@sjcrh/proteinpaint-types 2.98.1-0 → 2.98.1

package/dist/correlationVolcano.js

@@ -0,0 +1,11 @@
+import {
+  CorrelationVolcanoPayload,
+  validCorrelationVolcanoRequest,
+  validCorrelationVolcanoResponse
+} from "./chunk-DFSJACIQ.js";
+import "./chunk-Z6B6IQIY.js";
+export {
+  CorrelationVolcanoPayload,
+  validCorrelationVolcanoRequest,
+  validCorrelationVolcanoResponse
+};

package/dist/index.js

@@ -1,3 +1,8 @@
+import {
+  termdbTopTermsByTypePayload,
+  validTermdbTopTermsByTypeRequest,
+  validTermdbTopTermsByTypeResponse
+} from "./chunk-CU5TLT6P.js";
 import {
   termdbTopVariablyExpressedGenesPayload,
   validTermdbTopVariablyExpressedGenesRequest,
@@ -18,6 +23,11 @@ import {
   validWSImagesResponse,
   wsImagesPayload
 } from "./chunk-XLBSZOMF.js";
+import {
+  rootTermPayload,
+  validRootTermRequest,
+  validRootTermResponse
+} from "./chunk-GU7LIGHN.js";
 import {
   termdbSampleImagesPayload,
   validTermdbSampleImagesRequest,
@@ -54,10 +64,10 @@ import {
   validTermsByIdsResponse
 } from "./chunk-7K726NBK.js";
 import {
-  termdbTopTermsByTypePayload,
-  validTermdbTopTermsByTypeRequest,
-  validTermdbTopTermsByTypeResponse
-} from "./chunk-CU5TLT6P.js";
+  boxplotPayload,
+  validBoxPlotRequest,
+  validBoxPlotResponse
+} from "./chunk-X36QKCNU.js";
 import {
   termdbCategoriesPayload,
   validCategoriesRequest,
@@ -94,10 +104,10 @@ import {
   validPercentileResponse
 } from "./chunk-IORCECK2.js";
 import {
-  rootTermPayload,
-  validRootTermRequest,
-  validRootTermResponse
-} from "./chunk-GU7LIGHN.js";
+  hicstatPayload,
+  validHicstatRequest,
+  validHicstatResponse
+} from "./chunk-QX7QLUKY.js";
 import {
   isoformlstPayload,
   validIsoformLstRequest,
@@ -129,10 +139,10 @@ import {
   validDEResponse
 } from "./chunk-Z2WFGV6V.js";
 import {
-  boxplotPayload,
-  validBoxPlotRequest,
-  validBoxPlotResponse
-} from "./chunk-OAO3UWUX.js";
+  GdcMafPayload,
+  validGdcMafBuildRequest,
+  validGdcMafBuildResponse
+} from "./chunk-DIDZMC3G.js";
 import {
   gdcTopMutatedGenePayload,
   validGdcTopMutatedGeneRequest,
@@ -168,11 +178,6 @@ import {
   validHicGenomeRequest,
   validHicGenomeResponse
 } from "./chunk-W3QYIXXF.js";
-import {
-  hicstatPayload,
-  validHicstatRequest,
-  validHicstatResponse
-} from "./chunk-QX7QLUKY.js";
 import {
   brainImagingPayload,
   validBrainImagingRequest,
@@ -188,6 +193,11 @@ import {
   validBurdenRequest,
   validBurdenResponse
 } from "./chunk-RLFGMVJZ.js";
+import {
+  CorrelationVolcanoPayload,
+  validCorrelationVolcanoRequest,
+  validCorrelationVolcanoResponse
+} from "./chunk-DFSJACIQ.js";
 import {
   datasetPayload,
   validDatasetRequest,
@@ -208,13 +218,9 @@ import {
   validGdcMafRequest,
   validGdcMafResponse
 } from "./chunk-CETMA2FU.js";
-import {
-  GdcMafPayload,
-  validGdcMafBuildRequest,
-  validGdcMafBuildResponse
-} from "./chunk-DIDZMC3G.js";
 import "./chunk-Z6B6IQIY.js";
 export {
+  CorrelationVolcanoPayload,
   GdcMafPayload,
   boxplotPayload,
   brainImagingPayload,
@@ -266,6 +272,8 @@ export {
   validBurdenResponse,
   validCategoriesRequest,
   validCategoriesResponse,
+  validCorrelationVolcanoRequest,
+  validCorrelationVolcanoResponse,
   validDERequest,
   validDEResponse,
   validDZImagesRequest,

package/dist/termdb.boxplot.js

@@ -2,7 +2,7 @@ import {
   boxplotPayload,
   validBoxPlotRequest,
   validBoxPlotResponse
-} from "./chunk-OAO3UWUX.js";
+} from "./chunk-X36QKCNU.js";
 import "./chunk-Z6B6IQIY.js";
 export {
   boxplotPayload,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-types",
-  "version": "2.98.1-0",
+  "version": "2.98.1",
   "type": "module",
   "description": "Shared type definitions between ProteinPaint server and client code",
   "main": "src/index.ts",

package/src/dataset.ts

@@ -838,15 +838,18 @@ type SelectCohortValuesEntry = {
 }
 
 export type SelectCohortEntry = {
+	/** subcohort term in db. uses hardcoded type=multivalue */
 	term: { id: string; type: string }
 	/** Title above the cohort introduction/content in the about tab */
 	title?: string
 	/** Text above radio cohort options in the about tab. */
 	prompt: string
 	values: SelectCohortValuesEntry[]
+	/** cohort-related static html shown in about tab */
 	description?: string
-	/* If the description is dependent on the user pass a descriptionByUser dict instead */
-	descriptionByUser?: { [index: string]: string }
+	/** If the description is dependent on the user's role, 
+	define this callback to return description based on auth */
+	descriptionByUser?: (auth: any) => string
 	/** subtext shown at the very bottom of the cohort/about tab subheader */
 	asterisk?: string
 	//The profile has clearOnChange. The terms used in the plots are not always the same for the profile.
@@ -895,6 +898,22 @@ this is limited to only one term and doesn't allow switching between multiple te
 type Scatterplots = {
 	plots: ScatterPlotsEntry[]
 }
+/** this plot compares correlation of one feature against a bunch of variables across samples
+ */
+type CorrelationVolcano = {
+	/** fixed feature, is one numeric term */
+	feature: {
+		/** later expand to other types */
+		termType: 'geneExpression'
+	}
+	/** list of numeric variables to be compared against fixed feature*/
+	variables: {
+		/** later can expand */
+		type: 'dictionaryTerm'
+		/** when type=dictionaryTerm, is array of numeric term ids */
+		termIds?: string[]
+	}
+}
 
 type MatrixSettingsControlLabels = {
 	samples?: string
@@ -1142,7 +1161,6 @@ keep this setting here for reason of:
   */
 	useLower?: boolean
 
-	scatterplots?: Scatterplots
 	matrix?: Matrix
 	numericDictTermCluster?: NumericDictTermCluster
 	survival?: Survival
@@ -1280,6 +1298,8 @@ type AssayAvailability = {
 
 //Shared with genome.ts
 export type Cohort = {
+	/** if present, means correlation volcano plot analysis is enabled */
+	correlationVolcano?: CorrelationVolcano
 	cumburden?: {
 		files: {
 			fit: string
@@ -1295,6 +1315,7 @@ export type Cohort = {
 	matrixplots?: MatrixPlots
 	mutationset?: MutationSet[]
 	renamedChartTypes?: { singleCellPlot?: string; sampleScatter?: string }
+	/** if present, supplies premade scatter plots */
 	scatterplots?: Scatterplots
 	termdb: Termdb
 }

package/src/index.ts

@@ -8,6 +8,7 @@ export * from './routes/routeApi.ts'
 export * from './routes/brainImaging.ts'
 export * from './routes/brainImagingSamples.ts'
 export * from './routes/burden.ts'
+export * from './routes/correlationVolcano.ts'
 export * from './routes/dataset.ts'
 export * from './routes/dsdata.ts'
 export * from './routes/dzimages.ts'

package/src/routes/correlationVolcano.ts

@@ -0,0 +1,44 @@
+import type { RoutePayload } from './routeApi.js'
+import type { TermWrapper } from '../terms/tw.ts'
+import type { Filter } from '../filter.ts'
+
+/** */
+export type CorrelationVolcanoRequest = {
+	genome: string
+	dslabel: string
+	filter?: Filter
+	filter0?: any // gdc
+	/** feature tw */
+	featureTw: TermWrapper
+	/** variables */
+	variableTwLst: TermWrapper[]
+	/** correlation method */
+	correlationMethod: 'pearson' | 'spearman'
+	/** add new param */
+}
+
+export type CorrelationVolcanoResponse = {
+	/** each element is test result of one variable corresponding to variableTwLst */
+	variableItems: {
+		/** correlation coefficient, -1 to 1 */
+		correlation: number
+		/** pvalue */
+		original_pvalue: number
+		/** pvalue */
+		adjusted_pvalue: number
+		/** tw.$id, for client to match the item with variableTwLst */
+		tw$id: string
+		/** number of samples analyzed. samples not having complete data for all terms will be excluded, thus size may be lower than current cohort */
+		sampleSize: number
+	}[]
+}
+
+export const CorrelationVolcanoPayload: RoutePayload = {
+	request: {
+		typeId: 'CorrelationVolcanoRequest'
+	},
+	response: {
+		typeId: 'CorrelationVolcanoResponse'
+	}
+	//examples: []
+}

package/src/routes/termdb.boxplot.ts

@@ -1,18 +1,20 @@
 import type { RoutePayload } from './routeApi.js'
+import type { TermWrapper } from '../terms/tw.ts'
+import type { Filter } from '../filter.ts'
 
 /**Args set in Termdb vocab and from mass box plot */
 export type BoxPlotRequest = {
 	/** Args set in TermVocab */
 	/** term1 or term */
-	tw: any
+	tw: TermWrapper
 	genome: string
 	dslabel: string
 	/** sort plots by median value */
 	orderByMedian: boolean
 	/** term2 */
-	overlayTw?: any
-	filter: any
-	filter0: any
+	overlayTw?: TermWrapper
+	filter?: Filter
+	filter0?: any
 }
 
 export type BoxPlotResponse = {

package/dist/chunk-OAO3UWUX.js

@@ -1,311 +0,0 @@
-import {
-  __toESM,
-  require_lib
-} from "./chunk-Z6B6IQIY.js";
-
-// dist/termdb.boxplot.ts
-var import_typia = __toESM(require_lib(), 1);
-
-// src/routes/termdb.boxplot.ts
-var boxplotPayload = {
-  request: {
-    typeId: "BoxPlotRequest"
-  },
-  response: {
-    typeId: "BoxPlotResponse"
-  },
-  examples: [
-    {
-      request: {
-        body: {
-          tw: {
-            term: { id: "subcohort", type: "categorical" },
-            values: [{ key: "ABC", label: "ABC" }]
-          },
-          genome: "hg38-test",
-          dslabel: "TermdbTest",
-          orderByMedian: true
-        }
-      },
-      response: {
-        body: {
-          absMin: 0,
-          absMax: 100,
-          plots: [
-            {
-              boxplot: {
-                label: "ABC",
-                w1: 0,
-                w2: 100,
-                p05: 0,
-                p25: 25,
-                p50: 50,
-                p75: 75,
-                p95: 100,
-                iqr: 50,
-                out: [101, 102, 106]
-              },
-              color: "blue",
-              descrStats: [
-                { id: "total", label: "Total", value: 100 },
-                { id: "min", label: "Min", value: 0 },
-                { id: "p25", label: "25%", value: 25 },
-                { id: "median", label: "Median", value: 50 },
-                { id: "mean", label: "Mean", value: 50 },
-                { id: "p75", label: "75%", value: 75 },
-                { id: "max", label: "Max", value: 100 },
-                { id: "sd", label: "SD", value: 0 },
-                { id: "variance", label: "Variance", value: 0 },
-                { id: "iqr", label: "IQR", value: 50 }
-              ],
-              key: "ABC"
-            }
-          ],
-          uncomputableValues: [{ label: "uncomputable-test", value: 1 }]
-        }
-      }
-    }
-  ]
-};
-
-// dist/termdb.boxplot.ts
-var validBoxPlotRequest = (input) => {
-  const errors = [];
-  const __is = (input2) => {
-    const $io0 = (input3) => "string" === typeof input3.genome && "string" === typeof input3.dslabel && "boolean" === typeof input3.orderByMedian && true && true && 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, "string" === typeof input3.genome || $report(_exceptionable2, {
-        path: _path2 + ".genome",
-        expected: "string",
-        value: input3.genome
-      }), "string" === typeof input3.dslabel || $report(_exceptionable2, {
-        path: _path2 + ".dslabel",
-        expected: "string",
-        value: input3.dslabel
-      }), "boolean" === typeof input3.orderByMedian || $report(_exceptionable2, {
-        path: _path2 + ".orderByMedian",
-        expected: "boolean",
-        value: input3.orderByMedian
-      }), true, true, true].every((flag) => flag);
-      return ("object" === typeof input2 && null !== input2 || $report(true, {
-        path: _path + "",
-        expected: "BoxPlotRequest",
-        value: input2
-      })) && $vo0(input2, _path + "", true) || $report(true, {
-        path: _path + "",
-        expected: "BoxPlotRequest",
-        value: input2
-      });
-    })(input, "$input", true);
-  }
-  const success = 0 === errors.length;
-  return {
-    success,
-    errors,
-    data: success ? input : void 0
-  };
-};
-var validBoxPlotResponse = (input) => {
-  const errors = [];
-  const __is = (input2) => {
-    const $io0 = (input3) => (void 0 === input3.absMin || "number" === typeof input3.absMin) && (void 0 === input3.absMax || "number" === typeof input3.absMax) && (Array.isArray(input3.plots) && input3.plots.every((elem) => "object" === typeof elem && null !== elem && $io1(elem))) && (null === input3.uncomputableValues || Array.isArray(input3.uncomputableValues) && input3.uncomputableValues.every((elem) => "object" === typeof elem && null !== elem && $io5(elem)));
-    const $io1 = (input3) => "object" === typeof input3.boxplot && null !== input3.boxplot && $io2(input3.boxplot) && (void 0 === input3.color || "string" === typeof input3.color) && (Array.isArray(input3.descrStats) && input3.descrStats.every((elem) => "object" === typeof elem && null !== elem && $io4(elem))) && (void 0 === input3.isHidden || "boolean" === typeof input3.isHidden) && "string" === typeof input3.key && true && (void 0 === input3.seriesId || "string" === typeof input3.seriesId);
-    const $io2 = (input3) => (void 0 === input3.w1 || "number" === typeof input3.w1) && (void 0 === input3.w2 || "number" === typeof input3.w2) && "number" === typeof input3.p05 && "number" === typeof input3.p25 && "number" === typeof input3.p50 && "number" === typeof input3.p75 && "number" === typeof input3.p95 && "number" === typeof input3.iqr && (Array.isArray(input3.out) && input3.out.every((elem) => "object" === typeof elem && null !== elem && $io3(elem))) && "string" === typeof input3.label;
-    const $io3 = (input3) => "number" === typeof input3.value;
-    const $io4 = (input3) => "string" === typeof input3.id && "string" === typeof input3.label && "number" === typeof input3.value;
-    const $io5 = (input3) => "string" === typeof input3.label && "number" === typeof input3.value;
-    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) => [void 0 === input3.absMin || "number" === typeof input3.absMin || $report(_exceptionable2, {
-        path: _path2 + ".absMin",
-        expected: "(number | undefined)",
-        value: input3.absMin
-      }), void 0 === input3.absMax || "number" === typeof input3.absMax || $report(_exceptionable2, {
-        path: _path2 + ".absMax",
-        expected: "(number | undefined)",
-        value: input3.absMax
-      }), (Array.isArray(input3.plots) || $report(_exceptionable2, {
-        path: _path2 + ".plots",
-        expected: "Array<BoxPlotEntry>",
-        value: input3.plots
-      })) && input3.plots.map((elem, _index1) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
-        path: _path2 + ".plots[" + _index1 + "]",
-        expected: "BoxPlotEntry",
-        value: elem
-      })) && $vo1(elem, _path2 + ".plots[" + _index1 + "]", _exceptionable2) || $report(_exceptionable2, {
-        path: _path2 + ".plots[" + _index1 + "]",
-        expected: "BoxPlotEntry",
-        value: elem
-      })).every((flag) => flag) || $report(_exceptionable2, {
-        path: _path2 + ".plots",
-        expected: "Array<BoxPlotEntry>",
-        value: input3.plots
-      }), null === input3.uncomputableValues || (Array.isArray(input3.uncomputableValues) || $report(_exceptionable2, {
-        path: _path2 + ".uncomputableValues",
-        expected: "(Array<__type>.o1 | null)",
-        value: input3.uncomputableValues
-      })) && input3.uncomputableValues.map((elem, _index2) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
-        path: _path2 + ".uncomputableValues[" + _index2 + "]",
-        expected: "__type.o1",
-        value: elem
-      })) && $vo5(elem, _path2 + ".uncomputableValues[" + _index2 + "]", _exceptionable2) || $report(_exceptionable2, {
-        path: _path2 + ".uncomputableValues[" + _index2 + "]",
-        expected: "__type.o1",
-        value: elem
-      })).every((flag) => flag) || $report(_exceptionable2, {
-        path: _path2 + ".uncomputableValues",
-        expected: "(Array<__type>.o1 | null)",
-        value: input3.uncomputableValues
-      })].every((flag) => flag);
-      const $vo1 = (input3, _path2, _exceptionable2 = true) => [("object" === typeof input3.boxplot && null !== input3.boxplot || $report(_exceptionable2, {
-        path: _path2 + ".boxplot",
-        expected: "BoxPlotData & { label: string; }",
-        value: input3.boxplot
-      })) && $vo2(input3.boxplot, _path2 + ".boxplot", _exceptionable2) || $report(_exceptionable2, {
-        path: _path2 + ".boxplot",
-        expected: "BoxPlotData & { label: string; }",
-        value: input3.boxplot
-      }), void 0 === input3.color || "string" === typeof input3.color || $report(_exceptionable2, {
-        path: _path2 + ".color",
-        expected: "(string | undefined)",
-        value: input3.color
-      }), (Array.isArray(input3.descrStats) || $report(_exceptionable2, {
-        path: _path2 + ".descrStats",
-        expected: "Array<BoxPlotDescrStatsEntry>",
-        value: input3.descrStats
-      })) && input3.descrStats.map((elem, _index3) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
-        path: _path2 + ".descrStats[" + _index3 + "]",
-        expected: "BoxPlotDescrStatsEntry",
-        value: elem
-      })) && $vo4(elem, _path2 + ".descrStats[" + _index3 + "]", _exceptionable2) || $report(_exceptionable2, {
-        path: _path2 + ".descrStats[" + _index3 + "]",
-        expected: "BoxPlotDescrStatsEntry",
-        value: elem
-      })).every((flag) => flag) || $report(_exceptionable2, {
-        path: _path2 + ".descrStats",
-        expected: "Array<BoxPlotDescrStatsEntry>",
-        value: input3.descrStats
-      }), void 0 === input3.isHidden || "boolean" === typeof input3.isHidden || $report(_exceptionable2, {
-        path: _path2 + ".isHidden",
-        expected: "(boolean | undefined)",
-        value: input3.isHidden
-      }), "string" === typeof input3.key || $report(_exceptionable2, {
-        path: _path2 + ".key",
-        expected: "string",
-        value: input3.key
-      }), true, void 0 === input3.seriesId || "string" === typeof input3.seriesId || $report(_exceptionable2, {
-        path: _path2 + ".seriesId",
-        expected: "(string | undefined)",
-        value: input3.seriesId
-      })].every((flag) => flag);
-      const $vo2 = (input3, _path2, _exceptionable2 = true) => [void 0 === input3.w1 || "number" === typeof input3.w1 || $report(_exceptionable2, {
-        path: _path2 + ".w1",
-        expected: "(number | undefined)",
-        value: input3.w1
-      }), void 0 === input3.w2 || "number" === typeof input3.w2 || $report(_exceptionable2, {
-        path: _path2 + ".w2",
-        expected: "(number | undefined)",
-        value: input3.w2
-      }), "number" === typeof input3.p05 || $report(_exceptionable2, {
-        path: _path2 + ".p05",
-        expected: "number",
-        value: input3.p05
-      }), "number" === typeof input3.p25 || $report(_exceptionable2, {
-        path: _path2 + ".p25",
-        expected: "number",
-        value: input3.p25
-      }), "number" === typeof input3.p50 || $report(_exceptionable2, {
-        path: _path2 + ".p50",
-        expected: "number",
-        value: input3.p50
-      }), "number" === typeof input3.p75 || $report(_exceptionable2, {
-        path: _path2 + ".p75",
-        expected: "number",
-        value: input3.p75
-      }), "number" === typeof input3.p95 || $report(_exceptionable2, {
-        path: _path2 + ".p95",
-        expected: "number",
-        value: input3.p95
-      }), "number" === typeof input3.iqr || $report(_exceptionable2, {
-        path: _path2 + ".iqr",
-        expected: "number",
-        value: input3.iqr
-      }), (Array.isArray(input3.out) || $report(_exceptionable2, {
-        path: _path2 + ".out",
-        expected: "Array<__type>",
-        value: input3.out
-      })) && input3.out.map((elem, _index4) => ("object" === typeof elem && null !== elem || $report(_exceptionable2, {
-        path: _path2 + ".out[" + _index4 + "]",
-        expected: "__type",
-        value: elem
-      })) && $vo3(elem, _path2 + ".out[" + _index4 + "]", _exceptionable2) || $report(_exceptionable2, {
-        path: _path2 + ".out[" + _index4 + "]",
-        expected: "__type",
-        value: elem
-      })).every((flag) => flag) || $report(_exceptionable2, {
-        path: _path2 + ".out",
-        expected: "Array<__type>",
-        value: input3.out
-      }), "string" === typeof input3.label || $report(_exceptionable2, {
-        path: _path2 + ".label",
-        expected: "string",
-        value: input3.label
-      })].every((flag) => flag);
-      const $vo3 = (input3, _path2, _exceptionable2 = true) => ["number" === typeof input3.value || $report(_exceptionable2, {
-        path: _path2 + ".value",
-        expected: "number",
-        value: input3.value
-      })].every((flag) => flag);
-      const $vo4 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.id || $report(_exceptionable2, {
-        path: _path2 + ".id",
-        expected: "string",
-        value: input3.id
-      }), "string" === typeof input3.label || $report(_exceptionable2, {
-        path: _path2 + ".label",
-        expected: "string",
-        value: input3.label
-      }), "number" === typeof input3.value || $report(_exceptionable2, {
-        path: _path2 + ".value",
-        expected: "number",
-        value: input3.value
-      })].every((flag) => flag);
-      const $vo5 = (input3, _path2, _exceptionable2 = true) => ["string" === typeof input3.label || $report(_exceptionable2, {
-        path: _path2 + ".label",
-        expected: "string",
-        value: input3.label
-      }), "number" === typeof input3.value || $report(_exceptionable2, {
-        path: _path2 + ".value",
-        expected: "number",
-        value: input3.value
-      })].every((flag) => flag);
-      return ("object" === typeof input2 && null !== input2 || $report(true, {
-        path: _path + "",
-        expected: "BoxPlotResponse",
-        value: input2
-      })) && $vo0(input2, _path + "", true) || $report(true, {
-        path: _path + "",
-        expected: "BoxPlotResponse",
-        value: input2
-      });
-    })(input, "$input", true);
-  }
-  const success = 0 === errors.length;
-  return {
-    success,
-    errors,
-    data: success ? input : void 0
-  };
-};
-
-export {
-  boxplotPayload,
-  validBoxPlotRequest,
-  validBoxPlotResponse
-};