2 + ".size",
+        expected: "number",
+        value: input3.size
+      }), "string" === typeof input3.key || $report(_exceptionable2, {
+        path: _path2 + ".key",
+        expected: "string",
+        value: input3.key
+      })].every((flag) => flag);
       return ("object" === typeof input2 && null !== input2 || $report(true, {
         path: _path + "",
         expected: "DEResponse",

package/dist/{chunk-HR6GSKDC.js → chunk-UZH5HOBP.js}

@@ -64,7 +64,7 @@ var validWSImagesRequest = (input) => {
 var validWSImagesResponse = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => (void 0 === input3.wsiSessionId || "string" === typeof input3.wsiSessionId) && (void 0 === input3.browserImageInstanceId || "string" === typeof input3.browserImageInstanceId) && (Array.isArray(input3.slide_dimensions) && input3.slide_dimensions.every((elem) => "number" === typeof elem)) && "string" === typeof input3.status;
+    const $io0 = (input3) => (void 0 === input3.wsiSessionId || "string" === typeof input3.wsiSessionId) && (Array.isArray(input3.slide_dimensions) && input3.slide_dimensions.every((elem) => "number" === typeof elem)) && "string" === typeof input3.status && (void 0 === input3.error || "string" === typeof input3.error);
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -74,10 +74,6 @@ var validWSImagesResponse = (input) => {
         path: _path2 + ".wsiSessionId",
         expected: "(string | undefined)",
         value: input3.wsiSessionId
-      }), void 0 === input3.browserImageInstanceId || "string" === typeof input3.browserImageInstanceId || $report(_exceptionable2, {
-        path: _path2 + ".browserImageInstanceId",
-        expected: "(string | undefined)",
-        value: input3.browserImageInstanceId
       }), (Array.isArray(input3.slide_dimensions) || $report(_exceptionable2, {
         path: _path2 + ".slide_dimensions",
         expected: "Array<number>",
@@ -94,6 +90,10 @@ var validWSImagesResponse = (input) => {
         path: _path2 + ".status",
         expected: "string",
         value: input3.status
+      }), void 0 === input3.error || "string" === typeof input3.error || $report(_exceptionable2, {
+        path: _path2 + ".error",
+        expected: "(string | undefined)",
+        value: input3.error
       })].every((flag) => flag);
       return ("object" === typeof input2 && null !== input2 || $report(true, {
         path: _path + "",

package/dist/clearwsisession.js

@@ -1,9 +1,86 @@
 import {
-  clearWSImagesSessionsPayload,
-  validClearWSImagesSessionsRequest,
-  validClearWSImagesSessionsResponse
-} from "./chunk-QNBBWHEY.js";
-import "./chunk-CNSSF43V.js";
+  __toESM,
+  require_lib
+} from "./chunk-CNSSF43V.js";
+
+// 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) => {
+    const $io0 = (input3) => Array.isArray(input3.sessions);
+    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.sessions) || $report(_exceptionable2, {
+        path: _path2 + ".sessions",
+        expected: "Array<any>",
+        value: input3.sessions
+      })].every((flag) => flag);
+      return ("object" === typeof input2 && null !== input2 || $report(true, {
+        path: _path + "",
+        expected: "ClearWSImagesSessionsRequest",
+        value: input2
+      })) && $vo0(input2, _path + "", true) || $report(true, {
+        path: _path + "",
+        expected: "ClearWSImagesSessionsRequest",
+        value: input2
+      });
+    })(input, "$input", true);
+  }
+  const success = 0 === errors.length;
+  return {
+    success,
+    errors,
+    data: success ? input : void 0
+  };
+};
+var validClearWSImagesSessionsResponse = (input) => {
+  const errors = [];
+  const __is = (input2) => {
+    return "object" === typeof input2 && null !== input2 && "string" === typeof input2.message;
+  };
+  if (false === __is(input)) {
+    const $report = import_typia.createValidate.report(errors);
+    ((input2, _path, _exceptionable = true) => {
+      const $vo0 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.message || $report(_exceptionable2, {
+        path: _path2 + ".message",
+        expected: "string",
+        value: input3.message
+      })].every((flag) => flag);
+      return ("object" === typeof input2 && null !== input2 || $report(true, {
+        path: _path + "",
+        expected: "ClearWSImagesSessionsResponse",
+        value: input2
+      })) && $vo0(input2, _path + "", true) || $report(true, {
+        path: _path + "",
+        expected: "ClearWSImagesSessionsResponse",
+        value: input2
+      });
+    })(input, "$input", true);
+  }
+  const success = 0 === errors.length;
+  return {
+    success,
+    errors,
+    data: success ? input : void 0
+  };
+};
 export {
   clearWSImagesSessionsPayload,
   validClearWSImagesSessionsRequest,

package/dist/index.js

@@ -32,7 +32,7 @@ import {
   validWSImagesRequest,
   validWSImagesResponse,
   wsImagesPayload
-} from "./chunk-HR6GSKDC.js";
+} from "./chunk-UZH5HOBP.js";
 import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
@@ -82,7 +82,7 @@ import {
   diffExpPayload,
   validDERequest,
   validDEResponse
-} from "./chunk-2OBKIEPJ.js";
+} from "./chunk-3QALQGW4.js";
 import {
   boxplotPayload,
   validBoxPlotRequest,
@@ -203,11 +203,6 @@ import {
   validBurdenRequest,
   validBurdenResponse
 } from "./chunk-ZVTZJRGS.js";
-import {
-  clearWSImagesSessionsPayload,
-  validClearWSImagesSessionsRequest,
-  validClearWSImagesSessionsResponse
-} from "./chunk-QNBBWHEY.js";
 import {
   CorrelationVolcanoPayload,
   validCorrelationVolcanoRequest,
@@ -236,7 +231,6 @@ export {
   brainImagingPayload,
   brainImagingSamplesPayload,
   burdenPayload,
-  clearWSImagesSessionsPayload,
   datasetPayload,
   descrStatsPayload,
   diffExpPayload,
@@ -284,8 +278,6 @@ export {
   validBurdenResponse,
   validCategoriesRequest,
   validCategoriesResponse,
-  validClearWSImagesSessionsRequest,
-  validClearWSImagesSessionsResponse,
   validCorrelationVolcanoRequest,
   validCorrelationVolcanoResponse,
   validDERequest,

package/dist/termdb.DE.js

@@ -2,7 +2,7 @@ import {
   diffExpPayload,
   validDERequest,
   validDEResponse
-} from "./chunk-2OBKIEPJ.js";
+} from "./chunk-3QALQGW4.js";
 import "./chunk-CNSSF43V.js";
 export {
   diffExpPayload,

package/dist/wsimages.js

@@ -2,7 +2,7 @@ import {
   validWSImagesRequest,
   validWSImagesResponse,
   wsImagesPayload
-} from "./chunk-HR6GSKDC.js";
+} from "./chunk-UZH5HOBP.js";
 import "./chunk-CNSSF43V.js";
 export {
   validWSImagesRequest,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.111.0",
+  "version": "2.112.1-0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -243,7 +243,6 @@ type Population = {
 }
 
 /** primarily for prebuilding germline genetic association for survivorship portal
-accessible to client via termdb.js?for=mds3queryDetails
 part of state of genomeBrowser plot
 allowing for user modification
 */
@@ -334,7 +333,12 @@ so that it can work for a termdb-less ds, e.g. clinvar, where termdbConfig canno
 	}
 	allowSNPs?: boolean
 	vcfid4skewerName?: boolean
+	/** config on computing variant data and show as a custom mds3 tk */
 	details?: SnvindelComputeDetails
+	/** set to true to show mds3 tk by default when the ds have other genome browser track types besides this snvindel tk
+	if ds has only snvindel tk, then the tk will always be shown and no need to set this
+	*/
+	shown?: boolean
 }
 
 type SvFusion = {
@@ -452,44 +456,50 @@ type TopMutatedGenes = {
 	arguments?: GeneArgumentEntry[]
 }
 
-type TklstEntry = {
-	/** Determines the column to add the track via the assay names
-	 * shown at the top of the facet table.*/
-	assay?: string
-	/** track type (e.g. bigwig, bedj, etc.) */
-	type: string
-	/** Human readable name */
-	name: string
-	/** Corresponding sample id in the data file */
-	sampleID?: string
-	/** data file path */
-	file: string
-	/** The key for the second tier of the facet table*/
-	level1?: string
-	/** The key for the third tier of the facet table*/
-	level2?: string
-	/** Whether the track is shown by default */
-	defaultShown?: boolean
-	/** Track height */
-	stackheight?: number
-	/** Space added to the height of the track */
-	stackspace?: number
-	/** padding-top for the track */
-	toppad?: number
-	/** padding-bottom for the track */
-	bottompad?: number
-	/** Specifically for bedj tracks. if true, will render all items in a
-	 * single row and do not stack them */
-	onerow?: number | boolean
-}
-
-type TrackLstEntry = {
-	/** creates a facet table if true. */
-	isfacet: boolean
-	/** name shown for the facet table button from Tracks button*/
-	name: string
-	/** tk objs to show on click of the facet table */
-	tklst: TklstEntry[]
+/** setup for a set of genome browser tracks and/or facet tables, that can be selected for genomebrowser display
+ */
+type TrackLst = {
+	/** path to legacy json file containing a long array of 1 or more facets
+
+	[
+	  {
+         "isfacet": true,
+         "name": "PEDDEP Prepilot",
+         "tracks": [
+		   {
+		     name:str // required. used as *identifer* for a track
+			 sample:str // required. should match with a sample in db!
+			 assay:str // required. free string not controlled in dictionary yet. if missing the track won't appear in facet table
+			 type:str // properties inherent for each custom track
+			 file:str
+		   },
+		   ... more tk
+		 ]
+	  },
+	  { ... 2nd facet table }
+	]
+
+	*/
+	jsonFile: string
+
+	/*
+	alternative format that's easier to maintain than a giant json file
+	facetFiles:[
+		{
+			// name of this facet table
+			name: str
+			// a tabular file with columns "tkname/assay/sample/path/json"; last column json provides any customization for a track
+			// e.g. "Track 1 \t h3k4me3 \t sample1 \t path/to/file.bw \t {"scale":{..}}"
+			tabFile: string
+		}
+	]
+	*/
+
+	/** list of track names to show by default, should be found in json file
+	in json content above, allow a name to be shared by multiple tracks!
+	in such case, all tracks identified by given name will show/hide altogether
+	*/
+	activeTracks: string[]
 }
 
 type CnvSegment = {
@@ -712,6 +722,7 @@ type SCImages = {
 	label: string
 }
 
+/** genome browser LD track */
 type LdQuery = {
 	/** each track obj defines a ld track */
 	tracks: {
@@ -719,8 +730,6 @@ type LdQuery = {
 		name: string
 		/** relative path of ld .gz file */
 		file: string
-		/** dynamically added full path */
-		file0?: string
 		/** dynamically added */
 		nochr?: boolean
 		/** if to show by default */
@@ -779,6 +788,9 @@ type Mds3Queries = {
 	snvindel?: SnvIndelQuery
 	svfusion?: SvFusion
 	cnv?: CnvSegment
+	trackLst?: TrackLst
+	ld?: LdQuery
+	defaultCoord?: string
 	singleSampleMutation?: SingleSampleMutationQuery
 	NIdata?: NIdataQuery
 	geneExpression?: GeneExpressionQuery
@@ -793,15 +805,12 @@ type Mds3Queries = {
 		src: 'native' | 'gdc'
 		file: string
 	}
-	trackLst?: TrackLstEntry[]
 	singleCell?: SingleCellQuery
 	geneCnv?: {
 		bygene?: {
 			gdcapi: true
 		}
 	}
-	defaultCoord?: string
-	ld?: LdQuery
 	singleSampleGenomeQuantification?: SingleSampleGenomeQuantification
 	singleSampleGbtk?: SingleSampleGbtk
 	/** depreciated. replaced by WSImages */

package/src/routes/termdb.DE.ts

@@ -50,17 +50,33 @@ export type ExpressionInput = {
 
 export type DEResponse = {
 	/** Array containing objects of each gene containing foldchange, gene name, gene symbol, original pvalue, adjusted pvalue */
-	data: string
+	data: DataEntry[]
 	/** Effective sample size for group 1 */
 	sample_size1: number
 	/** Effective sample size for group 2 */
 	sample_size2: number
 	/** Method of DE used wilcoxon/edgeR */
 	method: string
-	/** Image name from edgeR describing the quality of the fitting from QL pipeline, this is only generated for edgeR not for wilcoxon method  */
-	ql_image?: any
-	/** Image name from edgeR showing the MDS plot of samples from both groups, this is only generated for edgeR not for wilcoxon method */
-	mds_image?: any
+	/** QL: Image describing the quality of the fitting from QL pipeline, this is only generated for edgeR not for wilcoxon method  */
+	/** MDS: Image showing the MDS plot of samples from both groups, this is only generated for edgeR not for wilcoxon method */
+	images?: DEImage[]
+}
+
+export type DataEntry = {
+	adjusted_p_value: number
+	original_p_value: number
+	fold_change: number
+	gene_name: string
+	gene_symbol: string
+}
+
+export type DEImage = {
+	/** Image source */
+	src: string
+	/** File size */
+	size: number
+	/** Image identifier */
+	key: string
 }
 
 export const diffExpPayload: RoutePayload = {

package/src/routes/wsimages.ts

@@ -10,11 +10,9 @@ export type WSImagesRequest = {
 export type WSImagesResponse = {
 	// TileServer image session id
 	wsiSessionId?: string
-	// Identifier for the image instance displayed in the browser
-	// In case the same image is displayed in multiple browser windows, a new id is generated
-	browserImageInstanceId?: string
 	slide_dimensions: number[]
 	status: string
+	error?: string
 }
 
 export const wsImagesPayload: RoutePayload = {

package/dist/chunk-QNBBWHEY.js

@@ -1,89 +0,0 @@
-import {
-  __toESM,
-  require_lib
-} from "./chunk-CNSSF43V.js";
-
-// 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) => {
-    const $io0 = (input3) => Array.isArray(input3.sessions);
-    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.sessions) || $report(_exceptionable2, {
-        path: _path2 + ".sessions",
-        expected: "Array<any>",
-        value: input3.sessions
-      })].every((flag) => flag);
-      return ("object" === typeof input2 && null !== input2 || $report(true, {
-        path: _path + "",
-        expected: "ClearWSImagesSessionsRequest",
-        value: input2
-      })) && $vo0(input2, _path + "", true) || $report(true, {
-        path: _path + "",
-        expected: "ClearWSImagesSessionsRequest",
-        value: input2
-      });
-    })(input, "$input", true);
-  }
-  const success = 0 === errors.length;
-  return {
-    success,
-    errors,
-    data: success ? input : void 0
-  };
-};
-var validClearWSImagesSessionsResponse = (input) => {
-  const errors = [];
-  const __is = (input2) => {
-    return "object" === typeof input2 && null !== input2 && "string" === typeof input2.message;
-  };
-  if (false === __is(input)) {
-    const $report = import_typia.createValidate.report(errors);
-    ((input2, _path, _exceptionable = true) => {
-      const $vo0 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.message || $report(_exceptionable2, {
-        path: _path2 + ".message",
-        expected: "string",
-        value: input3.message
-      })].every((flag) => flag);
-      return ("object" === typeof input2 && null !== input2 || $report(true, {
-        path: _path + "",
-        expected: "ClearWSImagesSessionsResponse",
-        value: input2
-      })) && $vo0(input2, _path + "", true) || $report(true, {
-        path: _path + "",
-        expected: "ClearWSImagesSessionsResponse",
-        value: input2
-      });
-    })(input, "$input", true);
-  }
-  const success = 0 === errors.length;
-  return {
-    success,
-    errors,
-    data: success ? input : void 0
-  };
-};
-
-export {
-  clearWSImagesSessionsPayload,
-  validClearWSImagesSessionsRequest,
-  validClearWSImagesSessionsResponse
-};