Allow adding pre built numberic dicterm cluster

client/mass/charts.js

@@ -290,41 +290,7 @@ function getChartTypeList(self, state) {
 			//use the app name defined in dataset file
 			label: state.termdbConfig.numericDictTermCluster?.appName || 'Numeric Dictionary Term cluster',
 			chartType: 'numericDictTermCluster',
-			clickTo: self.showTree_selectlst,
-			usecase: {
-				target: 'numericDictTermCluster',
-				detail: { exclude: state.termdbConfig.numericDictTermCluster?.exclude }
-			},
-			updateActionBySelectedTerms: (action, termlst) => {
-				const twlst = termlst.map(term => ({
-					term: structuredClone(term),
-					q: { mode: NumericModes.continuous }
-				}))
-				if (twlst.length == 1) {
-					// violin
-					action.config.chartType = 'summary'
-					action.config.term = twlst[0]
-					return
-				}
-				if (twlst.length == 2) {
-					// scatter
-					action.config.chartType = 'summary'
-					action.config.term = twlst[0]
-					action.config.term2 = twlst[1]
-					return
-				}
-				// 3 or more terms, launch clustering
-				action.config.chartType = 'hierCluster'
-				action.config.dataType = 'numericDictTerm'
-				action.config.termgroups = [
-					{
-						name:
-							state.termdbConfig.numericDictTermCluster?.settings?.termGroupName || 'Numercic Dictionary Term Cluster',
-						lst: twlst,
-						type: 'hierCluster'
-					}
-				]
-			}
+			clickTo: self.loadChartSpecificMenu
 		}
 	]
 

client/plots/numericDictTermCluster.js

@@ -0,0 +1,76 @@
+import { NumericModes } from '#shared/terms.js'
+
+export function makeChartBtnMenu(holder, chartsInstance) {
+	/*
+	holder: the holder in the tooltip
+	chartsInstance: MassCharts instance
+		termdbConfig is accessible at chartsInstance.state.termdbConfig{}
+		mass option is accessible at chartsInstance.app.opts{}
+	*/
+	chartsInstance.dom.tip.clear()
+	const menuDiv = holder.append('div')
+	if (chartsInstance.state.termdbConfig.numericDictTermClusterPlots) {
+		for (const plot of chartsInstance.state.termdbConfig.numericDictTermClusterPlots) {
+			/* plot: 
+			{
+				name=str
+			}
+			*/
+			menuDiv
+				.append('div')
+				.attr('class', 'sja_menuoption sja_sharp_border')
+				.text(plot.name)
+				.on('click', async () => {
+					chartsInstance.dom.tip.hide()
+					const config = await chartsInstance.app.vocabApi.getNumericDictTermClusterByName(plot.name)
+					chartsInstance.app.dispatch({
+						type: 'plot_create',
+						config
+					})
+				})
+		}
+	}
+
+	const chart = {
+		//use the app name defined in dataset file
+		label: chartsInstance.state.termdbConfig.numericDictTermCluster?.appName || 'Numeric Dictionary Term cluster',
+		chartType: 'numericDictTermCluster',
+		clickTo: self.showTree_selectlst,
+		usecase: {
+			target: 'numericDictTermCluster',
+			detail: { exclude: chartsInstance.state.termdbConfig.numericDictTermCluster?.exclude }
+		},
+		updateActionBySelectedTerms: (action, termlst) => {
+			const twlst = termlst.map(term => ({
+				term: structuredClone(term),
+				q: { mode: NumericModes.continuous }
+			}))
+			if (twlst.length == 1) {
+				// violin
+				action.config.chartType = 'summary'
+				action.config.term = twlst[0]
+				return
+			}
+			if (twlst.length == 2) {
+				// scatter
+				action.config.chartType = 'summary'
+				action.config.term = twlst[0]
+				action.config.term2 = twlst[1]
+				return
+			}
+			// 3 or more terms, launch clustering
+			action.config.chartType = 'hierCluster'
+			action.config.dataType = 'numericDictTerm'
+			action.config.termgroups = [
+				{
+					name:
+						chartsInstance.state.termdbConfig.numericDictTermCluster?.settings?.termGroupName ||
+						'Numercic Dictionary Term Cluster',
+					lst: twlst,
+					type: 'hierCluster'
+				}
+			]
+		}
+	}
+	chartsInstance.showTree_selectlst(chart)
+}

client/termdb/TermdbVocab.js

@@ -1157,6 +1157,18 @@ export class TermdbVocab extends Vocab {
 		})
 	}
 
+	async getNumericDictTermClusterByName(name) {
+		// find a pre-built numericDictTermCluster by name from this dataset
+		return await dofetch3('termdb', {
+			body: {
+				for: 'numericDictTermCluster',
+				getPlotDataByName: name,
+				genome: this.state.vocab.genome,
+				dslabel: this.state.vocab.dslabel
+			}
+		})
+	}
+
 	// following two methods are hardcoded at /gdc/*. TODO change to generic method to work for all datasets
 	async getTopMutatedGenes(arg) {
 		return await dofetch3('gdc/topMutatedGenes', { method: 'GET', body: arg })

release.txt

@@ -1 +1,2 @@
-
+Features:
+- numericDictTermCluster: allows adding pre-built numericDictTermCluster plots

server/routes/termdb.config.ts

@@ -120,6 +120,7 @@ function make(q, res, ds: Mds3WithCohort, genome) {
 	addRestrictAncestries(c, tdb)
 	addScatterplots(c, ds)
 	addMatrixplots(c, ds)
+	addNumericDictTermClusterPlots(c, ds)
 	addNonDictionaryQueries(c, ds, genome)
 
 	res.send({ termdbConfig: c })
@@ -157,6 +158,14 @@ function addMatrixplots(c, ds) {
 	})
 }
 
+function addNumericDictTermClusterPlots(c, ds) {
+	if (!ds.cohort.numericDictTermClusterPlots) return
+	// this dataset has premade numericDictTermClusterPlots. reveal numericDictTermCluster plot names to client
+	c.numericDictTermClusterPlots = ds.cohort.numericDictTermClusterPlots.plots.map(p => {
+		return { name: p.name }
+	})
+}
+
 /* ds.queries{} contains query methods for non-dictionary data types
 including genomic, molecular, imaging etc
 */

server/src/mds3.init.js

@@ -29,7 +29,7 @@ import { get_samples, get_active_groupset } from './termdb.sql.js'
 import { server_init_db_queries } from './termdb.server.init.ts'
 import { barchart_data } from './termdb.barchart.js'
 import { mayInitiateScatterplots } from './termdb.scatter.js'
-import { mayInitiateMatrixplots } from './termdb.matrix.js'
+import { mayInitiateMatrixplots, mayInitiateNumericDictionaryTermplots } from './termdb.matrix.js'
 import { add_bcf_variant_filter } from './termdb.snp.js'
 import { validate_query_NIdata } from '#routes/brainImagingSamples.ts'
 import { validate_query_singleCell } from '#routes/termdb.singlecellSamples.ts'
@@ -301,6 +301,8 @@ export async function validate_termdb(ds) {
 
 	await mayInitiateMatrixplots(ds)
 
+	await mayInitiateNumericDictionaryTermplots(ds)
+
 	if ('minTimeSinceDx' in tdb) {
 		if (!Number.isFinite(tdb.minTimeSinceDx)) throw 'termdb.minTimeSinceDx not number'
 		if (tdb.minTimeSinceDx <= 0) throw 'termdb.minTimeSinceDx<=0'

server/src/termdb.js

@@ -67,6 +67,7 @@ export function handle_request_closure(genomes) {
 			if (q.for == 'mds3queryDetails') return get_mds3queryDetails(res, ds)
 			if (q.for == 'termTypes') return res.send(await ds.getTermTypes(q))
 			if (q.for == 'matrix') return await get_matrix(q, req, res, ds, genome)
+			if (q.for == 'numericDictTermCluster') return await get_numericDictTermCluster(q, req, res, ds, genome)
 			if (q.for == 'getSamplesPerFilter') return await getSamplesPerFilter(q, ds, res)
 			if (q.for == 'mds3variantData') return await get_mds3variantData(q, res, ds, genome)
 			if (q.for == 'validateToken') {
@@ -328,6 +329,18 @@ async function get_matrix(q, req, res, ds, genome) {
 	res.send(data)
 }
 
+async function get_numericDictTermCluster(q, req, res, ds, genome) {
+	if (q.getPlotDataByName) {
+		// send back the config for premade numericDictTermCluster plot
+		if (!ds.cohort?.numericDictTermClusterPlots?.plots)
+			throw 'ds.cohort.get_numericDictTermClusterPlots.plots missing for the dataset'
+		const plot = ds.cohort.numericDictTermClusterPlots.plots.find(p => p.name === q.getPlotDataByName)
+		if (!plot) throw 'invalid name of premade numericDictTermCluster plot' // invalid name could be attack string, avoid returning it so it won't be printed in html
+		res.send(plot.numericDictTermClusterConfig)
+		return
+	}
+}
+
 async function get_ProfileFacilities(q, req, res, ds, tdb) {
 	const canDisplay = authApi.canDisplaySampleIds(req, ds)
 	let result = []

server/src/termdb.matrix.js

@@ -644,6 +644,26 @@ export async function mayInitiateMatrixplots(ds) {
 	}
 }
 
+/*
+works with "canned" NumericDictionaryTerm plot in a dataset, e.g. data from a text file
+called in mds3.init
+*/
+export async function mayInitiateNumericDictionaryTermplots(ds) {
+	if (!ds.cohort.numericDictTermClusterPlots) return
+	if (!Array.isArray(ds.cohort.numericDictTermClusterPlots.plots))
+		throw 'cohort.numericDictTermClusterPlots.plots is not array'
+	for (const p of ds.cohort.numericDictTermClusterPlots.plots) {
+		if (!p.name) throw '.name missing from one of numericDictTermClusterPlots.plots[]'
+		if (p.file) {
+			const numericDictTermClusterConfig = await read_file(path.join(serverconfig.tpmasterdir, p.file))
+			p.numericDictTermClusterConfig = JSON.parse(numericDictTermClusterConfig)
+			if (p.getConfig) p.numericDictTermClusterConfig = p.getConfig(p.numericDictTermClusterConfig)
+		} else {
+			throw 'unknown data source of one of numericDictTermClusterConfig.plots[]'
+		}
+	}
+}
+
 async function findListOfBins(q, tw, ds) {
 	// for non-dict terms which may lack tw.term.bins
 	if (tw.q.type == 'custom-bin') {

shared/types/src/dataset.ts

@@ -1028,10 +1028,23 @@ type MatrixPlotsEntry = {
 	getConfig?: (f: any) => void
 }
 
+type NumericDictTermClusterPlotsEntry = {
+	name: string
+	file: string
+	settings?: {
+		[key: string]: any
+	}
+	getConfig?: (f: any) => void
+}
+
 type MatrixPlots = {
 	plots: MatrixPlotsEntry[]
 }
 
+type NumericDictTermClusterPlots = {
+	plots: NumericDictTermClusterPlotsEntry[]
+}
+
 type AllowCaseDetails = {
 	sample_id_key: string
 	terms: string[]
@@ -1271,6 +1284,7 @@ export type Cohort = {
 	defaultChartType?: string
 	massNav?: MassNav
 	matrixplots?: MatrixPlots
+	numericDictTermClusterPlots?: NumericDictTermClusterPlots
 	mutationset?: MutationSet[]
 	renamedChartTypes?: { singleCellPlot?: string; sampleScatter?: string }
 	scatterplots?: Scatterplots