@sjcrh/proteinpaint-client 2.191.4 → 2.193.0

package/dist/barchart.integration.spec-OQYY54AQ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/test/barchart.integration.spec.js", "../termdb/test/vocabData.js"],
+  "sourcesContent": ["import tape from 'tape'\nimport { termjson } from '../../test/testdata/termjson'\nimport {\n\tgetSamplelstTw,\n\tgetCategoryGroupsetting,\n\tgetGeneVariantTw,\n\tgetGenesetMutTw,\n\tgetCategoricalTermcollectionTw,\n\tgetScctTw\n} from '../../test/testdata/data.ts'\nimport * as helpers from '../../test/front.helpers.js'\nimport { sleep, detectLst, detectGte, detectOne, Locator } from '../../test/test.helpers.js'\nimport { getFilterItemByTag } from '../../filter/filter'\nimport * as vocabData from '../../termdb/test/vocabData'\nimport { hideCategory } from '../barchart.events.js'\n\n/*\ntest sections\n\nterm1=categorical\nterm1=categorical (no values)\nterm1=termCollection categorical\nterm1=categorical, term2=defaultbins\nterm0=defaultbins, term1=categorical\nterm1=categorical, term2=categorical (patient-level)\nterm1=geneVariant no group\nterm1=geneVariant with groups\nterm1=geneVariant, term2=geneVariant using region but not gene\nterm1=geneVariant geneset with groups\nterm1=categorical, term2=geneVariant\nterm1=categorical (patient-level), term2=geneVariant\nterm1=geneExp, term2=geneVariant SKIPPED\nterm1=geneVariant, term2=geneExp\nterm1=geneExp\nterm1=numeric term2=geneExp with default bins\nterm1=geneExp, term2=categorical\nterm1=geneExp, term2=categorical (patient-level)\nterm1=condition, term2=gene exp with default bins\nterm1=TP53 gene exp, term2=BCR gene exp, both terms with default bins\nterm1=categorical, term0=gene exp with default bins\nterm1=scct\nseries visibility - q.hiddenValue\nseries visibility - numeric\nseries visibility - condition\n\nsingle barchart, categorical filter\nsingle barchart, categorical filter (patient-level)\nsingle geneExp barchart, categorical filter (patient-level)\nsingle barchart (patient-level), compound filter (patient-level + sample-level)\ngenevariant barchart, compound filter SKIPPED\nsingle barchart, TP53 mutation dtTerm filter\n\nclick non-group bar to add filter\nclick custom categorical group bar to add filter\nnumeric exclude range\nnumeric filter - only special value\ncustom vocab: categorical terms with numeric filter\ncustom vocab: numeric terms with categorical filter\nmax number of bins: exceeded\nno visible series data, no overlay\nall hidden + with overlay, legend click\nunhidden chart and legend\ncustomized bins\n */\n\ntape('\\n', function (test) {\n\ttest.comment('-***- plots/barchart -***-')\n\ttest.end()\n})\n\ntape('term1=categorical', function (test) {\n\ttest.timeoutAfter(3000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'diaggrp'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\ttestBarCount(barchart)\n\t\ttestAxisDimension(barchart)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tlet barDiv\n\tfunction testBarCount(barchart) {\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\tconst minBars = 5\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n\t\ttest.true(numBars > minBars, `should have more than ${minBars} Diagnosis Group bars`)\n\t\ttest.equal(numBars, numOverlays, 'should have equal numbers of bars and overlays')\n\t}\n\n\tfunction testAxisDimension(barchart) {\n\t\tconst xAxis = barDiv.select('.sjpcb-bar-chart-x-axis').node()\n\t\tconst seriesG = barDiv.select('.bars-series').node()\n\t\ttest.true(xAxis.getBBox().width >= seriesG.getBBox().width, 'x-axis width should be >= series width')\n\t}\n})\n\ntape('term1=categorical (no values)', function (test) {\n\ttest.timeoutAfter(3000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'diaggrp_novalues'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\ttestTw(barchart)\n\t\ttestBarCount(barchart)\n\t\ttestAxisDimension(barchart)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testTw(barchart) {\n\t\t// testing if term.values{} and term.samplecounts[] get filled\n\t\tconst tw = barchart.Inner.config.term\n\t\ttest.ok(tw.term.values && typeof tw.term.values == 'object', 'term.values{} should be an object')\n\t\ttest.ok(Array.isArray(tw.term.categories.lst), 'term.categories.lst[] should be an array')\n\t\ttest.equal(tw.term.categories.lst.length, 7, 'term.categories.lst[] should have 7 sample counts')\n\t}\n\n\tlet barDiv\n\tfunction testBarCount(barchart) {\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\tconst minBars = 5\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n\t\ttest.true(numBars > minBars, `should have more than ${minBars} Diagnosis Group bars`)\n\t\ttest.equal(numBars, numOverlays, 'should have equal numbers of bars and overlays')\n\t}\n\n\tfunction testAxisDimension(barchart) {\n\t\tconst xAxis = barDiv.select('.sjpcb-bar-chart-x-axis').node()\n\t\tconst seriesG = barDiv.select('.bars-series').node()\n\t\ttest.true(xAxis.getBBox().width >= seriesG.getBBox().width, 'x-axis width should be >= series width')\n\t}\n})\n\ntape('term1=termCollection categorical', function (test) {\n\ttest.timeoutAfter(3000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [{ chartType: 'summary', childType: 'barchart', term: getCategoricalTermcollectionTw() }]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\t\ttestBarCount(barDiv)\n\t\ttestBarOrder(barDiv)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testBarCount(barDiv) {\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\ttest.equal(numBars, 3, 'should render 3 bars, one per member term')\n\t}\n\n\tfunction testBarOrder(barDiv) {\n\t\t// Bars should appear in termIds order: CNV, Fusion, Germline\n\t\t// Each rowlabel g has transform=\"translate(x,y)\" where y increases with row index\n\t\tconst labelGs = barDiv.selectAll('[data-testid=\"sjpcb-bars-rowlabels\"] g').nodes()\n\t\ttest.equal(labelGs.length, 3, 'should have 3 row label elements')\n\t\tif (labelGs.length < 2) return\n\t\tconst yValues = labelGs.map(g => {\n\t\t\tconst t = g.getAttribute('transform') || ''\n\t\t\tconst m = t.match(/translate\\([^,]+,([^)]+)\\)/)\n\t\t\treturn m ? parseFloat(m[1]) : 0\n\t\t})\n\t\ttest.ok(\n\t\t\tyValues[0] < yValues[1] && yValues[1] < yValues[2],\n\t\t\t'row label y positions should increase in termIds order (CNV < Fusion < Germline)'\n\t\t)\n\t}\n})\n\ntape('term1=categorical, term2=defaultbins', function (test) {\n\ttest.timeoutAfter(5000)\n\ttest.plan(4)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: { id: 'diaggrp' },\n\t\t\t\t\tterm2: { id: 'agedx' }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet barDiv\n\tasync function runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\t/*helpers\n\t\t\t.rideInit({ arg: barchart, bus: barchart, eventType: 'postRender.test', preserve: true })\n\t\t\t.run(testBarCount)\n\t\t\t.run(testOverlayOrder)\n\t\t\t.run(triggerUncomputableOverlay, 200)\n\t\t\t.run(clickLegendToHideOverlay, 1000)\n\t\t\t.run(testHiddenOverlayData, 2000)\n\t\t\t.done(test)*/\n\n\t\tawait detectOne({ elem: barDiv.node(), selector: '.pp-bars-svg' })\n\t\ttestBarCount()\n\t\ttestOverlayOrder()\n\t\tawait triggerUncomputableOverlay(barchart)\n\t\tclickLegendToHideOverlay(barchart)\n\t\tawait testHiddenOverlayData(barchart)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testBarCount() {\n\t\t// no need to await, the bar order will tested after the initial postRender event\n\t\tconst minBars = 5\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n\t\ttest.true(numBars > minBars, `should have more than ${minBars} Diagnosis Group bars`)\n\t\ttest.true(numOverlays > numBars, 'number of overlays should be greater than bars')\n\t}\n\n\tfunction testOverlayOrder() {\n\t\t// no need to await, the bar order will tested after the initial postRender event\n\t\tconst bars_grp = barDiv.selectAll('.bars-cell-grp')\n\t\tconst legend_rows = barDiv.selectAll('.legend-row')\n\t\t//flag to indicate unordered bars\n\t\tlet overlay_ordered = true\n\t\tconst legend_ids = []\n\t\tlegend_rows.each(d => legend_ids.push(d.dataId))\n\t\t//check if each stacked bar is in same order as legend\n\t\tbars_grp.each(d => {\n\t\t\tif (!overlay_ordered) return\n\t\t\tconst bar_ids = d.visibleData.map(d => d.dataId)\n\t\t\toverlay_ordered = legend_ids\n\t\t\t\t.filter(id => bar_ids.includes(id))\n\t\t\t\t.reduce((bool, id, i) => bool && bar_ids[i] === id, overlay_ordered)\n\t\t})\n\t\ttest.true(overlay_ordered, 'overlay order is same as legend')\n\t}\n\n\tasync function triggerUncomputableOverlay(barchart) {\n\t\t//Await for legend rows to increase before moving on to the next function\n\t\tawait detectLst({\n\t\t\ttarget: barchart.Inner.dom.legendDiv.node(),\n\t\t\t// avoid detecting legend entries for descriptive stats,\n\t\t\t// term legend items have a corresponding icon as the first div,\n\t\t\t// making the second div (even-numbered child) the relevant target/selector\n\t\t\tselector: '.sjpp-htmlLegend:nth-child(even)',\n\t\t\tcount: 6,\n\t\t\tmatchAs: '>=',\n\t\t\ttrigger: () => {\n\t\t\t\tbarchart.Inner.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: 'diaggrp',\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tterm2: {\n\t\t\t\t\t\t\tid: 'aaclassic_5',\n\t\t\t\t\t\t\tterm: termjson['aaclassic_5'],\n\t\t\t\t\t\t\tq: termjson['aaclassic_5'].bins.default\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t}\n\n\tconst legendDataId = 'not exposed'\n\n\tasync function clickLegendToHideOverlay(barchart) {\n\t\t//await sleep(40)\n\t\tconst legendDiv = barchart.Inner.dom.legendDiv\n\t\tconst item = legendDiv\n\t\t\t.selectAll('.sjpp-htmlLegend')\n\t\t\t.filter(d => d.dataId == legendDataId)\n\t\t\t.node()\n\t\thideCategory(item.__data__, barchart.Inner, true)\n\t}\n\n\tasync function testHiddenOverlayData(barchart) {\n\t\tconst legendDiv = barchart.Inner.dom.legendDiv\n\t\t//Fix for removing sleep()\n\t\tconst item = await detectLst({ elem: legendDiv.node(), selector: '.sjpp-hidden-legend-item', matchAs: '>=' })\n\t\t// const item = legendDiv.selectAll('.legend-row').filter(function(d) {\n\t\t// \treturn +this.style.opacity < 1 && d.dataId == legendDataId\n\t\t// })\n\t\ttest.equal(item.length, 1, 'should hide a clicked uncomputable overlay legend')\n\t}\n})\n\ntape('term0=defaultbins, term1=categorical', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: { id: 'diaggrp' },\n\t\t\t\t\tterm0: { id: 'agedx' }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': testNumCharts\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction testNumCharts(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\t\tconst numCharts = barDiv.selectAll('.pp-sbar-div').size()\n\t\ttest.true(numCharts > 2, 'should have more than 2 charts by Age at Cancer Diagnosis')\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=categorical, term2=categorical (patient-level)', function (test) {\n\ttest.timeoutAfter(5000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: { id: 'diaggrp' },\n\t\t\t\t\tterm2: { id: 'sex' }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet barDiv\n\tasync function runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\tawait detectOne({ elem: barDiv.node(), selector: '.pp-bars-svg' })\n\t\ttestBarCount()\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testBarCount() {\n\t\t// no need to await, the bar order will tested after the initial postRender event\n\t\tconst minBars = 5\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n\t\ttest.true(numBars > minBars, `should have more than ${minBars} Diagnosis Group bars`)\n\t\ttest.true(numOverlays > numBars, 'number of overlays should be greater than bars')\n\t}\n})\n\ntape('term1=geneVariant with groups', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [{ chartType: 'summary', childType: 'barchart', term: getGeneVariantTw() }]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': testNumCharts\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction testNumCharts(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\t\tconst numCharts = barDiv.selectAll('.pp-sbar-div').size()\n\t\ttest.true(numCharts == 1, 'Should have 1 chart from gene variant term')\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=geneVariant, term2=geneVariant using region but not gene', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tchildType: 'barchart',\n\t\t\t\t\tterm: getGeneVariantTw(),\n\t\t\t\t\tterm2: getGeneVariantTw(true) // gives region but not gene\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': testNumCharts\n\t\t\t}\n\t\t}\n\t})\n\tfunction testNumCharts(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\t\tconst numCharts = barDiv.selectAll('.pp-sbar-div').size()\n\t\ttest.true(numCharts == 1, 'Should have 1 chart from gene variant term')\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=geneVariant geneset with groups', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tchildType: 'barchart',\n\t\t\t\t\tterm: getGenesetMutTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': testNumCharts\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction testNumCharts(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\t\tconst numCharts = barDiv.selectAll('.pp-sbar-div').size()\n\t\ttest.true(numCharts == 1, 'Should have 1 chart from gene variant gene set')\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=categorical, term2=geneVariant', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: { id: 'diaggrp' },\n\t\t\t\t\tterm2: { term: { type: 'geneVariant', gene: 'TP53' }, q: { type: 'predefined-groupset' } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': testNumCharts\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction testNumCharts(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\t\tconst numCharts = barDiv.selectAll('.pp-sbar-div').size()\n\t\ttest.true(numCharts == 1, 'Should have 1 chart from gene variant term')\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=categorical (patient-level), term2=geneVariant', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: { id: 'genetic_race' },\n\t\t\t\t\tterm2: { term: { type: 'geneVariant', gene: 'TP53' }, q: { type: 'predefined-groupset' } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet barDiv\n\tasync function runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\tawait detectOne({ elem: barDiv.node(), selector: '.pp-bars-svg' })\n\t\ttestBarCount()\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testBarCount() {\n\t\t// no need to await, the bar order will tested after the initial postRender event\n\t\tconst minBars = 2\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n\t\ttest.true(numBars > minBars, `should have more than ${minBars} bars`)\n\t\ttest.true(numOverlays > numBars, 'number of overlays should be greater than bars')\n\t}\n})\n\ntape('term1=geneExp, term2=geneVariant SKIPPED', function (test) {\n\ttest.timeoutAfter(10000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tterm2: { term: { type: 'geneVariant', gene: 'TP53' }, q: { type: 'predefined-groupset' } },\n\t\t\t\t\t// must set geneExp q.mode=discrete to show barchart, otherwise it will become violin and not trigger provied postRender for barchart\n\t\t\t\t\tterm: { term: { type: 'geneExpression', gene: 'TP53' }, q: { mode: 'discrete' } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': testNumCharts\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction testNumCharts(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\t\tconst numCharts = barDiv.selectAll('.pp-sbar-div').size()\n\t\ttest.true(numCharts == 1, 'Should have 1 chart from gene variant term')\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=geneVariant, term2=geneExp', function (test) {\n\ttest.timeoutAfter(10000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tchildType: 'barchart',\n\t\t\t\t\tterm: { term: { type: 'geneVariant', gene: 'TP53' }, q: { type: 'predefined-groupset' } },\n\t\t\t\t\tterm2: { term: { type: 'geneExpression', gene: 'TP53' } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': testNumCharts\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction testNumCharts(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\t\tconst numCharts = barDiv.selectAll('.pp-sbar-div').size()\n\t\ttest.true(numCharts == 1, 'Should have 1 chart from gene variant term')\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=geneExp', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tchildType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: { type: 'geneExpression', gene: 'TP53', name: 'TP53' },\n\t\t\t\t\t\tq: { mode: 'discrete' }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction runTests(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\n\t\tconst numBars = barDiv.selectAll('rect').size()\n\t\ttest.ok(\n\t\t\tbarDiv.selectAll('.pp-sbar-div').size() == 1 && barchart.Inner.config.term.bins.length && numBars,\n\t\t\t'Should correctly render a bar chart for a gene expression term = TP53'\n\t\t)\n\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=numeric term2=geneExp with default bins', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tchildType: 'barchart',\n\t\t\t\t\tterm: { id: 'agedx' },\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tterm: { type: 'geneExpression', gene: 'TP53' },\n\t\t\t\t\t\tq: { mode: 'discrete' }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction runTests(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\n\t\tconst numBarCalls = barDiv.selectAll('.bars-cell').size()\n\t\tconst tableRows = barDiv.selectAll('tr').size()\n\t\ttest.equal(\n\t\t\tnumBarCalls,\n\t\t\ttableRows - 1,\n\t\t\t'Should display the correct number of bars and table rows when overlaid by gene expression term.'\n\t\t)\n\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=geneExp, term2=categorical', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tchildType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: { gene: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'discrete' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tid: 'diaggrp'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\tasync function runTests(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\n\t\tconst numBarCells = await detectGte({ elem: barDiv.node(), selector: '.bars-cell', count: 22 })\n\t\tconst tableRows = await detectGte({ elem: barDiv.node(), selector: 'tr', count: 22 })\n\t\ttest.ok(\n\t\t\t// table has one row for header\n\t\t\tnumBarCells.length >= tableRows.length - 1,\n\t\t\t'Should display the correct number of cells and table rows when gene expression term is overlaid by a categorical term.'\n\t\t)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=geneExp, term2=categorical (patient-level)', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tchildType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: { gene: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'discrete' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tid: 'sex'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet barDiv\n\tasync function runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\tawait detectOne({ elem: barDiv.node(), selector: '.pp-bars-svg' })\n\t\ttestBarCount()\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testBarCount() {\n\t\t// no need to await, the bar order will tested after the initial postRender event\n\t\tconst minBars = 5\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n\t\ttest.true(numBars > minBars, `should have more than ${minBars} bars`)\n\t\ttest.true(numOverlays > numBars, 'number of overlays should be greater than bars')\n\t}\n})\n\ntape('term1=condition, term2=gene exp with default bins', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tchildType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'Hearing loss'\n\t\t\t\t\t},\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tterm: { gene: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'discrete' }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\tasync function runTests(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\n\t\tconst numBarCells = await detectGte({ elem: barDiv.node(), selector: '.bars-cell', count: 14 })\n\t\tconst tableRows = await detectGte({ elem: barDiv.node(), selector: 'tr', count: 14 })\n\t\ttest.ok(\n\t\t\t// table has one row for header\n\t\t\tnumBarCells.length >= tableRows.length - 1,\n\t\t\t'Should display the correct number of cells and table rows when gene expression term is overlaid by a conditional term.'\n\t\t)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=TP53 gene exp, term2=BCR gene exp, both terms with default bins', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tchildType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: { gene: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'discrete' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tterm: { gene: 'BCR', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'discrete' }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\tasync function runTests(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\n\t\tconst numBarCells = await detectGte({ elem: barDiv.node(), selector: '.bars-cell', count: 27 })\n\t\tconst tableRows = await detectGte({ elem: barDiv.node(), selector: 'tr', count: 28 })\n\t\ttest.ok(\n\t\t\tnumBarCells.length == tableRows.length - 1,\n\t\t\t'Should display the correct number of cells and table rows when gene expression term is overlaid by a gene expression term.'\n\t\t)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=categorical, term0=gene exp with default bins', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tchildType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'diaggrp'\n\t\t\t\t\t},\n\t\t\t\t\tterm0: {\n\t\t\t\t\t\tterm: { gene: 'TP53', name: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'discrete' }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\tasync function runTests(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\n\t\tconst numBarchart = await detectGte({ elem: barDiv.node(), selector: '.pp-bars-svg', count: 8 })\n\t\ttest.equal(\n\t\t\tnumBarchart.length,\n\t\t\t8,\n\t\t\t'Should display the correct number of barcharts when a categorical term is overlaid by a gene expression term.'\n\t\t)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=scct', function (test) {\n\ttest.timeoutAfter(3000)\n\n\tconst scctTw = getScctTw()\n\tscctTw.term.sample.name = 'UMAP'\n\n\trunpp({\n\t\tstate: {\n\t\t\tnav: { header_mode: 'hidden' },\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tterm: scctTw\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\tasync function runTests(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\t\tconst count = 1\n\n\t\tconst numBarchart = await detectGte({ elem: barDiv.node(), selector: '.pp-bars-svg', count })\n\t\ttest.equal(numBarchart.length, count, 'Should display a barchart for a single cell cell type term.')\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('series visibility - q.hiddenValues', function (test) {\n\ttest.timeoutAfter(5000)\n\ttest.plan(2)\n\n\tconst hiddenValues = { 1: true }\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'sex',\n\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\thiddenValues\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': testHiddenValues\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction testHiddenValues(barchart) {\n\t\tconst bar = barchart.Inner\n\t\ttest.deepEqual(\n\t\t\tbar.settings.exclude.cols.sort(),\n\t\t\tObject.keys(hiddenValues).sort(),\n\t\t\t'should have the correct number of hidden bars by q.hiddenValues'\n\t\t)\n\t\ttest.equal(\n\t\t\tbar.dom.holder.selectAll('.bars-cell').size(),\n\t\t\tbar.settings.cols.length - bar.settings.exclude.cols.length,\n\t\t\t'should render the correct number of visible bars'\n\t\t)\n\t\tif (test._ok) bar.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('series visibility - numeric', function (test) {\n\ttest.timeoutAfter(5000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tnav: { activeTab: 1 },\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: { id: 'aaclassic_5' }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runNumericExcludedTests\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction runNumericExcludedTests(barchart) {\n\t\thelpers\n\t\t\t.rideInit({ arg: barchart, bus: barchart, eventType: 'postRender.test' })\n\t\t\t.run(testHiddenByValuesAndOrder)\n\t\t\t.use(triggerHiddenLegendClick, { wait: 800 })\n\t\t\t.to(testRevealedBar, { wait: 100 })\n\t\t\t.use(triggerMenuClickToHide, { wait: 100 })\n\t\t\t.to(testHiddenLegendDisplay, { wait: 600 })\n\t\t\t.done(test)\n\t}\n\n\tfunction testHiddenByValuesAndOrder(barchart) {\n\t\tconst bar = barchart.Inner\n\t\tconst excluded = bar.settings.exclude.cols\n\t\ttest.true(\n\t\t\texcluded.length > 1 && excluded.length == Object.keys(bar.config.term.q.hiddenValues).length,\n\t\t\t'should have the correct number of excluded numeric series by q.hiddenValues'\n\t\t)\n\t\t// console.log(bar.dom.legendDiv.selectAll('.legend-row').nodes())\n\t\tconst foundHiddenLabels = bar.dom.legendDiv\n\t\t\t.selectAll('.sjpp-htmlLegend')\n\t\t\t.filter(d => d?.isHidden == true)\n\t\t\t.nodes()\n\n\t\ttest.equal(\n\t\t\tfoundHiddenLabels.length + 1,\n\t\t\texcluded.length,\n\t\t\t'should display the correct number of hidden legend labels'\n\t\t)\n\n\t\tconst barOrder = [...bar.dom.holder.node().querySelectorAll('.bars-cell-grp')].sort(\n\t\t\t(a, b) => a.__data__.data[0].y - b.__data__.data[0].y\n\t\t)\n\t\ttest.deepEqual(\n\t\t\tbarOrder.map(d => d.__data__.seriesId),\n\t\t\t['<5000', '5000 to <10000', '10000 to <15000', '15000 to <20000', '20000 to <25000', '\u226525000'],\n\t\t\t'should render the bars in the expected order'\n\t\t)\n\t}\n\n\tlet numHiddenLegendBeforeClick\n\tfunction triggerHiddenLegendClick(barchart) {\n\t\tnumHiddenLegendBeforeClick = barchart.Inner.settings.exclude.cols.length\n\t\tconst node = barchart.Inner.dom.legendDiv\n\t\t\t.selectAll('.sjpp-htmlLegend')\n\t\t\t.filter(d => d?.isHidden == true)\n\t\t\t.node()\n\t\thideCategory(node.__data__, barchart.Inner, false)\n\t}\n\n\tfunction testRevealedBar(barchart) {\n\t\tconst bar = barchart.Inner\n\t\tconst excluded = bar.settings.exclude.cols\n\t\ttest.equal(excluded.length, numHiddenLegendBeforeClick - 1, 'should adjust the number of excluded series data')\n\n\t\tconst foundHiddenLabels = bar.dom.legendDiv\n\t\t\t.selectAll('.legend-row')\n\t\t\t.filter(d => d?.isHidden == true)\n\t\t\t.nodes()\n\t\ttest.equal(\n\t\t\tfoundHiddenLabels.length + 1,\n\t\t\texcluded.length,\n\t\t\t'should adjust the number of hidden legend labels after clicking to reveal one'\n\t\t)\n\t}\n\n\tfunction triggerMenuClickToHide(barchart) {\n\t\tconst node = barchart.Inner.dom.holder\n\t\t\t.selectAll('.bars-cell-grp')\n\t\t\t.filter(d => d.seriesId == 'not exposed')\n\t\t\t.node()\n\t\t\t.dispatchEvent(new Event('click', { bubbles: true }))\n\t\tbarchart.Inner.app.tip.d\n\t\t\t.selectAll('.sja_menuoption')\n\t\t\t.filter(d => d.label.includes('Hide'))\n\t\t\t.node()\n\t\t\t.click()\n\t}\n\n\tfunction testHiddenLegendDisplay(barchart) {\n\t\ttest.equal(\n\t\t\tbarchart.Inner.dom.legendDiv\n\t\t\t\t.selectAll('.sjpp-htmlLegend')\n\t\t\t\t.filter(function () {\n\t\t\t\t\treturn this.innerHTML.includes('not exposed')\n\t\t\t\t})\n\t\t\t\t.size(),\n\t\t\t1,\n\t\t\t'should hide a special numeric value by menu click'\n\t\t)\n\t}\n})\n\ntape('series visibility and order - condition', function (test) {\n\ttest.timeoutAfter(5000)\n\n\tconst conditionHiddenValues = { '1: Mild': 1 }\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'Arrhythmias',\n\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\thiddenValues: conditionHiddenValues\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': testConditionHiddenValues\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction testConditionHiddenValues(barchart) {\n\t\tconst bar = barchart.Inner\n\t\tconst excluded = bar.settings.exclude.cols\n\t\t// exclude \"Unknown status\" and \"1: Mild\"\n\t\ttest.equal(excluded.length, 1, 'should have the correct number of hidden condition bars by q.hiddenValues')\n\t\tconst barOrder = [...bar.dom.holder.node().querySelectorAll('.bars-cell-grp')].sort(\n\t\t\t(a, b) => a.__data__.data[0].y - b.__data__.data[0].y\n\t\t)\n\t\ttest.deepEqual(\n\t\t\tbarOrder.map(d => d.__data__.seriesId),\n\t\t\t['0: No condition', '2: Moderate', '3: Severe', '4: Life-threatening'],\n\t\t\t'should render the bars in the expected order'\n\t\t)\n\t\tif (test._ok) bar.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('single barchart, categorical filter', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\ttermfilter: {\n\t\t\t\tfilter: {\n\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\tin: 1,\n\t\t\t\t\tjoin: '',\n\t\t\t\t\tlst: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\ttvs: { term: { id: 'diaggrp' }, values: [{ key: 'Acute lymphoblastic leukemia' }] }\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t},\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'agedx'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet barDiv\n\tasync function runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\tawait detectOne({ elem: barDiv.node(), selector: '.pp-bars-svg' })\n\t\ttestBarCount()\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testBarCount() {\n\t\t// no need to await, the bar order will tested after the initial postRender event\n\t\tconst minBars = 3\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n\t\ttest.true(numBars > minBars, `should have more than ${minBars} bars`)\n\t\ttest.true(numOverlays == numBars, 'number of overlays should equal number of bars')\n\t}\n})\n\ntape('single barchart, categorical filter (patient-level)', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\ttermfilter: {\n\t\t\t\tfilter: {\n\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\tin: 1,\n\t\t\t\t\tjoin: '',\n\t\t\t\t\tlst: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\ttvs: { term: { id: 'sex' }, values: [{ key: '2' }] }\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t},\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'agedx'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet barDiv\n\tasync function runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\tawait detectOne({ elem: barDiv.node(), selector: '.pp-bars-svg' })\n\t\ttestBarCount()\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testBarCount() {\n\t\t// no need to await, the bar order will tested after the initial postRender event\n\t\tconst minBars = 3\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n\t\ttest.true(numBars > minBars, `should have more than ${minBars} bars`)\n\t\ttest.true(numOverlays == numBars, 'number of overlays should equal number of bars')\n\t}\n})\n\ntape('single geneExp barchart, categorical filter (patient-level)', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\ttermfilter: {\n\t\t\t\tfilter: {\n\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\tin: 1,\n\t\t\t\t\tjoin: '',\n\t\t\t\t\tlst: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\ttvs: { term: { id: 'sex' }, values: [{ key: '2' }] }\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t},\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'summary',\n\t\t\t\t\tchildType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: { type: 'geneExpression', gene: 'TP53' },\n\t\t\t\t\t\tq: { mode: 'discrete' }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet barDiv\n\tasync function runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\tawait detectOne({ elem: barDiv.node(), selector: '.pp-bars-svg' })\n\t\ttestBarCount()\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testBarCount() {\n\t\t// no need to await, the bar order will tested after the initial postRender event\n\t\tconst minBars = 3\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n\t\ttest.true(numBars > minBars, `should have more than ${minBars} bars`)\n\t\ttest.true(numOverlays == numBars, 'number of overlays should equal number of bars')\n\t}\n})\n\ntape('single barchart (patient-level), compound filter (patient-level + sample-level)', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\ttermfilter: {\n\t\t\t\tfilter: {\n\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\tin: 1,\n\t\t\t\t\tjoin: 'and',\n\t\t\t\t\tlst: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\ttvs: { term: { id: 'diaggrp' }, values: [{ key: 'Wilms tumor' }] }\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\ttvs: { term: { id: 'sex' }, values: [{ key: '1' }] }\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t},\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'sex'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\ttest.equal(\n\t\t\tbarchart.Inner.dom.holder.node().querySelectorAll('.bars-cell-grp').length,\n\t\t\t1,\n\t\t\t'should show one bar series'\n\t\t)\n\t\ttest.equal(\n\t\t\tbarchart.Inner.dom.holder.node().querySelector('.bars-cell-grp').__data__.seriesId,\n\t\t\t'1',\n\t\t\t'should show one bar series that matches filter value'\n\t\t)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\n// skipped until non-dictionary terms can be filtered by patient-level terms\ntape.skip('genevariant barchart, compound filter', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\ttermfilter: {\n\t\t\t\tfilter: {\n\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\tjoin: 'or',\n\t\t\t\t\tin: true,\n\t\t\t\t\tlst: [\n\t\t\t\t\t\t{ type: 'tvs', tvs: { term: { id: 'sex' }, values: [{ key: '1' }] } },\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\ttvs: { term: { gene: 'TP53', name: 'TP53', type: 'geneExpression' }, ranges: [{ start: 1, stop: 10 }] }\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t},\n\t\t\tplots: [{ chartType: 'summary', childType: 'barchart', term: getGeneVariantTw() }]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\ttest.equal(\n\t\t\tbarchart.Inner.dom.holder.node().querySelectorAll('.bars-cell-grp').length,\n\t\t\t2,\n\t\t\t'should show two bar series'\n\t\t)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('single barchart, TP53 mutation dtTerm filter', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\ttermfilter: { filter: tp53dtTermFilter },\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: { id: 'agedx' }\n\t\t\t\t\t// since p53 mutation filter is applied at sample level, barchart term must be sample-level (agedx)\n\t\t\t\t\t// patient-level term (sex) won't show data\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\tfunction runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\ttest.equal(\n\t\t\tbarchart.Inner.dom.holder.node().querySelectorAll('.bars-cell-grp').length,\n\t\t\t2,\n\t\t\t'should show two bar series'\n\t\t)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('click non-group bar to add filter', function (test) {\n\ttest.timeoutAfter(8000)\n\ttest.plan(3)\n\n\tconst termfilter = { filter: [] }\n\trunpp({\n\t\tstate: {\n\t\t\tnav: {\n\t\t\t\tactiveCohort: 0\n\t\t\t},\n\t\t\ttermfilter,\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: { id: 'agedx', term: termjson['agedx'], q: termjson['agedx'].bins.less },\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tid: 'Arrhythmias',\n\t\t\t\t\t\tterm: termjson['Arrhythmias'],\n\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\thiddenValues: {\n\t\t\t\t\t\t\t\t'Unknown status': 1\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet barDiv\n\tasync function runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tif (barDiv) return\n\t\tbarchart.Inner.bus.on('postRender.test', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\ttriggerBarClick(barchart)\n\t\tawait detectLst({ elem: barchart.Inner.app.tip.d.node(), selector: '.sja_menuoption', count: 1, matchAs: '>=' })\n\t\ttriggerMenuClick(barchart)\n\t\tawait detectLst({\n\t\t\telem: barchart.Inner.app.Inner.dom.holder.node(),\n\t\t\tselector: '.sja_filter_item',\n\t\t\tcount: 1,\n\t\t\tmatchAs: '>='\n\t\t})\n\t\ttestTermValues(barchart)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tlet clickedData, currData\n\tfunction triggerBarClick(barchart) {\n\t\tconst elem = barDiv.node().querySelector('.bars-cell').querySelector('rect')\n\t\tclickedData = elem.__data__\n\t\tcurrData = barchart.Inner.currServerData\n\t\telem.dispatchEvent(new Event('click', { bubbles: true }))\n\t}\n\n\tfunction triggerMenuClick(barchart) {\n\t\tbarchart.Inner.app.tip.d\n\t\t\t.selectAll('.sja_menuoption')\n\t\t\t.filter(d => d.label.includes('filter'))\n\t\t\t.node()\n\t\t\t.dispatchEvent(new Event('click', { bubbles: true }))\n\t}\n\n\tfunction testTermValues(barchart) {\n\t\tconst config = barchart.Inner.state.config\n\t\tconst termfilter = barchart.Inner.app.Inner.state.termfilter\n\t\tconst filter = getFilterItemByTag(termfilter.filter, 'filterUiRoot')\n\t\ttest.equal(\n\t\t\tfilter && filter.lst.length,\n\t\t\t2,\n\t\t\t'should create two tvslst filters when a numeric term overlay is clicked'\n\t\t)\n\t\ttest.deepEqual(\n\t\t\tfilter.lst[0],\n\t\t\t{\n\t\t\t\ttype: 'tvs',\n\t\t\t\ttvs: {\n\t\t\t\t\tterm: config.term.term,\n\t\t\t\t\tranges: [currData.refs.bins[1].find(d => d.label == clickedData.seriesId)]\n\t\t\t\t}\n\t\t\t},\n\t\t\t'should create a numeric term-value filter with a ranges key'\n\t\t)\n\t\t// config.term2.q is frozen\n\t\tconst q = JSON.parse(JSON.stringify(config.term2.q))\n\t\tconst t2ValKey =\n\t\t\tconfig.term2 &&\n\t\t\tconfig.term2.term.values &&\n\t\t\tObject.keys(config.term2.term.values).filter(key => config.term2.term.values[key].label == clickedData.dataId)[0]\n\t\ttest.deepEqual(\n\t\t\tfilter.lst[1],\n\t\t\t{\n\t\t\t\ttype: 'tvs',\n\t\t\t\ttvs: Object.assign(\n\t\t\t\t\t{\n\t\t\t\t\t\tterm: config.term2.term,\n\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tkey: t2ValKey !== undefined ? t2ValKey : clickedData.dataId,\n\t\t\t\t\t\t\t\tlabel:\n\t\t\t\t\t\t\t\t\tclickedData.dataId in config.term2.term.values\n\t\t\t\t\t\t\t\t\t\t? config.term2.term.values[clickedData.dataId].label\n\t\t\t\t\t\t\t\t\t\t: clickedData.dataId\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t]\n\t\t\t\t\t},\n\t\t\t\t\tq\n\t\t\t\t)\n\t\t\t},\n\t\t\t'should create a condition term-value filter with bar_by_*, value_by_*, and other expected keys'\n\t\t)\n\t}\n})\n\ntape('click custom categorical group bar to add filter', function (test) {\n\ttest.timeoutAfter(3000)\n\n\tconst termfilter = { filter: [] }\n\tconst tw = getCategoryGroupsetting()\n\trunpp({\n\t\tstate: {\n\t\t\ttermfilter,\n\t\t\tplots: [{ chartType: 'barchart', term: tw }]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet barDiv\n\tfunction runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tif (barDiv) return\n\t\tbarchart.Inner.bus.on('postRender.test', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\thelpers\n\t\t\t.rideInit({ arg: barchart, bus: barchart, eventType: 'postRender.test' })\n\t\t\t.run(triggerBarClick, { wait: 600 })\n\t\t\t.use(triggerMenuClick, { wait: 500 })\n\t\t\t.to(testTermValues, { wait: 100 })\n\t\t\t.done(test)\n\t}\n\n\tlet clickedData\n\tfunction triggerBarClick(barchart) {\n\t\tconst elem = barDiv.node().querySelector('.bars-cell').querySelector('rect')\n\t\tclickedData = elem.__data__\n\t\telem.dispatchEvent(new Event('click', { bubbles: true }))\n\t}\n\n\tfunction triggerMenuClick(barchart) {\n\t\tbarchart.Inner.app.tip.d\n\t\t\t.selectAll('.sja_menuoption')\n\t\t\t.filter(d => d.label.includes('filter'))\n\t\t\t.node()\n\t\t\t.click() //dispatchEvent(new Event('click', { bubbles: true }))\n\t}\n\n\tfunction testTermValues(barchart) {\n\t\tconst config = barchart.Inner.state.config\n\t\tconst currData = barchart.Inner.currServerData\n\t\tconst termfilter = barchart.Inner.app.Inner.state.termfilter\n\t\tconst filter = getFilterItemByTag(termfilter.filter, 'filterUiRoot')\n\t\ttest.equal(\n\t\t\tfilter && filter.lst.length,\n\t\t\t1,\n\t\t\t'should create one tvslst filters when a numeric term overlay is clicked'\n\t\t)\n\t\ttest.deepEqual(\n\t\t\tfilter.lst[0],\n\t\t\t{\n\t\t\t\ttype: 'tvs',\n\t\t\t\ttvs: {\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tname: 'group',\n\t\t\t\t\t\ttype: 'samplelst',\n\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\tGroup: {\n\t\t\t\t\t\t\t\tkey: 'Group',\n\t\t\t\t\t\t\t\tlabel: 'Group',\n\t\t\t\t\t\t\t\tlist: [\n\t\t\t\t\t\t\t\t\t{ sampleId: '41' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '42' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '43' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '44' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '45' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '46' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '47' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '48' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '49' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '50' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '51' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '52' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '53' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '54' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '55' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '56' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '57' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '58' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '59' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '60' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '61' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '63' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '64' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '65' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '66' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '67' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '68' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '69' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '70' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '71' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '72' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '73' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '74' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '75' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '76' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '77' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '78' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '80' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '93' }\n\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t'Not in Group': {\n\t\t\t\t\t\t\t\tkey: 'Not in Group',\n\t\t\t\t\t\t\t\tlabel: 'Not in Group',\n\t\t\t\t\t\t\t\tcolor: '#aaa',\n\t\t\t\t\t\t\t\tlist: [\n\t\t\t\t\t\t\t\t\t{ sampleId: '41' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '42' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '43' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '44' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '45' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '46' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '47' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '48' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '49' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '50' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '51' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '52' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '53' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '54' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '55' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '56' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '57' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '58' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '59' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '60' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '61' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '63' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '64' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '65' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '66' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '67' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '68' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '69' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '70' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '71' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '72' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '73' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '74' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '75' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '76' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '77' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '78' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '80' },\n\t\t\t\t\t\t\t\t\t{ sampleId: '93' }\n\t\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\t\tin: false\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tnoEdit: true\n\t\t\t},\n\t\t\t'should create a customset filter with the clicked group.values array'\n\t\t)\n\t}\n})\n\n/* bar_by_children handling has been inactivated\ntape.skip('click custom subcondition group bar to add filter', function(test) {\n\ttest.timeoutAfter(3000)\n\n\tconst termfilter = { filter: [] }\n\tconst customset = {\n\t\tname: 'A vs. B vs. C',\n\t\tgroups: [\n\t\t\t{\n\t\t\t\tname: 'Test A',\n\t\t\t\ttype: 'values',\n\t\t\t\tvalues: [\n\t\t\t\t\t{\n\t\t\t\t\t\tkey: 'Sinus tachycardia',\n\t\t\t\t\t\tlabel: 'Sinus tachycardia'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tkey: 'Sinus bradycardia',\n\t\t\t\t\t\tlabel: 'Sinus bradycardia'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tname: 'Test B',\n\t\t\t\ttype: 'values',\n\t\t\t\tvalues: [\n\t\t\t\t\t{\n\t\t\t\t\t\tkey: 'Conduction abnormalities',\n\t\t\t\t\t\tlabel: 'Conduction abnormalities'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tkey: 'Atrioventricular heart block',\n\t\t\t\t\t\tlabel: 'Atrioventricular heart block'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t},\n\t\t\t{\n\t\t\t\tname: 'Test C',\n\t\t\t\ttype: 'values',\n\t\t\t\tvalues: [\n\t\t\t\t\t{\n\t\t\t\t\t\tkey: 'Prolonged QT interval',\n\t\t\t\t\t\tlabel: 'Prolonged QT interval'\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tkey: 'Cardiac dysrhythmia',\n\t\t\t\t\t\tlabel: 'Cardiac dysrhythmia'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t]\n\t}\n\trunpp({\n\t\tstate: {\n\t\t\ttermfilter,\n\t\t\tplots: [{\n\t\t\t\tchartType: 'barchart',\n\t\t\t\tterm: {\n\t\t\t\t\tid: 'Arrhythmias',\n\t\t\t\t\tterm: termjson['Arrhythmias'],\n\t\t\t\t\tq: {\n\t\t\t\t\t\tbar_by_children: true,\n\t\t\t\t\t\tvalue_by_max_grade: 1,\n\t\t\t\t\t\tgroupsetting: {\n\t\t\t\t\t\t\tdisabled: false,\n\t\t\t\t\t\t\tinuse: true,\n\t\t\t\t\t\t\t//predefined_groupset_idx: INT,\n\t\t\t\t\t\t\tcustomset\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet barDiv\n\tfunction runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tif (barDiv) return\n\t\tbarchart.Inner.bus.on('postRender.test', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\thelpers\n\t\t\t.rideInit({ arg: barchart, bus: barchart, eventType: 'postRender.test' })\n\t\t\t.run(triggerBarClick, { wait: 600 })\n\t\t\t.use(triggerMenuClick, { wait: 500 })\n\t\t\t.to(testTermValues, { wait: 100 })\n\t\t\t.done(test)\n\t}\n\n\tlet clickedData\n\tfunction triggerBarClick(barchart) {\n\t\tconst elem = barDiv\n\t\t\t.selectAll('.bars-cell')\n\t\t\t.selectAll('rect')\n\t\t\t.filter(d => d.colId == 'Test A')\n\t\t\t.node()\n\t\tclickedData = elem.__data__\n\t\telem.dispatchEvent(new Event('click', { bubbles: true }))\n\t}\n\n\tfunction triggerMenuClick(barchart) {\n\t\tbarchart.Inner.app.tip.d\n\t\t\t.selectAll('.sja_menuoption')\n\t\t\t.filter(d => d.label.includes('filter'))\n\t\t\t.node()\n\t\t\t.click()\n\t}\n\n\tfunction testTermValues(barchart) {\n\t\tconst config = barchart.Inner.state.config\n\t\tconst currData = barchart.Inner.currServerData\n\t\tconst termfilter = barchart.Inner.app.Inner.state.termfilter\n\t\tconst filter = getFilterItemByTag(termfilter.filter, 'filterUiRoot')\n\t\ttest.equal(\n\t\t\tfilter && filter.lst.length,\n\t\t\t1,\n\t\t\t'should create one tvslst filters when a numeric term overlay is clicked'\n\t\t)\n\t\ttest.deepEqual(\n\t\t\tfilter.lst[0],\n\t\t\t{\n\t\t\t\ttype: 'tvs',\n\t\t\t\ttvs: {\n\t\t\t\t\tterm: config.term.term,\n\t\t\t\t\tvalues: customset.groups[0].values,\n\t\t\t\t\tgroupset_label: customset.groups[0].name,\n\t\t\t\t\tbar_by_children: true,\n\t\t\t\t\tvalue_by_max_grade: 1\n\t\t\t\t}\n\t\t\t},\n\t\t\t'should create a customset filter with the clicked group.values array'\n\t\t)\n\t}\n})\n*/\n\ntape('numeric exclude range', function (test) {\n\ttest.timeoutAfter(3000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: { id: 'aaclassic_5', term: termjson['aaclassic_5'] },\n\t\t\t\t\tterm2: { id: 'sex' }\n\t\t\t\t}\n\t\t\t],\n\t\t\ttermfilter: {\n\t\t\t\tfilter: {\n\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\tjoin: 'and',\n\t\t\t\t\tin: true,\n\t\t\t\t\tlst: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\ttag: 'cohortFilter',\n\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\tterm: { id: 'subcohort', type: 'multivalue' },\n\t\t\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t\t\t{ key: 'ABC', label: 'ABC' }\n\t\t\t\t\t\t\t\t\t//{key:'XYZ',label:'XYZ'},\n\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\ttag: 'filterUiRoot',\n\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\tterm: termjson['aaclassic_5'],\n\t\t\t\t\t\t\t\t\t\tranges: [{ start: 10000, stopunbounded: true, startinclusive: false, stopinclusive: true }],\n\t\t\t\t\t\t\t\t\t\tisnot: true\n\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t]\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t},\n\t\t\tnav: {\n\t\t\t\theader_mode: 'with_tabs'\n\t\t\t},\n\t\t\tactiveCohort: -1\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': testBarCount\n\t\t\t}\n\t\t}\n\t})\n\n\tfunction testBarCount(barchart) {\n\t\tconst barDiv = barchart.Inner.dom.barDiv\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\ttest.equal(numBars, 8, 'should have 8 bars')\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\n// tape.skip('numeric filter - only special value', function (test) {\n// \ttest.timeoutAfter(5000)\n\n// \trunpp({\n// \t\tstate: {\n// \t\t\tplots: [\n// \t\t\t\t{\n// \t\t\t\t\tchartType: 'barchart',\n// \t\t\t\t\tterm: { id: 'aaclassic_5' }\n// \t\t\t\t}\n// \t\t\t],\n// \t\t\ttermfilter: {\n// \t\t\t\tfilter: {\n// \t\t\t\t\ttype: 'tvslst',\n// \t\t\t\t\tin: 1,\n// \t\t\t\t\tjoin: '',\n// \t\t\t\t\tlst: [\n// \t\t\t\t\t\t{\n// \t\t\t\t\t\t\ttype: 'tvs',\n// \t\t\t\t\t\t\ttvs: {\n// \t\t\t\t\t\t\t\tterm: termjson['aaclassic_5'],\n// \t\t\t\t\t\t\t\tranges: [{ value: -8888, label: 'test' }]\n// \t\t\t\t\t\t\t}\n// \t\t\t\t\t\t}\n// \t\t\t\t\t]\n// \t\t\t\t}\n// \t\t\t}\n// \t\t},\n// \t\tbarchart: {\n// \t\t\tcallbacks: {\n// \t\t\t\t'postRender.test': runNumericValueTests\n// \t\t\t}\n// \t\t}\n// \t})\n\n// \tfunction runNumericValueTests(barchart) {\n// \t\thelpers\n// \t\t\t.rideInit({ arg: barchart, bus: barchart, eventType: 'postRender.test' })\n// \t\t\t//.run(testNoBar, { wait: 300 })\n// \t\t\t//.use(triggerHiddenLegendClick, { wait: 300 })\n// \t\t\t.run(testHasBar, { wait: 300 })\n// \t\t\t.done(test)\n// \t}\n\n// \tfunction testNoBar(barchart) {\n// \t\tconst barDiv = barchart.Inner.dom.barDiv\n// \t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n// \t\ttest.equal(numBars, 0, 'should have 0 bar')\n// \t}\n\n// \tfunction triggerHiddenLegendClick(barchart) {\n// \t\tbarchart.Inner.dom.legendDiv.node().querySelector('.legend-row').click()\n// \t}\n\n// \tfunction testHasBar(barchart) {\n// \t\tconst barDiv = barchart.Inner.dom.barDiv\n// \t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n// \t\ttest.equal(\n// \t\t\tnumBars,\n// \t\t\t1,\n// \t\t\t'should have 1 bar, forced to be visible on first render to avoid confusion with a blank barchart'\n// \t\t)\n// \t}\n// })\n\n// tape.skip('custom vocab: categorical terms with numeric filter', test => {\n// \ttest.timeoutAfter(3000)\n\n// \tconst custom_runpp = helpers.getRunPp('termdb', {\n// \t\tdebug: 1,\n// \t\tstate: {\n// \t\t\tnav: {\n// \t\t\t\theader_mode: 'search_only'\n// \t\t\t},\n// \t\t\tvocab: vocabData.getExample()\n// \t\t}\n// \t})\n\n// \tcustom_runpp({\n// \t\tstate: {\n// \t\t\ttermfilter: {\n// \t\t\t\tfilter: {\n// \t\t\t\t\ttype: 'tvslst',\n// \t\t\t\t\tjoin: '',\n// \t\t\t\t\tlst: [\n// \t\t\t\t\t\t{\n// \t\t\t\t\t\t\ttype: 'tvs',\n// \t\t\t\t\t\t\ttvs: {\n// \t\t\t\t\t\t\t\tterm: vocabData.terms.find(t => t.id == 'd'),\n// \t\t\t\t\t\t\t\tranges: [{ start: 0.1, startinclusive: false, stopunbounded: true }]\n// \t\t\t\t\t\t\t}\n// \t\t\t\t\t\t}\n// \t\t\t\t\t]\n// \t\t\t\t}\n// \t\t\t},\n// \t\t\tplots: [\n// \t\t\t\t{\n// \t\t\t\t\tchartType: 'barchart',\n// \t\t\t\t\tterm: {\n// \t\t\t\t\t\tterm: vocabData.terms.find(t => t.id == 'c')\n// \t\t\t\t\t}\n// \t\t\t\t}\n// \t\t\t]\n// \t\t},\n// \t\tbarchart: {\n// \t\t\tcallbacks: {\n// \t\t\t\t'postRender.test': runTests\n// \t\t\t}\n// \t\t}\n// \t})\n\n// \tfunction runTests(barchart) {\n// \t\tbarchart.on('postRender.test', null)\n// \t\ttestBarCount(barchart)\n// \t\tif (test._ok) barchart.Inner.app.destroy()\n// \t\ttest.end()\n// \t}\n\n// \tlet barDiv\n// \tfunction testBarCount(barchart) {\n// \t\tbarDiv = barchart.Inner.dom.barDiv\n// \t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n// \t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n// \t\ttest.equal(numBars, 2, 'should have 2 bars')\n// \t\ttest.equal(numBars, numOverlays, 'should have equal numbers of bars and overlays')\n// \t}\n// })\n\n// tape.skip('custom vocab: numeric terms with categorical filter', test => {\n// \ttest.timeoutAfter(3000)\n// \tconst vocab = vocabData.getExample()\n// \tconst custom_runpp = helpers.getRunPp('termdb', {\n// \t\tdebug: 1,\n// \t\tstate: {\n// \t\t\tnav: {\n// \t\t\t\theader_mode: 'search_only'\n// \t\t\t},\n// \t\t\tvocab\n// \t\t}\n// \t})\n\n// \tconst dterm = vocab.terms.find(t => t.id == 'd')\n// \tcustom_runpp({\n// \t\tstate: {\n// \t\t\ttermfilter: {\n// \t\t\t\tfilter: {\n// \t\t\t\t\ttype: 'tvslst',\n// \t\t\t\t\tjoin: '',\n// \t\t\t\t\tlst: [\n// \t\t\t\t\t\t{\n// \t\t\t\t\t\t\ttype: 'tvs',\n// \t\t\t\t\t\t\ttvs: {\n// \t\t\t\t\t\t\t\tterm: vocab.terms.find(t => t.id == 'c'),\n// \t\t\t\t\t\t\t\tvalues: [{ key: 1 }]\n// \t\t\t\t\t\t\t}\n// \t\t\t\t\t\t}\n// \t\t\t\t\t]\n// \t\t\t\t}\n// \t\t\t},\n// \t\t\tplots: [\n// \t\t\t\t{\n// \t\t\t\t\tchartType: 'barchart',\n// \t\t\t\t\tterm: {\n// \t\t\t\t\t\tterm: dterm,\n// \t\t\t\t\t\tq: dterm.bins.default\n// \t\t\t\t\t}\n// \t\t\t\t}\n// \t\t\t]\n// \t\t},\n// \t\tbarchart: {\n// \t\t\tcallbacks: {\n// \t\t\t\t'postRender.test': runTests\n// \t\t\t}\n// \t\t}\n// \t})\n\n// \tfunction runTests(barchart) {\n// \t\tbarchart.on('postRender.test', null)\n// \t\ttestBarCount(barchart)\n// \t\tif (test._ok) barchart.Inner.app.destroy()\n// \t\ttest.end()\n// \t}\n\n// \tlet barDiv\n// \tfunction testBarCount(barchart) {\n// \t\tbarDiv = barchart.Inner.dom.barDiv\n// \t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n// \t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n// \t\ttest.equal(numBars, 5, 'should have 5 bars')\n// \t\ttest.equal(numBars, numOverlays, 'should have equal numbers of bars and overlays')\n// \t}\n// })\n\ntape('max number of bins: exceeded', test => {\n\ttest.timeoutAfter(3000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: termjson['aaclassic_5'],\n\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\ttype: 'regular-bin',\n\t\t\t\t\t\t\tbin_size: 1000,\n\t\t\t\t\t\t\tstopinclusive: true,\n\t\t\t\t\t\t\tfirst_bin: { startunbounded: true, stop: 1, stopinclusive: true, bin: 'first' },\n\t\t\t\t\t\t\tnumDecimals: 1,\n\t\t\t\t\t\t\tlast_bin: { start: 30000, bin: 'last', stopunbounded: true },\n\t\t\t\t\t\t\tstartinclusive: false\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet barDiv\n\tasync function runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\ttestBarCount(barchart)\n\t\ttriggerExceedMaxBin(barchart)\n\t\tawait testExceedMaxBin(barchart)\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testBarCount(barchart) {\n\t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n\t\ttest.equal(numBars, 22, 'should have 22 age bars')\n\t}\n\n\tfunction triggerExceedMaxBin(barchart) {\n\t\tbarchart.Inner.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: 'aaclassic_5',\n\t\t\tconfig: {\n\t\t\t\tterm: {\n\t\t\t\t\tid: 'aaclassic_5',\n\t\t\t\t\tterm: barchart.Inner.config.term.term,\n\t\t\t\t\tq: {\n\t\t\t\t\t\ttype: 'regular-bin',\n\t\t\t\t\t\tbin_size: 100,\n\t\t\t\t\t\tstopinclusive: true,\n\t\t\t\t\t\tfirst_bin: { startunbounded: true, stop: 1, stopinclusive: true, bin: 'first' },\n\t\t\t\t\t\tnumDecimals: 1,\n\t\t\t\t\t\tlast_bin: { start: 30000, bin: 'last', stopunbounded: true },\n\t\t\t\t\t\tstartinclusive: false\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t}\n\n\tasync function testExceedMaxBin(barchart) {\n\t\t//Fix for removing sleep()\n\t\tconst barLoc = Locator.init(barchart.Inner.dom.holder.node())\n\t\tconst numBars = await barLoc.shows('.bars-cell-grp', { visibility: false, count: 22 }).get()\n\t\ttest.equal(numBars.length, 22, 'should hide the previously rendered 22 age bars on error and not re-render')\n\t\tconst errorbar = await barLoc.shows('.sja_errorbar').get(0)\n\t\ttest.true(errorbar?.innerText.includes('max_num_bins_reached'), 'should show a max number of bins error')\n\t}\n})\n\ntape('minimum sample size', test => {\n\ttest.timeoutAfter(3000)\n\tconst runpp = helpers.getRunPp('mass', {\n\t\tstate: {\n\t\t\tvocab: {\n\t\t\t\tdslabel: 'ProtectedTest',\n\t\t\t\tgenome: 'hg38-test'\n\t\t\t}\n\t\t},\n\t\tdebug: 1\n\t})\n\n\trunpp({\n\t\tstate: {\n\t\t\ttermfilter: {\n\t\t\t\tfilter: {\n\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\tjoin: 'and',\n\t\t\t\t\tlst: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\tterm: termjson.agedx,\n\t\t\t\t\t\t\t\tranges: [{ start: 1, startinclusive: true, stop: 3, stopinclusive: true }]\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t},\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\tterm: termjson.sex,\n\t\t\t\t\t\t\t\tvalues: [{ key: '1' }]\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t},\n\t\t\tnav: {\n\t\t\t\tactiveTab: 1\n\t\t\t},\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: termjson['diaggrp']\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests,\n\t\t\t\terror: runTests\n\t\t\t}\n\t\t},\n\t\tdebug: 1\n\t})\n\n\tlet barDiv, errDiv\n\tasync function runTests(barchart) {\n\t\tbarchart.on('postRender.test', null).on('error', null)\n\t\tbarDiv = barchart.Inner.dom.barDiv\n\t\terrDiv = barchart.Inner.dom.errdiv\n\t\tawait testBarCount(0, 'with stricter filter')\n\t\ttest.true(errDiv.text().includes('has less than 10 samples'), 'should display the expected error message')\n\t\ttest.notEqual(errDiv.style('display'), 'none', 'should have a visible red error div')\n\t\tawait triggerClearedError(barchart)\n\t}\n\n\tasync function testBarCount(expected, testcase) {\n\t\tif (expected > 0) {\n\t\t\tconst numBars = await Locator.init(barDiv.node()).shows('.bars-cell-grp', { count: expected }).length()\n\t\t\ttest.equal(numBars, expected, `should have ${expected} bars ${testcase}`)\n\t\t\treturn\n\t\t}\n\n\t\tconst numBars = await Locator.init(barDiv.node()).find('.bars-cell-grp').length()\n\t\t//const numBars = await Locator.init(barDiv.node())[method]('.bars-cell-grp').length()\n\t\ttest.equal(numBars, expected, `should have ${expected} bars ${testcase}`)\n\t}\n\n\tasync function triggerClearedError(barchart) {\n\t\tbarchart.on('postRender.test', testClearedError).on('error', testClearedError)\n\t\tawait barchart.Inner.app.dispatch({\n\t\t\ttype: 'filter_replace',\n\t\t\tfilter: {\n\t\t\t\ttype: 'tvslst',\n\t\t\t\tjoin: '',\n\t\t\t\tin: true,\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\tterm: termjson.agedx,\n\t\t\t\t\t\t\tranges: [{ start: 1, startinclusive: true, stop: 3, stopinclusive: true }]\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t})\n\t}\n\n\tasync function testClearedError(barchart) {\n\t\tbarchart.on('postRender.test', null).on('error', null)\n\t\tawait testBarCount(3, 'with looser filter')\n\t\ttest.equal(errDiv.text(), '', 'should have an empty error message')\n\t\ttest.equal(errDiv.style('display'), 'none', 'should have a hidden red error div')\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('no visible series data, no overlay', function (test) {\n\ttest.timeoutAfter(3000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tnav: {\n\t\t\t\theader_mode: 'search_only'\n\t\t\t},\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'barchart',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'cisplateq_5'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tbarchart: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(barchart) {\n\t\tbarchart.on('postRender.test', null)\n\t\tconst barLoc = Locator.init(barchart.Inner.dom.holder)\n\t\t//const bars = await barDiv.shows('.bars-cell-grp').length()\n\t\tconst banner = await barLoc.shows('[data-testid=\"sjpp-barchart-banner\"]').get()\n\n\t\ttest.equal(banner.length, 1, 'should show the banner')\n\n\t\ttest.true(\n\t\t\tbanner[0]?.innerText.includes('No visible barchart data '),\n\t\t\t'should show a banner for no visible data to render'\n\t\t)\n\n\t\ttest.equal(await barLoc.shows('.sjpp-hidden-legend-item').length(), 1, 'should show a legend entry')\n\n\t\tif (test._ok) barchart.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\n// tape.skip('all hidden + with overlay, legend click', function (test) {\n// \ttest.timeoutAfter(9000)\n\n// \trunpp({\n// \t\tstate: {\n// \t\t\tnav: {\n// \t\t\t\theader_mode: 'search_only'\n// \t\t\t},\n// \t\t\tplots: [\n// \t\t\t\t{\n// \t\t\t\t\tchartType: 'barchart',\n// \t\t\t\t\tterm: {\n// \t\t\t\t\t\tid: 'cisplateq_5'\n// \t\t\t\t\t},\n// \t\t\t\t\tterm2: {\n// \t\t\t\t\t\tid: 'sex'\n// \t\t\t\t\t}\n// \t\t\t\t}\n// \t\t\t]\n// \t\t},\n// \t\tbarchart: {\n// \t\t\tcallbacks: {\n// \t\t\t\t'postRender.test': runTests\n// \t\t\t}\n// \t\t}\n// \t})\n\n// \tfunction runTests(barchart) {\n// \t\tbarchart.on('postRender.test', null)\n\n// \t\thelpers\n// \t\t\t.rideInit({ arg: barchart, bus: barchart, eventType: 'postRender.test' })\n// \t\t\t.run(testBarCount)\n// \t\t\t.run(triggerBarClick)\n// \t\t\t.use(triggerMenuClick, { wait: 1100 })\n// \t\t\t.to(testRemovedOverlayByMenu, { wait: 100 })\n// \t\t\t.use(triggerUnhideOverlay, { wait: 1100 })\n// \t\t\t.to(testUnhiddenOverlay, { wait: 100 })\n// \t\t\t.use(triggerOverlayHideByLegendClick, { wait: 1000 })\n// \t\t\t.to(testhiddenOverlayByLegendClick, { wait: 100 })\n// \t\t\t.done(test)\n// \t}\n\n// \tlet barDiv\n// \tfunction testBarCount(barchart) {\n// \t\tbarDiv = barchart.Inner.dom.barDiv\n// \t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n// \t\ttest.equal(\n// \t\t\tnumBars,\n// \t\t\t1,\n// \t\t\t'should have 1 visible bar on first render when Object.keys(q.hiddenValues).length > chart.serieses.length'\n// \t\t)\n// \t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n// \t\ttest.equal(\n// \t\t\tnumOverlays,\n// \t\t\t2,\n// \t\t\t'should have 2 visible overlays on first render when Object.keys(q.hiddenValues).length > chart.serieses.length'\n// \t\t)\n// \t\ttest.equal(\n// \t\t\tbarchart.Inner.dom.banner.style('display'),\n// \t\t\t'none',\n// \t\t\t'should hide the banner when at least one chart is visible'\n// \t\t)\n// \t}\n\n// \tlet clickedData\n// \tfunction triggerBarClick(barchart) {\n// \t\tconst elem = barDiv.node().querySelector('.bars-cell').querySelector('rect')\n// \t\telem.dispatchEvent(new Event('click', { bubbles: true }))\n// \t}\n\n// \tfunction triggerMenuClick(barchart) {\n// \t\tbarchart.Inner.app.tip.d\n// \t\t\t.selectAll('.sja_menuoption')\n// \t\t\t.filter(d => d.label.includes('Hide \"Female\"'))\n// \t\t\t.node()\n// \t\t\t.dispatchEvent(new Event('click', { bubbles: true }))\n// \t}\n\n// \tfunction testRemovedOverlayByMenu(barchart) {\n// \t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n// \t\ttest.equal(numBars, 1, 'should have 1 visible bar after hiding an overlay')\n// \t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n// \t\ttest.equal(numOverlays, 1, 'should have 1 visible overlay left after hiding an overlay')\n// \t}\n\n// \tfunction triggerUnhideOverlay(barchart) {\n// \t\tbarchart.Inner.dom.legendDiv\n// \t\t\t.selectAll('.legend-row')\n// \t\t\t.filter(d => d.dataId == '2')\n// \t\t\t.node()\n// \t\t\t.firstChild.dispatchEvent(new Event('click', { bubbles: true }))\n// \t}\n\n// \tfunction testUnhiddenOverlay(barchart) {\n// \t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n// \t\ttest.equal(numBars, 1, 'should have 1 visible bar after unhiding an overlay')\n// \t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n// \t\ttest.equal(numOverlays, 2, 'should have 2 visible overlays after unhiding an overlay')\n// \t}\n\n// \tfunction triggerOverlayHideByLegendClick(barchart) {\n// \t\tbarchart.Inner.dom.legendDiv\n// \t\t\t.select('.legend-row')\n// \t\t\t.node()\n// \t\t\t.firstChild.dispatchEvent(new Event('click', { bubbles: true }))\n// \t}\n\n// \tfunction testhiddenOverlayByLegendClick(barchart) {\n// \t\tconst numBars = barDiv.selectAll('.bars-cell-grp').size()\n// \t\ttest.equal(numBars, 1, 'should have 1 visible bar after hiding an overlay by legend click')\n// \t\tconst numOverlays = barDiv.selectAll('.bars-cell').size()\n// \t\ttest.equal(numOverlays, 1, 'should have 1 visible overlays after hiding an overlay by legend click')\n// \t}\n// })\n\n// tape.skip('unhidden chart and legend', test => {\n// \ttest.timeoutAfter(8000)\n\n// \trunpp({\n// \t\tstate: {\n// \t\t\tnav: {\n// \t\t\t\theader_mode: 'search_only'\n// \t\t\t},\n// \t\t\tplots: [\n// \t\t\t\t{\n// \t\t\t\t\tchartType: 'barchart',\n// \t\t\t\t\tterm: {\n// \t\t\t\t\t\tterm: termjson['aaclassic_5'],\n// \t\t\t\t\t\tq: {\n// \t\t\t\t\t\t\ttype: 'regular-bin',\n// \t\t\t\t\t\t\tbin_size: 10000,\n// \t\t\t\t\t\t\tstopinclusive: true,\n// \t\t\t\t\t\t\tfirst_bin: { startunbounded: true, stop: 1, stopinclusive: true, bin: 'first' },\n// \t\t\t\t\t\t\tnumDecimals: 1,\n// \t\t\t\t\t\t\tlast_bin: { start: 30000, bin: 'last', stopunbounded: true },\n// \t\t\t\t\t\t\tstartinclusive: false\n// \t\t\t\t\t\t}\n// \t\t\t\t\t}\n// \t\t\t\t}\n// \t\t\t]\n// \t\t},\n// \t\tbarchart: {\n// \t\t\tcallbacks: {\n// \t\t\t\t'postRender.test': runTests\n// \t\t\t}\n// \t\t}\n// \t})\n\n// \tasync function runTests(barchart) {\n// \t\thelpers\n// \t\t\t.rideInit({ arg: barchart, bus: barchart, eventType: 'postRender.test', preserve: true })\n// \t\t\t.run(testVisibleChart)\n// \t\t\t.run(triggerHideChart, 300)\n// \t\t\t.run(testHiddenChart, 300)\n// \t\t\t.run(triggerShowChart, 300)\n// \t\t\t.run(testReshownChart, 300)\n// \t\t\t.done(test)\n// \t}\n\n// \tfunction testVisibleChart(barchart) {\n// \t\ttest.notEqual(\n// \t\t\tbarchart.Inner.dom.holder.node().style.display,\n// \t\t\t'none',\n// \t\t\t'should start with both visible and not overlapping'\n// \t\t)\n// \t}\n\n// \tfunction triggerHideChart(barchart) {\n// \t\tbarchart.Inner.app.dispatch({\n// \t\t\ttype: 'plot_hide',\n// \t\t\tid: 'aaclassic_5'\n// \t\t})\n// \t}\n\n// \tfunction testHiddenChart(barchart) {\n// \t\ttest.equal(barchart.Inner.dom.holder.node().style.display, 'none', 'should trigger hiding both chart and legend')\n// \t}\n\n// \tfunction triggerShowChart(barchart) {\n// \t\t// issue to fix: clicking the view button will cause the stat table\n// \t\t// to overlap from the bottom of the chart\n// \t\tbarchart.Inner.dom.holder.node().parentNode.querySelector('.termview').click()\n\n// \t\t// same result when using dispatch\n// \t\t/*barchart.Inner.app.dispatch({\n// \t\t\ttype: 'plot_show',\n// \t\t\tid: 'aaclassic_5'\n// \t\t})*/\n// \t}\n\n// \tfunction testReshownChart(barchart) {\n// \t\ttest.true(\n// \t\t\t+barchart.Inner.dom.holder.select('svg').property('height').baseVal.value > 100,\n// \t\t\t'should not have a small barchart svg when reshowing a barchart, not overlap with legend'\n// \t\t)\n// \t}\n// })\n\n// tape.skip('customized bins', test => {\n// \ttest.timeoutAfter(3000)\n\n// \trunpp({\n// \t\tstate: {\n// \t\t\tnav: {\n// \t\t\t\theader_mode: 'search_only'\n// \t\t\t},\n// \t\t\tplots: [\n// \t\t\t\t{\n// \t\t\t\t\tchartType: 'barchart',\n// 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\"geneVariant\"\n// for filter, search for \"termfilter\"\nconst tp53dtTermFilter = {\n\ttype: 'tvslst',\n\tin: true,\n\tjoin: '',\n\tlst: [\n\t\t{\n\t\t\ttype: 'tvs',\n\t\t\ttvs: {\n\t\t\t\tterm: {\n\t\t\t\t\tid: 'snvindel_somatic',\n\t\t\t\t\tquery: 'snvindel',\n\t\t\t\t\tname: 'SNV/indel (somatic)',\n\t\t\t\t\tparent_id: null,\n\t\t\t\t\tisleaf: true,\n\t\t\t\t\ttype: 'dtsnvindel',\n\t\t\t\t\tdt: 1,\n\t\t\t\t\tvalues: {\n\t\t\t\t\t\tM: { label: 'MISSENSE' },\n\t\t\t\t\t\tF: { label: 'FRAMESHIFT' },\n\t\t\t\t\t\tWT: { label: 'Wildtype' }\n\t\t\t\t\t},\n\t\t\t\t\tname_noOrigin: 'SNV/indel',\n\t\t\t\t\torigin: 'somatic',\n\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\tname: 'TP53',\n\t\t\t\t\t\tgenes: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tkind: 'gene',\n\t\t\t\t\t\t\t\tid: 'TP53',\n\t\t\t\t\t\t\t\tgene: 'TP53',\n\t\t\t\t\t\t\t\tname: 'TP53',\n\t\t\t\t\t\t\t\ttype: 'geneVariant'\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t],\n\t\t\t\t\t\ttype: 'geneVariant'\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\tvalues: [\n\t\t\t\t\t{\n\t\t\t\t\t\tkey: 'M',\n\t\t\t\t\t\tlabel: 'MISSENSE',\n\t\t\t\t\t\tvalue: 'M',\n\t\t\t\t\t\tbar_width_frac: null\n\t\t\t\t\t}\n\t\t\t\t],\n\t\t\t\tgenotype: 'variant',\n\t\t\t\tmcount: 'any'\n\t\t\t}\n\t\t}\n\t],\n\ttag: 'filterUiRoot'\n}\n\n/*************************\n reusable helper functions\n**************************/\n\nconst runpp = helpers.getRunPp('mass', {\n\tstate: {\n\t\tnav: {\n\t\t\tactiveTab: 1\n\t\t},\n\t\tvocab: {\n\t\t\tdslabel: 'TermdbTest',\n\t\t\tgenome: 'hg38-test'\n\t\t}\n\t},\n\tdebug: 1\n})\n", "export const terms = [\n\t{\n\t\tid: 'a',\n\t\tname: 'AAA',\n\t\tparent_id: null,\n\t\tincluded_types: ['categorical', 'integer', 'float', 'condition', 'survival'],\n\t\tchild_types: ['categorical', 'integer', 'float', 'condition', 'survival']\n\t},\n\t{\n\t\tid: 'b',\n\t\tname: 'BBB',\n\t\tparent_id: null,\n\t\tincluded_types: ['categorical', 'integer', 'float', 'condition', 'survival'],\n\t\tchild_types: ['categorical', 'integer', 'float', 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{\n\t\t\tdisabled: true\n\t\t},\n\t\tincluded_types: ['condition'],\n\t\tchild_types: []\n\t},\n\t{\n\t\ttype: 'categorical',\n\t\tid: 'f',\n\t\tname: 'FFF',\n\t\tparent_id: 'b',\n\t\tisleaf: true,\n\t\tgroupsetting: {\n\t\t\tdisabled: true\n\t\t},\n\t\tvalues: {\n\t\t\t1: { label: 'Yes' },\n\t\t\t0: { label: 'No' }\n\t\t},\n\t\tincluded_types: ['categorical'],\n\t\tchild_types: []\n\t},\n\t{\n\t\ttype: 'categorical',\n\t\tid: 'g',\n\t\tname: 'CCC',\n\t\tparent_id: 'ab',\n\t\tisleaf: true,\n\t\tgroupsetting: {\n\t\t\tdisabled: true\n\t\t},\n\t\tvalues: {\n\t\t\t1: { label: 'Yes' },\n\t\t\t0: { label: 'No' }\n\t\t},\n\t\tincluded_types: ['categorical'],\n\t\tchild_types: []\n\t},\n\t{\n\t\ttype: 'survival',\n\t\tid: 's',\n\t\tname: 'Survival term',\n\t\tisleaf: true,\n\t\tvalues: {\n\t\t\t1: { label: 'Deceased' },\n\t\t\t0: { label: 'Alive' }\n\t\t}\n\t},\n\t{\n\t\ttype: 'termCollection',\n\t\tname: 'age percentages',\n\t\ttermlst: [{ id: 'agedx' }, { id: 'a_death' }, { id: 'a_ndi' }, { id: 'agelastvisit' }],\n\t\tnumerators: ['agedx']\n\t}\n]\n\nconst vocab = JSON.stringify({\n\troute: null,\n\tterms,\n\tsampleannotation: {\n\t\t1: {\n\t\t\tc: 1,\n\t\t\td: 0.1\n\t\t},\n\t\t2: {\n\t\t\tc: 0,\n\t\t\td: 0.5\n\t\t},\n\t\t3: {\n\t\t\tc: 1,\n\t\t\td: 0.8\n\t\t},\n\t\t4: {\n\t\t\tc: 1,\n\t\t\td: 0.2\n\t\t},\n\t\t5: {\n\t\t\tc: 0,\n\t\t\td: 0.4\n\t\t},\n\t\t6: {\n\t\t\tc: 1,\n\t\t\td: 0.3\n\t\t},\n\t\t7: {\n\t\t\tc: 0,\n\t\t\td: 0.5\n\t\t},\n\t\t8: {\n\t\t\tc: 1,\n\t\t\td: 0.9\n\t\t},\n\t\t9: {\n\t\t\tc: 0,\n\t\t\td: 0.05\n\t\t},\n\t\t10: {\n\t\t\tc: 1,\n\t\t\td: 1.1\n\t\t}\n\t}\n})\n\nexport function getExample() {\n\treturn JSON.parse(vocab)\n}\n"],
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+  "names": ["tape", "d", "termfilter", "runpp", "numBars"]
+}

package/dist/barchart2-AT5FXOUY.js

@@ -0,0 +1,314 @@
+import {
+  ABBREV_COHORT,
+  FULL_COHORT,
+  getDefaultProfilePlotSettings,
+  getProfilePlotConfig,
+  profilePlot
+} from "./chunk-JEZUPG4J.js";
+import {
+  fillTwLst
+} from "./chunk-L7VDSIM7.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-UXDVUCXU.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-KM4JBR26.js";
+import "./chunk-COYULNJF.js";
+import {
+  dofetch3
+} from "./chunk-6G4YOMWW.js";
+import "./chunk-7IYJZZQI.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-IVXCWCKS.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import {
+  axisTop
+} from "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import {
+  linear
+} from "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/profile/barchart2.ts
+var stepx = 500;
+var barwidth = 400;
+var ProfileBarchart2 = class extends profilePlot {
+  constructor(opts) {
+    super(opts, "profileBarchart2");
+    this.rowCount = 0;
+    this.additionalInputs = [];
+  }
+  static {
+    this.type = "profileBarchart2";
+  }
+  async init(appState) {
+    await super.init(appState);
+    const config = appState.plots.find((p) => p.id === this.id);
+    this.componentNames = config.plotByComponent.map((elem) => ({
+      value: elem.profileComponent.name,
+      label: elem.profileComponent.name
+    }));
+    const profileComponentInput = {
+      label: "Component",
+      type: "dropdown",
+      chartType: "profileBarchart2",
+      options: this.componentNames,
+      settingsKey: "profileComponent",
+      callback: (value) => this.setProfileComponent(value)
+    };
+    this.additionalInputs.push(profileComponentInput);
+  }
+  setProfileComponent(value) {
+    this.settings.profileComponent = value;
+    this.app.dispatch({ type: "plot_edit", id: this.id, config: this.config });
+  }
+  async main() {
+    this.dom.loadingDiv.style("display", "");
+    try {
+      await super.main();
+      this.configProfileComponent = this.config.plotByComponent.find((comp) => comp.profileComponent.name == this.settings.profileComponent) || this.config.plotByComponent[0];
+      this.rowCount = 0;
+      this.scoreTerms = [];
+      for (const group of this.configProfileComponent.groups)
+        for (const row of group.rows) {
+          this.rowCount++;
+          if (row.term1) this.scoreTerms.push(row.term1);
+          if (row.term2) this.scoreTerms.push(row.term2);
+        }
+      await this.setControls(this.additionalInputs);
+      this.profileComponent = this.settings.profileComponent || this.componentNames[0].value;
+      this.plot();
+    } catch (e) {
+      console.error(e);
+      throw `${e} [profileBarchart2 main()]`;
+    } finally {
+      this.dom.loadingDiv.style("display", "none");
+    }
+  }
+  /**
+   * Override setControls() to fetch data from the dedicated barchart2 route.
+   * The base class setControls() builds filter UI and sets this.filter but
+   * skips the data fetch for profileBarchart2 (see profilePlot.ts).
+   * This method calls termdb/profileBarchart2Scores, which derives the facility
+   * term server-side and returns aggregated (median) percentages.
+   */
+  async setControls(additionalInputs = []) {
+    await super.setControls(additionalInputs);
+    this.data = await this.fetchAggregatedScores();
+    if (this.data && "error" in this.data) throw this.data.error;
+  }
+  async fetchAggregatedScores() {
+    return dofetch3("termdb/profileBarchart2Scores", {
+      body: {
+        genome: this.state.vocab.genome,
+        dslabel: this.state.vocab.dslabel,
+        scoreTerms: this.scoreTerms.map((t) => ({
+          score: { term: { id: t.score.term.id }, q: t.score.q },
+          maxScore: typeof t.maxScore === "number" ? t.maxScore : { term: { id: t.maxScore.term.id }, q: t.maxScore.q }
+        })),
+        filterByUserSites: this.settings?.filterByUserSites,
+        filter: this.filter
+      }
+    });
+  }
+  onMouseOut(event) {
+    if (event.target.tagName == "rect" && event.target.getAttribute("fill-opacity") == 0.3) {
+      event.target.setAttribute("fill-opacity", 0);
+    }
+  }
+  onMouseOver(event) {
+    if (event.target.tagName == "rect" && event.target.getAttribute("fill-opacity") == 0) {
+      event.target.setAttribute("fill-opacity", 0.3);
+    }
+  }
+  plot() {
+    const { hasSubjectiveData } = this.createSvg();
+    this.drawTitleAndDefs(hasSubjectiveData);
+    this.drawColumnHeaders(hasSubjectiveData);
+    const yEnd = this.drawComponentRows(hasSubjectiveData);
+    this.drawGuideLines(yEnd, hasSubjectiveData);
+    this.drawLegend(yEnd, hasSubjectiveData);
+  }
+  createSvg() {
+    const hasSubjectiveData = this.configProfileComponent.hasSubjectiveData;
+    const width = this.state.activeCohort == ABBREV_COHORT ? 1e3 : 1300;
+    const height = this.rowCount * 32 + 450;
+    this.dom.svg = this.dom.plotDiv.append("svg").attr("width", width).attr("height", height);
+    return { width, height, hasSubjectiveData };
+  }
+  drawTitleAndDefs(_hasSubjectiveData) {
+    const title = this.state.activeCohort == ABBREV_COHORT ? `Score-based Results for the ${this.profileComponent} Component by Module and Domain Compared with End-User Impression` : `Objective ${this.profileComponent == "Patients and Outcomes" ? "" : "and Subjective "}Score-based Results for the ${this.profileComponent} Component by Module and Domain`;
+    this.dom.svg.append("text").attr("transform", `translate(50, 30)`).attr("font-weight", "bold").text(title);
+    const color = this.configProfileComponent.profileComponent.color;
+    this.dom.svg.append("defs").append("pattern").attr("id", `${this.id}_diagonalHatch`).attr("patternUnits", "userSpaceOnUse").attr("width", 4).attr("height", 4).append("path").attr("d", "M-1,1 l2,-2 M0,4 l4,-4 M3,5 l2,-2").attr("stroke-width", 1).attr("stroke", color);
+  }
+  drawColumnHeaders(hasSubjectiveData) {
+    const svg = this.dom.svg;
+    const config = this.config;
+    for (const [i, c] of config.columnNames.entries()) {
+      if (i == 1 && !hasSubjectiveData) break;
+      const x = (i % 2 == 0 ? 400 : 900) + 10;
+      const y = 70;
+      svg.append("text").attr("transform", `translate(${x}, ${y})`).attr("text-anchor", "start").style("font-weight", "bold").text(c);
+      this.drawAxis(x, y + 30);
+    }
+  }
+  drawAxis(x, y) {
+    const xAxisScale = linear().domain([0, 100]).range([0, barwidth]);
+    this.dom.svg.append("g").attr("transform", `translate(${x}, ${y})`).call(axisTop(xAxisScale));
+  }
+  drawComponentRows(hasSubjectiveData) {
+    const svg = this.dom.svg;
+    const step = 30;
+    let y = 70;
+    for (const group of this.configProfileComponent.groups) {
+      svg.append("text").attr("transform", `translate(${50}, ${y + 40})`).attr("text-anchor", "start").text(`${group.label}`).style("font-weight", "bold");
+      y += step + 20;
+      for (const row of group.rows) {
+        const g = svg.append("g");
+        g.append("rect").attr("transform", `translate(${20}, ${y - 6})`).attr("x", 0).attr("y", 0).attr("width", hasSubjectiveData ? 1500 : 850).attr("height", 30).attr("fill", "#f8d335").attr("fill-opacity", 0);
+        const x = 400;
+        if (row.term1) this.drawRect(x, y, row, "term1", g);
+        if (row.term2) this.drawRect(x + stepx, y, row, "term2", g);
+        y += step;
+      }
+    }
+    return y;
+  }
+  drawRect(x, y, row, field, g) {
+    const hasSubjectiveData = this.configProfileComponent.hasSubjectiveData;
+    const d = row[field];
+    let subjectiveTerm = false;
+    if ((row.name == "Total Module" || row.name == "End-user Impression*") && !row.term2) subjectiveTerm = true;
+    const termColor = d.score.term.color;
+    const value = this.getPercentage(d);
+    const isFirst = field == "term1" || field == "term2" && !row.term1;
+    const pairValue = field == "term1" ? this.getPercentage(row.term2) : this.getPercentage(row.term1);
+    const width = value ? value / 100 * barwidth : 0;
+    if (value) {
+      const isObjective = this.state.activeCohort == FULL_COHORT && this.settings.profileComponent == "Patients and Outcomes" ? true : !subjectiveTerm && (pairValue || !hasSubjectiveData);
+      const rect = g.append("rect").attr("transform", `translate(${x + 10}, ${y})`).attr("pointer-events", "none").attr("x", 0).attr("y", 0).attr("width", width).attr("height", 20);
+      if (isObjective) rect.attr("fill", termColor);
+      else {
+        const termid = this.id + d.score.term.id;
+        g.append("defs").append("pattern").attr("id", termid).attr("patternUnits", "userSpaceOnUse").attr("width", 4).attr("height", 4).append("path").attr("d", "M-1,1 l2,-2 M0,4 l4,-4 M3,5 l2,-2").attr("stroke-width", 1).attr("stroke", termColor);
+        rect.attr("fill", `url(#${termid})`);
+      }
+    }
+    const text = g.append("text").attr("pointer-events", "none").attr("text-anchor", "end").text(`${value || 0}%`);
+    if (width > 0) text.attr("transform", `translate(${x + width + 55}, ${y + 15})`);
+    else if (!pairValue && field == "term1") text.attr("transform", `translate(${x + 35}, ${y + 15})`);
+    if (isFirst)
+      g.append("text").attr("transform", `translate(${field == "term1" ? x : x - stepx}, ${y + 15})`).attr("text-anchor", "end").text(row.name).attr("pointer-events", "none");
+  }
+  drawGuideLines(yEnd, hasSubjectiveData) {
+    this.drawGuide(410, 120, 50, yEnd, "B");
+    this.drawGuide(410, 120, 75, yEnd, "A");
+    if (!hasSubjectiveData) return;
+    this.drawGuide(910, 120, 50, yEnd, "B");
+    this.drawGuide(910, 120, 75, yEnd, "A");
+  }
+  drawGuide(x, y, percent, y2, text) {
+    const svg = this.dom.svg;
+    const x1 = x + percent / 100 * barwidth;
+    svg.append("line").style("stroke", "#aaa").style("stroke-width", 1).style("stroke-dasharray", "5, 5").attr("x1", x1).attr("y1", y).attr("x2", x1).attr("y2", y2);
+    svg.append("text").attr("transform", `translate(${x1 + 0.125 * barwidth}, ${y2 + 20})`).attr("text-anchor", "middle").text(text).style("font-weight", "bold");
+    if (percent == 50)
+      svg.append("text").attr("transform", `translate(${x1 - 0.25 * barwidth}, ${y2 + 20})`).attr("text-anchor", "middle").text("C").style("font-weight", "bold");
+  }
+  drawLegend(yEnd, hasSubjectiveData) {
+    this.legendG = this.dom.svg.append("g").attr("data-testid", "sjpp-profileBarchart2-legend").attr("transform", `translate(400,${yEnd + 90})`);
+    this.filterG = this.dom.svg.append("g").attr("transform", `translate(0,${yEnd + 90})`);
+    if (!this.isComparison) {
+      this.legendG.append("text").attr("text-anchor", "left").style("font-weight", "bold").text("Overall Score").attr("transform", `translate(0, -5)`);
+      this.addLegendItem("A", "More than 75% of possible scorable items", 1);
+      this.addLegendItem("B", "50-75% of possible scorable items", 2);
+      this.addLegendItem("C", "Less than 50% of possible scorable items", 3);
+      if (this.state.activeCohort == ABBREV_COHORT) {
+        this.addEndUserImpressionNote(this.legendG.append("g"));
+      } else this.addPOCNote(this.legendG.append("g"));
+    }
+    this.addFilterLegend();
+    if (!hasSubjectiveData) return;
+    const color = this.configProfileComponent.profileComponent.color;
+    const svg = this.dom.svg;
+    const y = yEnd + 40;
+    let x = 600;
+    const lineG = svg.append("g");
+    this.drawLegendRect(x, y, "and", color, lineG);
+    x += 300;
+    this.drawLegendRect(x, y, "or", color, lineG);
+  }
+  drawLegendRect(x, y, operator, color, lineG) {
+    const rect = lineG.append("g").attr("transform", `translate(${x}, ${y})`).append("rect").attr("x", 0).attr("y", 0).attr("width", 20).attr("height", 20);
+    if (operator == "and") rect.attr("fill", color);
+    else rect.attr("fill", `url(#${this.id}_diagonalHatch)`);
+    const text = this.dom.svg.append("text").attr("transform", `translate(${x + 25}, ${y + 15})`).attr("text-anchor", "start").text("Objective ");
+    text.append("tspan").attr("font-weight", "bold").text(operator);
+    text.append("tspan").text(" Subjective data");
+  }
+};
+async function getPlotConfig(opts, app, _activeCohort) {
+  try {
+    const activeCohort = _activeCohort === void 0 ? app.getState().activeCohort : _activeCohort;
+    const defaults = await getProfilePlotConfig(activeCohort, app, opts);
+    if (!defaults) throw "default config not found in termdbConfig.plotConfigByCohort.profileBarchart2";
+    defaults.settings = { profileBarchart2: getDefaultProfilePlotSettings() };
+    let config = structuredClone(defaults);
+    config = copyMerge(config, opts);
+    config.settings.controls = { isOpen: false };
+    const twlst = [];
+    for (const profileComponent of config.plotByComponent) {
+      profileComponent.hasSubjectiveData = false;
+      for (const group of profileComponent.groups)
+        for (const row of group.rows) {
+          if (row.term1) {
+            row.term1.score.q = row.term1.maxScore.q = { mode: "continuous" };
+            twlst.push(row.term1.score);
+            twlst.push(row.term1.maxScore);
+          }
+          if (row.term2) {
+            row.term2.score.q = row.term2.maxScore.q = { mode: "continuous" };
+            twlst.push(row.term2.score);
+            twlst.push(row.term2.maxScore);
+          }
+          if (row.term1 && row.term2) profileComponent.hasSubjectiveData = true;
+        }
+    }
+    await fillTwLst(twlst, app.vocabApi);
+    return config;
+  } catch (e) {
+    throw `${e} [profileBarchart2 getPlotConfig()]`;
+  }
+}
+var profileBarchart2Init = getCompInit(ProfileBarchart2);
+var componentInit = profileBarchart2Init;
+function getDefaultProfileBarchart2Settings() {
+  return {};
+}
+export {
+  componentInit,
+  getDefaultProfileBarchart2Settings,
+  getPlotConfig,
+  profileBarchart2Init
+};
+//# sourceMappingURL=barchart2-AT5FXOUY.js.map