@sjcrh/proteinpaint-types 2.187.0 → 2.188.0

package/dist/termdb.categories.js

@@ -2,7 +2,7 @@ import {
   termdbCategoriesPayload,
   validCategoriesRequest,
   validCategoriesResponse
-} from "./chunk-RY4Y5ESC.js";
+} from "./chunk-JEQGBUK2.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbCategoriesPayload,

package/dist/termdb.chat.js

@@ -1,6 +1,6 @@
 import {
   ChatPayload
-} from "./chunk-FRXRNCDV.js";
+} from "./chunk-DI4Q26E7.js";
 import {
   __toESM,
   require_lib
@@ -56,7 +56,7 @@ var validChatRequest = (input) => {
     const $io25 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "isoformExpression" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && (void 0 === input3.kind || "isoform" === input3.kind) && "string" === typeof input3.isoform && (void 0 === input3.gene || "string" === typeof input3.gene) && (void 0 === input3.chr || "string" === typeof input3.chr) && (void 0 === input3.start || "number" === typeof input3.start) && (void 0 === input3.stop || "number" === typeof input3.stop);
     const $io26 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "isoformExpression" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && (void 0 === input3.kind || "coord" === input3.kind) && (void 0 === input3.isoform || "string" === typeof input3.isoform) && (void 0 === input3.gene || "string" === typeof input3.gene) && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop;
     const $io27 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "metaboliteIntensity" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.metabolite && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
-    const $io28 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "proteomeAbundance" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.protein && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && ("object" === typeof input3.proteomeDetails && null !== input3.proteomeDetails && ("string" === typeof input3.proteomeDetails.organism && "string" === typeof input3.proteomeDetails.assay && "string" === typeof input3.proteomeDetails.cohort));
+    const $io28 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "proteomeAbundance" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.protein && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins)) && ("object" === typeof input3.dataTypeDetails && null !== input3.dataTypeDetails && ("string" === typeof input3.dataTypeDetails.organism && "string" === typeof input3.dataTypeDetails.assay && "string" === typeof input3.dataTypeDetails.cohort));
     const $io30 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "date" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
     const $io31 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "ssGSEA" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && (void 0 === input3.genes || Array.isArray(input3.genes) && input3.genes.every((elem) => "string" === typeof elem)) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
     const $io32 = (input3) => "string" === typeof input3.id && "string" === typeof input3.name && "dnaMethylation" === input3.type && (void 0 === input3.child_types || Array.isArray(input3.child_types) && input3.child_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.hashtmldetail || "boolean" === typeof input3.hashtmldetail) && (void 0 === input3.included_types || Array.isArray(input3.included_types) && input3.included_types.every((elem) => "string" === typeof elem)) && (void 0 === input3.isleaf || "boolean" === typeof input3.isleaf) && (void 0 === input3.values || "object" === typeof input3.values && null !== input3.values && false === Array.isArray(input3.values) && $io5(input3.values)) && (void 0 === input3.skipValuesBuild || "boolean" === typeof input3.skipValuesBuild) && (void 0 === input3.valueConversion || "object" === typeof input3.valueConversion && null !== input3.valueConversion && $io7(input3.valueConversion)) && (void 0 === input3.continuousColorScale || "object" === typeof input3.continuousColorScale && null !== input3.continuousColorScale && $io15(input3.continuousColorScale)) && (void 0 === input3.unit || "string" === typeof input3.unit) && "string" === typeof input3.chr && "number" === typeof input3.start && "number" === typeof input3.stop && ("gene" === input3.genomicFeatureType || "promoter" === input3.genomicFeatureType || "region" === input3.genomicFeatureType || "enhancer" === input3.genomicFeatureType) && (void 0 === input3.bins || "object" === typeof input3.bins && null !== input3.bins && $io16(input3.bins));
@@ -1666,14 +1666,14 @@ var validChatRequest = (input) => {
         path: _path2 + ".bins",
         expected: "(PresetNumericBins | undefined)",
         value: input3.bins
-      }), ("object" === typeof input3.proteomeDetails && null !== input3.proteomeDetails || $report(_exceptionable2, {
-        path: _path2 + ".proteomeDetails",
+      }), ("object" === typeof input3.dataTypeDetails && null !== input3.dataTypeDetails || $report(_exceptionable2, {
+        path: _path2 + ".dataTypeDetails",
         expected: "ProteomeDetails",
-        value: input3.proteomeDetails
-      })) && $vo29(input3.proteomeDetails, _path2 + ".proteomeDetails", _exceptionable2) || $report(_exceptionable2, {
-        path: _path2 + ".proteomeDetails",
+        value: input3.dataTypeDetails
+      })) && $vo29(input3.dataTypeDetails, _path2 + ".dataTypeDetails", _exceptionable2) || $report(_exceptionable2, {
+        path: _path2 + ".dataTypeDetails",
         expected: "ProteomeDetails",
-        value: input3.proteomeDetails
+        value: input3.dataTypeDetails
       })].every((flag) => flag);
       const $vo29 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.organism || $report(_exceptionable2, {
         path: _path2 + ".organism",
@@ -3542,7 +3542,7 @@ var validChatResponse = (input) => {
   const __is = (input2) => {
     const $io0 = (input3) => "text" === input3.type && "string" === typeof input3.text;
     const $io1 = (input3) => "html" === input3.type && "string" === typeof input3.html;
-    const $io2 = (input3) => "plot" === input3.type && ("object" === typeof input3.plot && null !== input3.plot && true);
+    const $io2 = (input3) => "plot" === input3.type && ("object" === typeof input3.plot && null !== input3.plot && true) && (void 0 === input3.msg || "string" === typeof input3.msg);
     const $iu0 = (input3) => (() => {
       if ("text" === input3.type)
         return $io0(input3);
@@ -3587,6 +3587,10 @@ var validChatResponse = (input) => {
         path: _path2 + ".plot",
         expected: "object",
         value: input3.plot
+      }), void 0 === input3.msg || "string" === typeof input3.msg || $report(_exceptionable2, {
+        path: _path2 + ".msg",
+        expected: "(string | undefined)",
+        value: input3.msg
       })].every((flag) => flag);
       const $vo3 = (input3, _path2, _exceptionable2 = true) => true;
       const $vu0 = (input3, _path2, _exceptionable2 = true) => (() => {

package/dist/termdb.chat2.js

@@ -1,13 +1,15 @@
 import {
   validChatRequest,
   validChatResponse
-} from "./chunk-DVMD6CBJ.js";
+} from "./chunk-MNT3GF7M.js";
 import {
-  ChatPayload
-} from "./chunk-FRXRNCDV.js";
+  ChatPayload,
+  createAmbiguousPoints
+} from "./chunk-DI4Q26E7.js";
 import "./chunk-YNHC5SXO.js";
 export {
   ChatPayload,
+  createAmbiguousPoints,
   validChatRequest,
   validChatResponse
 };

package/dist/termdb.cluster.js

@@ -2,7 +2,7 @@ import {
   termdbClusterPayload,
   validTermdbClusterRequest,
   validTermdbClusterResponse
-} from "./chunk-SGMHY5K7.js";
+} from "./chunk-TEXOICIS.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbClusterPayload,

package/dist/termdb.dapVolcano.js

@@ -0,0 +1,11 @@
+import {
+  dapVolcanoPayload,
+  validDapVolcanoRequest,
+  validDapVolcanoResponse
+} from "./chunk-QNH3PKJK.js";
+import "./chunk-YNHC5SXO.js";
+export {
+  dapVolcanoPayload,
+  validDapVolcanoRequest,
+  validDapVolcanoResponse
+};

package/dist/termdb.descrstats.js

@@ -2,7 +2,7 @@ import {
   descrStatsPayload,
   validDescrStatsRequest,
   validDescrStatsResponse
-} from "./chunk-MMNSJ72P.js";
+} from "./chunk-TQQWSHFM.js";
 import "./chunk-YNHC5SXO.js";
 export {
   descrStatsPayload,

package/dist/termdb.diffMeth.js

@@ -2,7 +2,7 @@ import {
   diffMethPayload,
   validDiffMethRequest,
   validDiffMethResponse
-} from "./chunk-FEMYT7FL.js";
+} from "./chunk-JDF7A2LY.js";
 import "./chunk-YNHC5SXO.js";
 export {
   diffMethPayload,

package/dist/termdb.dmr.js

@@ -2,7 +2,7 @@ import {
   TermdbDmrPayload,
   validTermdbDmrRequest,
   validTermdbDmrResponse
-} from "./chunk-46DTJOK5.js";
+} from "./chunk-MVB7LQS5.js";
 import "./chunk-YNHC5SXO.js";
 export {
   TermdbDmrPayload,

package/dist/termdb.numericcategories.js

@@ -2,7 +2,7 @@ import {
   numericCategoriesPayload,
   validNumericCategoriesRequest,
   validNumericCategoriesResponse
-} from "./chunk-VWLYQ33F.js";
+} from "./chunk-LQYSPLDQ.js";
 import "./chunk-YNHC5SXO.js";
 export {
   numericCategoriesPayload,

package/dist/termdb.percentile.js

@@ -2,7 +2,7 @@ import {
   percentilePayload,
   validPercentileRequest,
   validPercentileResponse
-} from "./chunk-I3QGRA7O.js";
+} from "./chunk-MKYLCBTP.js";
 import "./chunk-YNHC5SXO.js";
 export {
   percentilePayload,

package/dist/termdb.runChart.js

@@ -1,10 +1,12 @@
 import {
+  isRunChartSuccess,
   runChartPayload,
   validRunChartRequest,
   validRunChartResponse
-} from "./chunk-TWNJZBZK.js";
+} from "./chunk-2VJRTZE2.js";
 import "./chunk-YNHC5SXO.js";
 export {
+  isRunChartSuccess,
   runChartPayload,
   validRunChartRequest,
   validRunChartResponse

package/dist/termdb.singlecellDEgenes.js

@@ -2,7 +2,7 @@ import {
   termdbSingleCellDEgenesPayload,
   validTermdbSingleCellDEgenesRequest,
   validTermdbSingleCellDEgenesResponse
-} from "./chunk-OCH5BJCV.js";
+} from "./chunk-BZVFHGN3.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleCellDEgenesPayload,

package/dist/termdb.singlecellSamples.js

@@ -2,7 +2,7 @@ import {
   termdbSingleCellSamplesPayload,
   validTermdbSingleCellSamplesRequest,
   validTermdbSingleCellSamplesResponse
-} from "./chunk-VCEWZVLZ.js";
+} from "./chunk-IS74WYQF.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbSingleCellSamplesPayload,

package/dist/termdb.termsbyids.js

@@ -2,7 +2,7 @@ import {
   termsByIdsPayload,
   validTermsByIdsRequest,
   validTermsByIdsResponse
-} from "./chunk-F2QRI6B2.js";
+} from "./chunk-SDZIGJY3.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termsByIdsPayload,

package/dist/termdb.topTermsByType.js

@@ -2,7 +2,7 @@ import {
   termdbTopTermsByTypePayload,
   validTermdbTopTermsByTypeRequest,
   validTermdbTopTermsByTypeResponse
-} from "./chunk-AYTV7V46.js";
+} from "./chunk-LC6KLHCJ.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopTermsByTypePayload,

package/dist/termdb.topVariablyExpressedGenes.js

@@ -2,7 +2,7 @@ import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
   validTermdbTopVariablyExpressedGenesResponse
-} from "./chunk-DPJUULKQ.js";
+} from "./chunk-V3JDD3ZG.js";
 import "./chunk-YNHC5SXO.js";
 export {
   termdbTopVariablyExpressedGenesPayload,

package/dist/termdb.violinBox.js

@@ -1,10 +1,16 @@
 import {
+  isBoxPlotResponse,
+  isErrorResponse,
+  isViolinResponse,
   validViolinBoxRequest,
   validViolinBoxResponse,
   violinBoxPayload
-} from "./chunk-IIWTMQJZ.js";
+} from "./chunk-DDKGTDDB.js";
 import "./chunk-YNHC5SXO.js";
 export {
+  isBoxPlotResponse,
+  isErrorResponse,
+  isViolinResponse,
   validViolinBoxRequest,
   validViolinBoxResponse,
   violinBoxPayload

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.187.0",
+  "version": "2.188.0",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",
@@ -11,12 +11,12 @@
     "./checkers": "./dist/index.js"
   },
   "imports": {
-    "#shared": "@sjcrh/proteinpaint-shared"
+    "#shared": "@sjcrh/proteinpaint-shared",
+    "#shared/devTs": "@sjcrh/proteinpaint-shared/devTs"
   },
   "scripts": {
     "generate": "node dev.mjs",
-    "predev": "tsx emitCheckers.ts",
-    "dev": "node --watch-path=src --watch-path=checkers dev.mjs",
+    "dev": "node --watch-path=src/routes dev.mjs",
     "prepare": "ts-patch install",
     "build": "./build.sh",
     "prepack": "./build.sh",

package/src/dataset.ts

@@ -499,9 +499,8 @@ export type GeneArgumentEntry = {
 }
 
 type TopVariablyExpressedGenesQuery = {
-	/** Denotes either gdc specific data requests or common
-	 * data request processing */
-	src: 'gdcapi' | 'native' | string
+	/** ds supplied getter. if not, dynamically adds one during launch */
+	getGenes?: (f: any) => void
 	/** Specifies the dom element rendered in the menu */
 	arguments?: GeneArgumentEntry[]
 }
@@ -717,6 +716,7 @@ type ProteomeCohortConfig = {
 	prior: { d0: number; s0sq: number }
 	controlFilter: ProteomeFilter[]
 	caseFilter: ProteomeFilter[]
+	DAPfile?: string
 }
 
 type ProteomeAssayConfig = {
@@ -875,8 +875,7 @@ type GDCSingleCellPlot = {
 	colorColumns: ColorColumn[]
 	coordsColumns: { x: number; y: number }
 	/** if true the plot is shown by default. otherwise hidden
-	 * Will not be needed when the singleCellPlot is depreciated.
-	 */
+	 * Will not be needed when the singleCellPlot is deprecated.*/
 	selected?: boolean
 }
 
@@ -914,8 +913,15 @@ type SingleCellPlot = {
 	/** list of columns in tabular text file that define cell categories and can be used to color the cells in the plot. must have categorical values
 	 */
 	colorColumns: ColorColumn[]
-	/** if true the plot is shown by default. otherwise hidden */
+	/** if true the plot is shown by default. otherwise hidden.
+	 * Old implementation. Maybe deleted when singleCellPlot is deprecated.*/
 	selected?: boolean
+	/** Plot is a meta analysis result and treated differently in the UI */
+	isMetaResult?: boolean
+	/** optional for meta analysis result plots. May define the "sampleId" for the
+	 * server requests. If not provided, the file name or the plot name with the
+	 * spaces replaced with '_' is used. */
+	sampleId?: string
 }
 export type SingleCellDataNative = SingleCellDataBase & {
 	src: 'native'
@@ -1092,8 +1098,7 @@ type Mds3Queries = {
 	/** Used to create the top mutated genes UI in the gene
 	 * set edit ui and data requests. */
 	topMutatedGenes?: TopMutatedGenes
-	/** Used to create the top variably expressed UI in the gene
-	 * set edit ui. Also used for data requests */
+	/** get top variably expressed genes */
 	topVariablyExpressedGenes?: TopVariablyExpressedGenesQuery
 	metaboliteIntensity?: {
 		src: 'native'
@@ -1103,7 +1108,7 @@ type Mds3Queries = {
 	singleCell?: SingleCellQuery
 	singleSampleGenomeQuantification?: SingleSampleGenomeQuantification
 	singleSampleGbtk?: SingleSampleGbtk
-	/** depreciated. replaced by WSImages */
+	/** deprecated. replaced by WSImages */
 	DZImages?: DZImages
 	WSImages?: WSImages
 	images?: Images
@@ -1135,7 +1140,7 @@ type Images = {
 	folder: string
 }
 
-/** Depreciated. deep zoom image shown via openseadragon, with precomputed tiles.
+/** Deprecated. deep zoom image shown via openseadragon, with precomputed tiles.
  * this is replaced by WSImages and should not be used anymore */
 export type DZImages = {
 	// type of the image, e.g. H&E
@@ -1248,6 +1253,8 @@ type DataDownloadCatch = {
 
 type ScatterPlotsEntry = {
 	name: string
+	description?: string
+	descriptionShort?: string
 	dimension: number
 	file: string
 	coordsColumns?: { x: number; y: number; z?: number }

package/src/index.ts

@@ -44,6 +44,7 @@ export * from './routes/termdb.cluster.ts'
 export * from './routes/termdb.cohort.summary.ts'
 export * from './routes/termdb.cohorts.ts'
 export * from './routes/termdb.DE.ts'
+export * from './routes/termdb.dapVolcano.ts'
 export * from './routes/termdb.diffMeth.ts'
 export * from './routes/termdb.descrstats.ts'
 export * from './routes/termdb.dmr.ts'

package/src/routes/aiProjectSelectedWSImages.ts

@@ -1,5 +1,6 @@
 import type { RoutePayload } from './routeApi.ts'
 import type { WSImage } from './samplewsimages.ts'
+import type { FlagStatus } from '#shared/devTs'
 
 export type AiProjectSelectedWSImagesRequest = {
 	genome: string
@@ -13,16 +14,23 @@ export type AiProjectSelectedWSImagesResponse = {
 	wsimages: WSImage[]
 }
 
+export interface FlagPredictionInfo {
+	flag: FlagStatus
+	timestamp: string
+}
+
 // TODO move to another class
 export interface TileSelection {
 	zoomCoordinates: [number, number]
 	class?: string
+	flag: FlagStatus
+	id: string
+	timestamp: string
 }
 
 export interface Annotation extends TileSelection {
 	class: string
 	status: number
-	timestamp: string
 }
 
 export interface Prediction extends TileSelection {

package/src/routes/deleteWSITileSelection.ts

@@ -6,8 +6,7 @@ export type DeleteWSITileSelectionRequest = {
 	dslabel: string
 	projectId: number
 	tileSelection: TileSelection
-	predictionClassId: string
-	tileSelectionType: number
+	classID: number
 	wsimage: string
 }
 

package/src/routes/genesetEnrichment.ts

@@ -38,6 +38,8 @@ export type GenesetEnrichmentRequest = {
 	num_permutations?: number
 	/** Method used for GSEA blitzgsea/cerno */
 	method: 'blitzgsea' | 'cerno'
+	/** DAP-specific parameters: organism/assay/cohort identify the DAP file */
+	dapParams?: { organism: string; assay: string; cohort: string }
 }
 
 type blitzgsea_geneset_attributes = {

package/src/routes/saveWSIAnnotation.ts

@@ -1,9 +1,10 @@
+import type { TileSelection } from '../index.ts'
 import type { RoutePayload } from './routeApi.ts'
 
 export type SaveWSIAnnotationRequest = {
 	genome: string
 	dslabel: string
-	coordinates: [number, number]
+	tileSelection: TileSelection
 	classId: number
 	projectId: number
 	wsimage: string

package/src/routes/termdb.DE.ts

@@ -7,9 +7,9 @@ export type DERequest = {
 	dslabel: string
 	/* Object containing two arrays of RNA seq count for DE analysis */
 	samplelst: any //{number[]; number[];}
-	/** Relative cpm cutoff for filtering a gene compared to all samples and genes in dataset */
+	/** Minimum count per sample for edgeR's filterByExpr */
 	min_count: number
-	/** Minimum total read count required for each sample */
+	/** Minimum total count across samples for edgeR's filterByExpr */
 	min_total_count: number
 	/** Minimum normalized expression threshold to retain only genes with sufficient expression */
 	cpm_cutoff: number
@@ -134,10 +134,6 @@ export type ExpressionInput = {
 	data_type: 'do_DE'
 	/** File containing raw gene counts for DE analysis */
 	input_file: string
-	/** Relative cpm cutoff for filtering a gene compared to all samples and genes in dataset */
-	min_count: number
-	/** Minimum total read count required for each sample */
-	min_total_count: number
 	/** Type of storage file: HDF5 or text. Text will be deprecated in the future */
 	storage_type: 'HDF5' | 'text'
 	/** Confounding variable1 for DE analysis. Maybe array of string (Gender: Male/female) or number (Age). For now supporting 1 confounding variable. */
@@ -154,6 +150,12 @@ export type ExpressionInput = {
 	DE_method: 'wilcoxon' | 'limma' | 'edgeR'
 	/** Cutoff for when mds plot will be generated for edgeR and limma test */
 	mds_cutoff: number
+	/** Minimum count per sample for edgeR's filterByExpr */
+	min_count: number
+	/** Minimum total count across samples for edgeR's filterByExpr */
+	min_total_count: number
+	/** Minimum normalized expression threshold to retain only genes with sufficient expression */
+	cpm_cutoff: number
 }
 
 /** Response when DERequest.preAnalysis === true. Returns per-group sample
@@ -188,7 +190,7 @@ export type DEResponse = DEPreAnalysisResponse | DEFullResponse
  * singlecell DE genes, each of which extends this with route-specific fields. */
 export type DataEntry = {
 	original_p_value: number
-	adjusted_p_value: number
+	adjusted_p_value?: number
 	fold_change: number
 }
 

package/src/routes/termdb.chat2.ts

@@ -2,6 +2,10 @@ import type { Filter } from '../filter.ts'
 import type { RoutePayload } from './routeApi.js'
 
 /** */
+// Helps track ambiguous points in the LLM reasoning process for debugging and improvement purposes.
+// Create a fresh array per request/pipeline run to avoid sharing mutable state across module consumers.
+export const createAmbiguousPoints = (): string[] => []
+
 export type ChatRequest = {
 	genome: string
 	dslabel: string
@@ -24,11 +28,12 @@ export type HtmlResponse = {
 export type PlotResponse = {
 	type: 'plot'
 	plot: object
+	msg?: string
 	/** Specifies what action to take e.g. Summary plot or no action. Will add more chart types later */
 }
 
 export type LlmConfig = {
-	provider: 'SJ' | 'ollama' | 'huggingface'
+	provider: 'SJ' | 'ollama' | 'huggingface' | 'azure'
 	EmbeddingProvider: 'SJ' | 'ollama' | 'huggingface'
 	EmbeddingProviderApi: string
 	api: string
@@ -137,7 +142,7 @@ export type none_type = {
 }
 
 /** Top-level classification returned by classifyQuery: plot or notplot (subtype determined separately by plot.ts) */
-export type QueryClassification = { type: 'plot' } | { type: 'notplot' }
+export type QueryClassification = { type: 'plot' } | { type: 'notplot' } | { type: 'binaryQuery' }
 
 /** Specific plot type returned by classifyPlotType in plot.ts */
 export type PlotType = 'summary' | 'dge' | 'survival' | 'matrix' | 'samplescatter' | 'hiercluster' | 'lollipop'

package/src/routes/termdb.dapVolcano.ts

@@ -0,0 +1,35 @@
+import type { RoutePayload } from './routeApi.js'
+import type { ErrorResponse } from './errorResponse.ts'
+import type { DataEntry, VolcanoData, VolcanoRenderRequest } from './termdb.DE.js'
+
+export type DapVolcanoRequest = {
+	genome: string
+	dslabel: string
+	organism: string
+	assay: string
+	cohort: string
+	volcanoRender?: VolcanoRenderRequest
+	countsOnly?: boolean
+}
+
+export type DapEntry = DataEntry & {
+	gene_name: string
+	gene: string
+}
+
+export type DapVolcanoResponse =
+	| ErrorResponse
+	| {
+			sample_size1: number
+			sample_size2: number
+			data?: VolcanoData<DapEntry>
+	  }
+
+export const dapVolcanoPayload: RoutePayload = {
+	request: {
+		typeId: 'DapVolcanoRequest'
+	},
+	response: {
+		typeId: 'DapVolcanoResponse'
+	}
+}

package/src/routes/termdb.singlecellSamples.ts

@@ -17,7 +17,7 @@ export type SingleCellSample = {
 		sampleName: any
 		experimentID?: string
 	}[]
-
+	isMetaResult?: boolean // whether this sample is a meta result. if so, sample name is from plot.sampleId or plot.name and experimentID is not used
 	// a sample may have additional fields that will be displayed in table, see singleCell.samples.sampleColumns[]
 }
 

package/src/routes/termdb.topVariablyExpressedGenes.ts

@@ -24,11 +24,7 @@ export type TermdbTopVariablyExpressedGenesRequest = {
 	/** optional parameter defined in gdc dataset. not used for non-gdc ds */
 	min_median_log2_uqfpkm?: number
 	/** filter extreme values (in native implementation): true/false */
-	filter_extreme_values?: number
-	/** min_count of fpkm when filter_extreme_values (in native implementation) = true */
-	min_count?: number
-	/** min_total_count of fpkm when filter_extreme_values (in native implementation) = true */
-	min_total_count?: number
+	filter_extreme_values?: boolean | number
 	/** Filter type: variance/inter-quartile region (in native implementation) */
 	rank_type?: {
 		type: 'var' | 'iqr'
@@ -36,6 +32,8 @@ export type TermdbTopVariablyExpressedGenesRequest = {
 	filter?: Filter
 	/** JSON, optional GDC cohort filter to restrict cases */
 	filter0?: any //GdcFilter0
+	/** helps ds getter */
+	ds?: any
 }
 
 type ValidResponse = {

package/src/terms/proteomeAbundance.ts

@@ -21,7 +21,7 @@ export type ProteomeAbundanceTerm = NumericBaseTerm & {
 	bins?: PresetNumericBins
 	unit?: string
 	/** organism, assay and cohort this term belongs to */
-	proteomeDetails: ProteomeDetails
+	dataTypeDetails: ProteomeDetails
 }
 
 export type ProteomeAbundanceTW = NumTW & { term: ProteomeAbundanceTerm }