@sjcrh/proteinpaint-types 2.158.0 → 2.160.1-0

package/dist/{chunk-4LOGWDCZ.js → chunk-3EVYVWI2.js}

@@ -21,7 +21,7 @@ var termdbSingleCellDEgenesPayload = {
 var validTermdbSingleCellDEgenesRequest = (input) => {
   const errors = [];
   const __is = (input2) => {
-    return "object" === typeof input2 && null !== input2 && ("string" === typeof input2.genome && "string" === typeof input2.dslabel && "string" === typeof input2.sample && "string" === typeof input2.columnName && "string" === typeof input2.categoryName);
+    return "object" === typeof input2 && null !== input2 && ("string" === typeof input2.genome && "string" === typeof input2.dslabel && "string" === typeof input2.sample && "string" === typeof input2.termId && "string" === typeof input2.categoryName);
   };
   if (false === __is(input)) {
     const $report = import_typia.createValidate.report(errors);
@@ -38,10 +38,10 @@ var validTermdbSingleCellDEgenesRequest = (input) => {
         path: _path2 + ".sample",
         expected: "string",
         value: input3.sample
-      }), "string" === typeof input3.columnName || $report(_exceptionable2, {
-        path: _path2 + ".columnName",
+      }), "string" === typeof input3.termId || $report(_exceptionable2, {
+        path: _path2 + ".termId",
         expected: "string",
-        value: input3.columnName
+        value: input3.termId
       }), "string" === typeof input3.categoryName || $report(_exceptionable2, {
         path: _path2 + ".categoryName",
         expected: "string",

package/dist/{chunk-UGYLBYUU.js → chunk-5L4VF3ZL.js}

@@ -74,7 +74,15 @@ var validTermdbSingleSampleMutationResponse = (input) => {
         return Array.isArray(value) && value.every((elem) => "object" === typeof elem && null !== elem && $io5(elem));
       return true;
     });
-    const $io5 = (input3) => (void 0 === input3.nameHtml || "string" === typeof input3.nameHtml) && (void 0 === input3.name || "string" === typeof input3.name) && (void 0 === input3.inuse || "boolean" === typeof input3.inuse) && (Array.isArray(input3.mlst) && input3.mlst.every((elem) => "object" === typeof elem && null !== elem && false === Array.isArray(elem) && $io2(elem)));
+    const $io5 = (input3) => (void 0 === input3.nameHtml || "string" === typeof input3.nameHtml) && (void 0 === input3.name || "string" === typeof input3.name) && (void 0 === input3.inuse || "boolean" === typeof input3.inuse) && (Array.isArray(input3.mlst) && input3.mlst.every((elem) => "object" === typeof elem && null !== elem && false === Array.isArray(elem) && $io2(elem))) && (void 0 === input3.attrs || "object" === typeof input3.attrs && null !== input3.attrs && false === Array.isArray(input3.attrs) && $io6(input3.attrs));
+    const $io6 = (input3) => Object.keys(input3).every((key) => {
+      const value = input3[key];
+      if (void 0 === value)
+        return true;
+      if (RegExp(/(.*)/).test(key))
+        return "string" === typeof value;
+      return true;
+    });
     const $iu0 = (input3) => (() => {
       if (void 0 !== input3.status)
         return $io0(input3);
@@ -200,7 +208,27 @@ var validTermdbSingleSampleMutationResponse = (input) => {
         path: _path2 + ".mlst",
         expected: "Array<object>",
         value: input3.mlst
+      }), void 0 === input3.attrs || ("object" === typeof input3.attrs && null !== input3.attrs && false === Array.isArray(input3.attrs) || $report(_exceptionable2, {
+        path: _path2 + ".attrs",
+        expected: "(__type.o3 | undefined)",
+        value: input3.attrs
+      })) && $vo6(input3.attrs, _path2 + ".attrs", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".attrs",
+        expected: "(__type.o3 | undefined)",
+        value: input3.attrs
       })].every((flag) => flag);
+      const $vo6 = (input3, _path2, _exceptionable2 = true) => [false === _exceptionable2 || Object.keys(input3).map((key) => {
+        const value = input3[key];
+        if (void 0 === value)
+          return true;
+        if (RegExp(/(.*)/).test(key))
+          return "string" === typeof value || $report(_exceptionable2, {
+            path: _path2 + $join(key),
+            expected: "string",
+            value
+          });
+        return true;
+      }).every((flag) => flag)].every((flag) => flag);
       const $vu0 = (input3, _path2, _exceptionable2 = true) => (() => {
         if (void 0 !== input3.status)
           return $vo0(input3, _path2, _exceptionable2);

package/dist/{chunk-5BNDT4E6.js → chunk-GDZUCVIB.js}

@@ -20,7 +20,7 @@ var termdbSampleScatterPayload = {
 var validTermdbSampleScatterRequest = (input) => {
   const errors = [];
   const __is = (input2) => {
-    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && true && true && true && true && (void 0 === input3.coordTWs || Array.isArray(input3.coordTWs)) && (void 0 === input3.plotName || "string" === typeof input3.plotName) && true && true && true;
+    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && true && true && true && true && (void 0 === input3.coordTWs || Array.isArray(input3.coordTWs)) && (void 0 === input3.plotName || "string" === typeof input3.plotName) && true && true && (void 0 === input3.chartType || "string" === typeof input3.chartType) && true;
     return "object" === typeof input2 && null !== input2 && $io0(input2);
   };
   if (false === __is(input)) {
@@ -42,7 +42,11 @@ var validTermdbSampleScatterRequest = (input) => {
         path: _path2 + ".plotName",
         expected: "(string | undefined)",
         value: input3.plotName
-      }), true, true, true].every((flag) => flag);
+      }), true, true, void 0 === input3.chartType || "string" === typeof input3.chartType || $report(_exceptionable2, {
+        path: _path2 + ".chartType",
+        expected: "(string | undefined)",
+        value: input3.chartType
+      }), true].every((flag) => flag);
       return ("object" === typeof input2 && null !== input2 || $report(true, {
         path: _path + "",
         expected: "TermdbSampleScatterRequest",

package/dist/index.js

@@ -42,17 +42,17 @@ import {
   termdbSampleScatterPayload,
   validTermdbSampleScatterRequest,
   validTermdbSampleScatterResponse
-} from "./chunk-5BNDT4E6.js";
+} from "./chunk-GDZUCVIB.js";
 import {
   termdbSingleSampleMutationPayload,
   validTermdbSingleSampleMutationRequest,
   validTermdbSingleSampleMutationResponse
-} from "./chunk-UGYLBYUU.js";
+} from "./chunk-5L4VF3ZL.js";
 import {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,
   validTermdbSingleCellDEgenesResponse
-} from "./chunk-4LOGWDCZ.js";
+} from "./chunk-3EVYVWI2.js";
 import {
   termdbSingleCellDataPayload,
   validTermdbSingleCellDataRequest,

package/dist/termdb.sampleScatter.js

@@ -2,7 +2,7 @@ import {
   termdbSampleScatterPayload,
   validTermdbSampleScatterRequest,
   validTermdbSampleScatterResponse
-} from "./chunk-5BNDT4E6.js";
+} from "./chunk-GDZUCVIB.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbSampleScatterPayload,

package/dist/termdb.singleSampleMutation.js

@@ -2,7 +2,7 @@ import {
   termdbSingleSampleMutationPayload,
   validTermdbSingleSampleMutationRequest,
   validTermdbSingleSampleMutationResponse
-} from "./chunk-UGYLBYUU.js";
+} from "./chunk-5L4VF3ZL.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleSampleMutationPayload,

package/dist/termdb.singlecellDEgenes.js

@@ -2,7 +2,7 @@ import {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,
   validTermdbSingleCellDEgenesResponse
-} from "./chunk-4LOGWDCZ.js";
+} from "./chunk-3EVYVWI2.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleCellDEgenesPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.158.0",
+  "version": "2.160.1-0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -756,28 +756,40 @@ export type SingleCellSamples = {
 	extraSampleTabLabel?: string
 }
 
-export type SingleCellDataGdc = {
-	src: 'gdcapi'
+type SingleCellDataBase = {
+	/** when a sample has multiple tsne plots, this flag allows allows all plots to share one cell type legend */
 	sameLegend: boolean
-	get?: (q: any) => any
+	/** name of ref cells? */
 	refName?: string
+	/** dynamically added getter */
+	get?: (q: any) => any
+	/** width and height of the plots */
+	settings?: { [key: string]: any }
+	/** In development
+	 * Replacing colorColumns in gdc plot objs.*/
+	twLst?: object[]
+}
+
+export type SingleCellDataGdc = SingleCellDataBase & {
+	src: 'gdcapi'
 	plots: GDCSingleCellPlot[]
-	settings?: { [key: string]: string }
 }
 
 export type SingleCellDEgeneGdc = {
 	src: 'gdcapi'
-	/** Column name.
-this must be the colorColumn from one of the plots. so that at the client app, as soon as the plot data have been loaded and maps rendered, client will find out the cell groups based on this columnName value, and show a drop down of these groups on UI. user selects a group, and pass it as request body to backend to get DE genes for this group
+	/** termId = Column name.
+this must be the colorColumn from one of the plots. In the client app, as soon as the plot data loads and maps renders, client finds the cell groups based on this columnName value, and shows a drop down of these groups on UI. user selects a group, and passes it as request body to backend to get DE genes for this group
 */
-	columnName: string
+	termId: string
 }
 
 type GDCSingleCellPlot = {
 	name: string
 	colorColumns: ColorColumn[]
 	coordsColumns: { x: number; y: number }
-	/** if true the plot is shown by default. otherwise hidden */
+	/** if true the plot is shown by default. otherwise hidden
+	 * Will not be needed when the singleCellPlot is depreciated.
+	 */
 	selected?: boolean
 }
 
@@ -818,19 +830,10 @@ type SingleCellPlot = {
 	/** if true the plot is shown by default. otherwise hidden */
 	selected?: boolean
 }
-export type SingleCellDataNative = {
+export type SingleCellDataNative = SingleCellDataBase & {
 	src: 'native'
-	/** when a sample has multiple tsne plots, this flag allows allows all plots to share one cell type legend */
-	sameLegend: boolean
 	/** available tsne type of plots for each sample */
 	plots: SingleCellPlot[]
-	/** name of ref cells? */
-	refName?: string
-	/** dynamically added getter */
-	get?: (q: any) => any
-	/** width and height of the plots */
-
-	settings?: { [key: string]: any }
 }
 
 export type SingleCellQuery = {
@@ -1380,24 +1383,23 @@ export type Termdb = {
 	 * in order to minimize the ease of extracting identifiable information from aggregate data
 	 * in server response
 	 *
-	 * returns: {minSampleSize, canAccess}, see below
+	 * returns: {minSize, canAccess}, see below
 	 */
 	checkAccessToSampleData?: (
 		/** req.query as processed through app middleware (pre-parsed, may have req.body props, __protectec__, etc) */
 		q: any,
 		data: {
-			/** the number of samples with matching data from one or more queried terms */
-			sampleCount: number
-			/** option to specify sample names that is accessible to the current user,
-			 * not using sample ID since portal embedder and token generator does not
-			 * know the internal sample ID-to-name mapping */
-			sampleNames?: string[]
+			/** the number of samples or sites with matching data from one or more queried terms */
+			count: number
+			/** option to specify sample names or sites that are accessible to the current user,
+			 */
+			names?: string[]
 		}
 	) => {
-		/** the required minimum sample size for the current user,
+		/** the required minimum size for the current user to access certain data,
 		 * may be dependent on login status or other context
 		 * */
-		minSampleSize: number
+		minSize: number
 		/** whether downstreadm backend code can proceed */
 		canAccess: boolean
 	}
@@ -1562,6 +1564,7 @@ keep this setting here for reason of:
 	}
 	//terms  are shown in the dictionary based on term and user role.
 	isTermVisible?: (clientAuthResult: any, ids: string) => boolean
+	hiddenIds?: string[]
 	getAdditionalFilter?: (__protected__: any, term: any) => Filter | undefined
 }
 

package/src/routes/termdb.sampleScatter.ts

@@ -13,6 +13,7 @@ export type TermdbSampleScatterRequest = {
 	plotName?: string
 	filter?: any
 	filter0?: any
+	chartType?: string
 	__protected__?: any // auth token for accessing protected data
 }
 

package/src/routes/termdb.singleSampleMutation.ts

@@ -14,7 +14,7 @@ type ValidResponse = {
 	mlst: object[]
 	/** total number of items for each dt, useful to indicate snvindel limited to 10k for a hypermutator */
 	dt2total?: { dt: number; total: number }[]
-	/** this declares alternative data for some dt, e.g. a gdc case has cnv results from both snp array and wgs
+	/** declares presence of alternative data for some dt, e.g. a gdc case has cnv results from both snp array and wgs
 	key: dt value
 	value: array of objects, each is a distinct set of data points for this dt
 		on ui, selecting an object will allow to show this data in disco plot
@@ -30,6 +30,10 @@ type ValidResponse = {
 			inuse?: boolean
 			/** required list of events from this data */
 			mlst: object[]
+			/** optional info about this source */
+			attrs?: {
+				[index: string]: string
+			}
 		}[]
 	}
 }

package/src/routes/termdb.singlecellDEgenes.ts

@@ -7,12 +7,15 @@ export type TermdbSingleCellDEgenesRequest = {
 	/** Dataset label */
 	dslabel: string
 	/** Sample name
-	for GDC the value is "seurat.analysis.tsv" file UUID rather than sample name. the file contains the analysis results for an experiment
-	*/
+	for GDC the value is "seurat.analysis.tsv" file UUID 
+	rather than sample name. the file contains the analysis 
+	results for an experiment */
 	sample: string
-	/** column name to provide cell groups/clustering, for which DE genes are precomputed.  */
-	columnName: string
-	/** User selected cell group/cluster, corresponds to columnName, for which DE genes will be returned to client */
+	/** column name to provide cell groups/clustering,
+	 * for which DE genes are precomputed.  */
+	termId: string
+	/** User selected cell group/cluster, corresponds to termId,
+	 * for which DE genes will be returned to client */
 	categoryName: string
 }