@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/violin.integration.spec-JVODKUCL.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/test/violin.integration.spec.js", "../plots/test/helpers.spec.ts"],
+  "sourcesContent": ["import tape from 'tape'\nimport { getRunPp } from '../../test/front.helpers.js'\nimport {\n\tgetSamplelstTw,\n\tgetCategoryGroupsetting,\n\tgetGenesetMutTw,\n\tgetSsgseaTw,\n\tgetGeneVariantTw,\n\tgetScgeneexpTw,\n\tgetScctTw\n} from '../../test/testdata/data.ts'\nimport { fillTermWrapper } from '#termsetting'\nimport { getFilterItemByTag, filterJoin } from '#filter'\nimport { sleep, detectOne, detectGte, detectLst, whenVisible } from '../../test/test.helpers.js'\nimport { testViolinByCount } from './helpers.spec'\nimport { SINGLECELL_CELLTYPE } from '#types'\n\n/**************\n test sections\n\nagedx/sex, basic rendering\nagedx/sex, basic controls\ntest label clicking, filtering and hovering\ntest hide option on label clicking\nterm1=categorical, term2=numeric\nterm1=numeric, term2=cat groupsetting\nterm1=numeric, term2=survival\nterm1=numeric, term2=geneVariant\nterm1=numeric, term2=geneVariant geneset\nterm1=numeric, term2=condition\nterm1=geneExp, term2=categorical\nterm1=geneExp, term2=cat groupsetting\nterm1=geneExp, term2=geneVariant\nterm1=geneExp, term2=geneVariant geneset\nterm1=ssgsea, term2=categorical\nterm1=ssgsea, term2=cat groupsetting\nterm1=ssgsea, term2=geneVariant\nterm1=ssgsea, term2=geneVariant geneset\nterm1=geneExp, term2=survival (SKIPPED)\nterm1=geneExp, term2=survival\nterm1=numeric, term2=samplelst\nterm1=geneexp, term2=samplelst\nterm1=ssgsea, term2=samplelst\nterm=agedx, term2=geneExp with regular bins\nterm=agedx, term2=geneExp with custom bins\nterm1=numeric, term0=categorical\nterm1=numeric, term2=numeric, term0=categorical\ntest uncomputable categories legend\nLoad linear regression-violin UI\nterm1=singleCellExpression, term2=singleCellCellType\nterm1=dnameth, term2=geneExp\n\n***************/\n\ntape('\\n', function (test) {\n\ttest.comment('-***- plots/violin -***-')\n\ttest.end()\n})\n\ntape('agedx/sex, basic rendering', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [open_state]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tviolin.on('postRender.test', null)\n\t\tconst legendDiv = violin.Inner.dom.legendDiv\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tconst violinDivControls = violin.Inner.dom.controls\n\t\tconst violinDivData = violin.Inner.data.charts\n\n\t\tawait testViolinByCount(test, violinDiv, 2)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\ttestPlotTitle(violinDiv, violinDivControls) //test if label in ts-pill is same as title on svg.\n\t\ttestPvalue(violin, violinDiv, violinDivData)\n\t\ttestDescrStats(violin, legendDiv)\n\t\tawait testMedianRendering(violin, violinDiv)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testPlotTitle(violinDiv, violinDivControls) {\n\t\tconst label = violinDiv.node().querySelector('.sjpp-numeric-term-label').innerHTML\n\t\ttest.equal(\n\t\t\t(violinDivControls.node().querySelector('.ts_pill').innerHTML = label),\n\t\t\tlabel,\n\t\t\t'Plot title is same as ts-pill label'\n\t\t)\n\t}\n\n\tfunction testPvalue(violin, violinDiv, violinDivData) {\n\t\tconst violinPvalueDiv = violinDiv.selectAll('.sjpp-tableHolder')\n\t\ttest.equal(violinPvalueDiv.size(), 1, 'Should have 1 p-value table')\n\t\tconst pvalues = violinDivData[''].pvalues\n\t\ttest.equal(\n\t\t\t+pvalues[0][2].html,\n\t\t\t+violinPvalueDiv.node().querySelectorAll('.sjpp_table_item')[5].innerHTML,\n\t\t\t`Should render correct p-value of ${+violinPvalueDiv.node().querySelectorAll('.sjpp_table_item')[5].innerHTML}.`\n\t\t)\n\t}\n\n\tfunction testDescrStats(violin, legendDiv) {\n\t\ttest.equal(\n\t\t\t+legendDiv.node().querySelectorAll('.legend-row')[0].innerText.split(':')[1],\n\t\t\t+violin.Inner.config.term.q.descrStats.total.value,\n\t\t\t'Should render Total n values.'\n\t\t)\n\t\ttest.equal(\n\t\t\t+legendDiv.node().querySelectorAll('.legend-row')[1].innerText.split(':')[1],\n\t\t\t+violin.Inner.config.term.q.descrStats.min.value,\n\t\t\t'Should render Minimum value.'\n\t\t)\n\t\ttest.equal(\n\t\t\t+legendDiv.node().querySelectorAll('.legend-row')[2].innerText.split(':')[1],\n\t\t\t+violin.Inner.config.term.q.descrStats.p25.value,\n\t\t\t'Should render 1st quartile value.'\n\t\t)\n\t\ttest.equal(\n\t\t\t+legendDiv.node().querySelectorAll('.legend-row')[3].innerText.split(':')[1],\n\t\t\t+violin.Inner.config.term.q.descrStats.median.value,\n\t\t\t'Should render Median value.'\n\t\t)\n\t\ttest.equal(\n\t\t\t+legendDiv.node().querySelectorAll('.legend-row')[4].innerText.split(':')[1],\n\t\t\t+violin.Inner.config.term.q.descrStats.p75.value,\n\t\t\t'Should render 3rd quartile value.'\n\t\t)\n\t\ttest.equal(\n\t\t\t+legendDiv.node().querySelectorAll('.legend-row')[5].innerText.split(':')[1],\n\t\t\t+violin.Inner.config.term.q.descrStats.max.value,\n\t\t\t'Should render Max value.'\n\t\t)\n\t\ttest.equal(\n\t\t\t+legendDiv.node().querySelectorAll('.legend-row')[6].innerText.split(':')[1],\n\t\t\t+violin.Inner.config.term.q.descrStats.mean.value,\n\t\t\t'Should render Mean value.'\n\t\t)\n\t\ttest.equal(\n\t\t\t+legendDiv.node().querySelectorAll('.legend-row')[7].innerText.split(':')[1],\n\t\t\t+violin.Inner.config.term.q.descrStats.stdDev.value,\n\t\t\t'Should render Standard deviation.'\n\t\t)\n\t}\n\tasync function testMedianRendering(violin, violinDiv) {\n\t\tconst median = await detectGte({\n\t\t\telem: violinDiv.node(),\n\t\t\tselector: '.sjpp-median-line',\n\t\t\tcount: 2\n\t\t})\n\t\ttest.ok(median, 'Should render median line(s)')\n\t\ttest.equal(median.length, violin.Inner.data.charts[''].plots.length, 'Should render correct number of median lines')\n\t\tconst medianValues = median.map(({ __data__: { summaryStats } }) => {\n\t\t\tconst { value } = summaryStats.median\n\t\t\treturn value\n\t\t})\n\t\tconst sumStatsValues = violin.Inner.data.charts[''].plots.map(({ summaryStats }) => {\n\t\t\tconst { value } = summaryStats.median\n\t\t\treturn value\n\t\t})\n\n\t\ttest.equal(\n\t\t\tmedianValues[0],\n\t\t\tsumStatsValues[0],\n\t\t\t`Should render median correctly for plot ${violin.Inner.data.charts[''].plots[0].label}`\n\t\t)\n\t\ttest.equal(\n\t\t\tmedianValues[1],\n\t\t\tsumStatsValues[1],\n\t\t\t`Should render median correctly for plot ${violin.Inner.data.charts[''].plots[1].label}`\n\t\t)\n\t}\n})\n\ntape('agedx/sex, basic controls', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [open_state]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tviolin.on('postRender.test', null)\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait changeSvgw(violin, violinDiv)\n\t\tawait changeMedianSize(violin, violinDiv)\n\t\tawait changeOrientation(violin, violinDiv) // test orientation by changing to vertical\n\t\tawait changeDataSymbol(violin, violinDiv) //test change in Data symbol\n\t\tawait changeStrokeWidth(violin) //test change in stroke width\n\t\tawait changeSymbolSize(violin) //test change in symbol size\n\t\tawait changeScaleToLog(violin, violinDiv) //test change in axis scale\n\t\tawait changeOverlayTerm(violin, violinDiv) //test change in term2/overlay term\n\t\tawait changeModeToDiscrete(violin) //test change in q: {mode: 'Discrete'} to display barchart\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tasync function changeSvgw(violin, violinDiv) {\n\t\tconst svgw = 333\n\t\tawait violin.Inner.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: violin.Inner.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tviolin: { svgw }\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\ttest.equal(violin.Inner.app.Inner.state.plots[0].settings.violin.svgw, svgw, 'svgw changed in state')\n\t}\n\tasync function changeMedianSize(violin, violinDiv) {\n\t\tconst testMedianLength = 10\n\t\tconst testMedianThickness = 10\n\t\tconst medianEle = await detectGte({\n\t\t\telem: violinDiv.node(),\n\t\t\tselector: '.sjpp-median-line',\n\t\t\tcount: 1,\n\t\t\tasync trigger() {\n\t\t\t\tawait violin.Inner.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: violin.Inner.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\tviolin: {\n\t\t\t\t\t\t\t\tmedianLength: testMedianLength,\n\t\t\t\t\t\t\t\tmedianThickness: testMedianThickness\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\ttest.ok(medianEle, 'Median exists')\n\t\ttest.equal(\n\t\t\tviolin.Inner.app.Inner.state.plots[0].settings.violin.medianLength,\n\t\t\ttestMedianLength,\n\t\t\t'Should change Median length in state'\n\t\t)\n\t\ttest.equal(\n\t\t\tviolin.Inner.app.Inner.state.plots[0].settings.violin.medianLength,\n\t\t\ttestMedianLength,\n\t\t\t'Should change Median thickness in state'\n\t\t)\n\t}\n\tasync function changeOrientation(violin, violinDiv) {\n\t\tawait violin.Inner.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: violin.Inner.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tviolin: {\n\t\t\t\t\t\torientation: 'vertical'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\ttest.equal(\n\t\t\tviolin.Inner.app.Inner.state.plots[0].settings.violin.orientation,\n\t\t\t'vertical',\n\t\t\t'Should change orientation to vertical in state'\n\t\t)\n\t}\n\n\tasync function changeDataSymbol(violin, violinDiv) {\n\t\tawait violin.Inner.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: violin.Inner.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tviolin: {\n\t\t\t\t\t\tdatasymbol: 'rug'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\ttest.true(\n\t\t\tviolin.Inner.app.Inner.state.plots[0].settings.violin.datasymbol === 'rug',\n\t\t\t'Should change Data Symbol to Ticks'\n\t\t)\n\t}\n\n\tasync function changeStrokeWidth(violin) {\n\t\tconst testStrokeWidth = 1\n\t\tawait violin.Inner.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: violin.Inner.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tviolin: {\n\t\t\t\t\t\tstrokeWidth: testStrokeWidth\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\ttest.true(\n\t\t\tviolin.Inner.app.Inner.state.plots[0].settings.violin.strokeWidth === testStrokeWidth,\n\t\t\t`Should change stroke width to ${testStrokeWidth}`\n\t\t)\n\t}\n\n\tasync function changeSymbolSize(violin) {\n\t\tconst testSymSize = 10\n\t\tawait violin.Inner.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: violin.Inner.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tviolin: {\n\t\t\t\t\t\tradius: testSymSize\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\ttest.true(\n\t\t\tviolin.Inner.app.Inner.state.plots[0].settings.violin.radius === testSymSize,\n\t\t\t`Symbol size changed to ${testSymSize}`\n\t\t)\n\t}\n\n\tasync function changeOverlayTerm(violin, violinDiv) {\n\t\tconst term2 = await fillTermWrapper({ id: 'genetic_race' }, violin.Inner.app.vocabApi)\n\n\t\tawait violin.Inner.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: violin.Inner.id,\n\t\t\tconfig: {\n\t\t\t\tterm2\n\t\t\t}\n\t\t})\n\t\ttest.true(violin.Inner.app.Inner.state.plots[0].term2.term.id === 'genetic_race', 'Overlay term changed')\n\t}\n\n\tasync function changeScaleToLog(violin, violinDiv) {\n\t\tconst showLogScale = await detectOne({\n\t\t\telem: violinDiv.node(),\n\t\t\tselector: '.sjpp-logscale',\n\t\t\tasync trigger() {\n\t\t\t\tawait violin.Inner.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: violin.Inner.id,\n\t\t\t\t\tconfig: {\n\t\t\t\t\t\tsettings: {\n\t\t\t\t\t\t\tviolin: {\n\t\t\t\t\t\t\t\tisLogScale: true,\n\t\t\t\t\t\t\t\tplotThickness: 150\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\ttest.ok(showLogScale, 'Log scale exists')\n\t\ttest.true(violin.Inner.app.Inner.state.plots[0].settings.violin.isLogScale, 'Axis scale rendered in log')\n\t}\n\n\tasync function changeModeToDiscrete(violin, violinDiv) {\n\t\tviolin.Inner.app.dispatch({\n\t\t\tid: violin.Inner.id,\n\t\t\ttype: 'plot_edit',\n\t\t\tconfig: {\n\t\t\t\tterm: await fillTermWrapper({ id: 'agedx', q: { mode: 'discrete' } }, violin.Inner.app.vocabApi)\n\t\t\t}\n\t\t})\n\t\tawait sleep(20)\n\t\ttest.true(violin.Inner.app.Inner.state.plots[0].term.q.mode === 'discrete', \"q.mode changed to 'Discrete' \")\n\t}\n})\n\ntape('test label clicking, filtering and hovering', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tnav: {\n\t\t\t\theader_mode: 'hide_search'\n\t\t\t},\n\t\t\tplots: [open_state]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tviolin.on('postRender.test', null)\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tconst violinDivData = violin.Inner.data.charts[''].plots\n\t\tconst violinSettings = violin.Inner.config.settings.violin\n\n\t\t// before filtering there are two violins, one for each sex\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\t// filter to just one sex\n\t\tawait testFiltering(violin, violinSettings, violinDivData)\n\t\t// after filtering, just one sex is left\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 1)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\t//This function tests filtering based on range provided.\n\tasync function testFiltering(violin) {\n\t\tconst tvslst = {\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: 'and',\n\t\t\tlst: [\n\t\t\t\t{\n\t\t\t\t\ttvs: {\n\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\tgroupsetting: { disabled: true },\n\t\t\t\t\t\t\tid: 'sex',\n\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\tname: 'Sex',\n\t\t\t\t\t\t\ttype: 'categorical',\n\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t1: { label: 'Male' },\n\t\t\t\t\t\t\t\t2: { label: 'Female' }\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t},\n\t\t\t\t\t\tvalues: [{ key: '2' }]\n\t\t\t\t\t},\n\t\t\t\t\ttype: 'tvs'\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\ttvs: {\n\t\t\t\t\t\tranges: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tstart: 12.289737495475805,\n\t\t\t\t\t\t\t\tstop: 16.794964344698805\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t],\n\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\tid: 'agedx',\n\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\tname: 'Age (years) at Cancer Diagnosis',\n\t\t\t\t\t\t\ttype: 'float',\n\t\t\t\t\t\t\tbins: {\n\t\t\t\t\t\t\t\tdefault: {\n\t\t\t\t\t\t\t\t\ttype: 'regular-bin',\n\t\t\t\t\t\t\t\t\tbin_size: 5,\n\t\t\t\t\t\t\t\t\tstartinclusive: true,\n\t\t\t\t\t\t\t\t\tfirst_bin: {\n\t\t\t\t\t\t\t\t\t\tstartunbounded: true,\n\t\t\t\t\t\t\t\t\t\tstop: 5\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\tlabel_offset: 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\tconst filterUiRoot = getFilterItemByTag(violin.Inner.state.termfilter.filter, 'filterUiRoot')\n\t\tconst filter = filterJoin([filterUiRoot, tvslst])\n\t\tfilter.tag = 'filterUiRoot'\n\t\tawait violin.Inner.app.dispatch({\n\t\t\ttype: 'filter_replace',\n\t\t\tfilter\n\t\t})\n\t\ttest.ok(true, 'Filtering works as expected upon given range(start, stop) of values')\n\t}\n})\n\ntape('test hide option on label clicking', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tnav: {\n\t\t\t\theader_mode: 'hide_search'\n\t\t\t},\n\t\t\tplots: [open_state]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tviolin.on('postRender.test', null)\n\t\tconst legendDiv = violin.Inner.dom.legendDiv\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\n\t\ttestHideOption(violin, legendDiv) //test filter on label clicking\n\t\tawait testHiddenValues(violin, legendDiv, violinDiv)\n\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tfunction testHideOption(violin) {\n\t\tconst q = {\n\t\t\thiddenValues: { [violin.Inner.data.charts[''].plots[0].label]: 1 },\n\t\t\tisAtomic: true,\n\t\t\ttype: 'values'\n\t\t}\n\t\tviolin.Inner.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: violin.Inner.id,\n\t\t\tconfig: {\n\t\t\t\tterm2: {\n\t\t\t\t\tisAtomic: true,\n\t\t\t\t\tid: violin.Inner.config.term2.id,\n\t\t\t\t\tterm: violin.Inner.config.term2.term,\n\t\t\t\t\tq: q\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\ttest.ok(true, 'label Clicking and Hide option ok!')\n\t}\n\n\tasync function testHiddenValues(violin, legendDiv, violinDiv) {\n\t\tconst htmlLegends = await detectGte({ elem: legendDiv.node(), selector: '.sjpp-htmlLegend' })\n\t\ttest.ok(htmlLegends, 'Legend exists')\n\n\t\tconst hiddenKeys = Object.keys(violin.Inner.config.term2.q.hiddenValues)\n\t\ttest.equal(\n\t\t\tObject.keys(violin.Inner.config.term2.q.hiddenValues)[0],\n\t\t\thtmlLegends[8].innerHTML,\n\t\t\t'q.hiddenValues match legend'\n\t\t)\n\t\tconst unhideLegendValue = htmlLegends.filter(c => hiddenKeys.find(k => c.__data__.text === k))\n\t\tunhideLegendValue[0].dispatchEvent(new Event('click'), { bubbles: true })\n\t\tconst hiddenValueRendered = await detectGte({\n\t\t\telem: violinDiv.node(),\n\t\t\tselector: '[data-testid=\"sjpp-violin-label\"]',\n\t\t\tcount: 2\n\t\t})\n\t\ttest.ok(hiddenValueRendered, 'hidden value rendered')\n\n\t\ttest.equal(\n\t\t\thiddenValueRendered[0].__data__.label,\n\t\t\tunhideLegendValue[0].innerHTML,\n\t\t\t'Clicking on hidden legend value renders the hidden plot'\n\t\t)\n\t}\n})\n\ntape('term1=categorical, term2=numeric', 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: 'violin',\n\t\t\t\t\tterm: { id: 'diaggrp' },\n\t\t\t\t\tterm2: { id: 'agedx', q: { mode: 'continuous' } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 7)\n\t\tawait testViolinByCount(test, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=numeric, term2=cat groupsetting', 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: 'violin',\n\t\t\t\t\tterm: { id: 'agedx', q: { mode: 'continuous' } },\n\t\t\t\t\tterm2: getCategoryGroupsetting()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tawait testViolinByCount(test, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=numeric, term2=survival', function (test) {\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: 'violin',\n\t\t\t\t\tterm: { id: 'agedx', q: { mode: 'continuous' } },\n\t\t\t\t\tterm2: { id: 'efs' }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 2)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=numeric, term2=geneVariant', function (test) {\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: 'violin',\n\t\t\t\t\tterm: { id: 'agedx', q: { mode: 'continuous' } },\n\t\t\t\t\tterm2: getGeneVariantTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 1)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=numeric, term2=geneVariant geneset', function (test) {\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: 'violin',\n\t\t\t\t\tterm: { id: 'agedx', q: { mode: 'continuous' } },\n\t\t\t\t\tterm2: getGenesetMutTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 1)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=numeric, term2=condition', function (test) {\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: 'violin',\n\t\t\t\t\tterm: { id: 'agedx', q: { mode: 'continuous' } },\n\t\t\t\t\tterm2: { id: 'Hearing loss' }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 1)\n\t\tawait testConditionTermOrder(violin, violinDiv)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 5)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\tasync function testConditionTermOrder(violin, violinDiv) {\n\t\tconst groups = await detectGte({ elem: violinDiv.node(), selector: '.sjpp-vp-path', count: 1 })\n\t\ttest.ok(groups, 'Condition groups exist')\n\t\ttest.deepEqual(\n\t\t\tgroups.filter((k, i) => i % 2 == 0).map(k => k.__data__.label),\n\t\t\tviolin.Inner.data.charts[''].plots.filter(plot => plot.plotValueCount > 5).map(k => k.label),\n\t\t\t'Order of conditional categories in term2 is accurate'\n\t\t)\n\t}\n})\n\ntape('term1=geneExp, term2=categorical', function (test) {\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: 'violin',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: { gene: 'TP53', name: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: { id: 'diaggrp' }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: { callbacks: { 'postRender.test': runTests } }\n\t})\n\tasync function runTests(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 2)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 7)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=geneExp, term2=cat groupsetting', function (test) {\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: 'violin',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: { gene: 'TP53', name: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: getCategoryGroupsetting()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 2)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=geneExp, term2=geneVariant', function (test) {\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: 'violin',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: { gene: 'TP53', name: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: getGeneVariantTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 1)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=geneExp, term2=geneVariant geneset', function (test) {\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: 'violin',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: { gene: 'TP53', name: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: getGenesetMutTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 1)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=ssgsea, term2=categorical', function (test) {\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: 'violin',\n\t\t\t\t\tterm: getSsgseaTw(),\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\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 2)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 7)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=ssgsea, term2=cat groupsetting', function (test) {\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: 'violin',\n\t\t\t\t\tterm: getSsgseaTw(),\n\t\t\t\t\tterm2: getCategoryGroupsetting()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 2)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=ssgsea, term2=geneVariant', function (test) {\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: 'violin',\n\t\t\t\t\tterm: getSsgseaTw(),\n\t\t\t\t\tterm2: getGeneVariantTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 1)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=ssgsea, term2=geneVariant geneset', function (test) {\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: 'violin',\n\t\t\t\t\tterm: getSsgseaTw(),\n\t\t\t\t\tterm2: getGenesetMutTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 1)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\n// this returns no data thus breaks\ntape.skip('term1=geneExp, term2=survival (SKIPPED)', function (test) {\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: 'violin',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: { gene: 'TP53', name: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolin(violin, violinDiv)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\tasync function testViolin(violin, violinDiv) {\n\t\tconst groups = await detectGte({ elem: violinDiv.node(), selector: '.sjpp-vp-path', count: 2 })\n\t\ttest.ok(groups, 'survival groups exist')\n\t}\n})\n\ntape('term1=numeric, term2=samplelst', function (test) {\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: 'violin',\n\t\t\t\t\tterm: { id: 'agedx', q: { mode: 'continuous' } },\n\t\t\t\t\tterm2: getSamplelstTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 2)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\ntape('term1=geneexp, term2=samplelst', function (test) {\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: 'violin',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: { gene: 'TP53', name: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: getSamplelstTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 2)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\ntape('term1=ssgsea, term2=samplelst', function (test) {\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: 'violin',\n\t\t\t\t\tterm: getSsgseaTw(),\n\t\t\t\t\tterm2: getSamplelstTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 2)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 2)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term=agedx, term2=geneExp with regular bins', function (test) {\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: 'violin',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'agedx',\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tterm: { gene: 'TP53', name: 'TP53', type: 'geneExpression' },\n\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\ttype: 'regular-bin',\n\t\t\t\t\t\t\tstartinclusive: true,\n\t\t\t\t\t\t\tbin_size: 5,\n\t\t\t\t\t\t\tfirst_bin: {\n\t\t\t\t\t\t\t\tstop: 5\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tlast_bin: {\n\t\t\t\t\t\t\t\tstart: 35\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tmode: 'discrete'\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\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 4)\n\t\t// FIXME list sample breaks with tvs.ranges[] not found\n\t\t//await testLabelHoverClick(test, violin, violinDiv, 8)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term=agedx, term2=geneExp with custom bins', function (test) {\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: 'violin',\n\t\t\t\t\tterm: { id: 'agedx', q: { mode: 'continuous' } },\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tterm: { gene: 'TP53', type: 'geneExpression', bins: { type: 'custom-bin' } },\n\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\ttype: 'custom-bin',\n\t\t\t\t\t\t\tmode: 'discrete',\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\tstartunbounded: true,\n\t\t\t\t\t\t\t\t\tstop: 10,\n\t\t\t\t\t\t\t\t\tstartinclusive: true,\n\t\t\t\t\t\t\t\t\tstopinclusive: false,\n\t\t\t\t\t\t\t\t\tlabel: '<10'\n\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\t\tstart: 10,\n\t\t\t\t\t\t\t\t\tstartinclusive: true,\n\t\t\t\t\t\t\t\t\tstopinclusive: false,\n\t\t\t\t\t\t\t\t\tstop: 15,\n\t\t\t\t\t\t\t\t\tlabel: '10 to <15'\n\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\t\tstart: 15,\n\t\t\t\t\t\t\t\t\tstartinclusive: true,\n\t\t\t\t\t\t\t\t\tstopinclusive: false,\n\t\t\t\t\t\t\t\t\tstopunbounded: true,\n\t\t\t\t\t\t\t\t\tlabel: '\u226515'\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\tstartinclusive: 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\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 3)\n\t\t// FIXME list sample breaks with tvs.ranges[] not found\n\t\t//await testLabelHoverClick(test, violin, violinDiv, 3)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=numeric, term0=categorical', function (test) {\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: 'violin',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'agedx',\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tterm0: {\n\t\t\t\t\t\tid: 'sex',\n\t\t\t\t\t\tisAtomic: true\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolin(violin, violinDiv)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\tasync function testViolin(violin, violinDiv) {\n\t\tconst chartDivs = await detectGte({ elem: violinDiv.node(), selector: '.sjpp-vp-chartDiv' })\n\t\ttest.equal(chartDivs.length, 2, 'Should have 2 charts')\n\t\tconst violinPaths = await detectGte({ elem: violinDiv.node(), selector: '.sjpp-vp-path' })\n\t\ttest.equal(violinPaths.length, 4, 'Should have 4 paths')\n\t}\n})\n\ntape('term1=numeric, term2=numeric, term0=categorical', function (test) {\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: 'violin',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'agedx',\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tid: 'aaclassic_5',\n\t\t\t\t\t\tisAtomic: true\n\t\t\t\t\t},\n\t\t\t\t\tterm0: {\n\t\t\t\t\t\tid: 'sex',\n\t\t\t\t\t\tisAtomic: true\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolin(violin, violinDiv)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\tasync function testViolin(violin, violinDiv) {\n\t\tconst chartDivs = await detectGte({ elem: violinDiv.node(), selector: '.sjpp-vp-chartDiv' })\n\t\ttest.equal(chartDivs.length, 2, 'Should have 2 charts')\n\t\tconst violinPaths = await detectGte({ elem: violinDiv.node(), selector: '.sjpp-vp-path' })\n\t\ttest.equal(violinPaths.length, 6, 'Should have 6 paths')\n\t}\n})\n\ntape('test uncomputable categories legend', function (test) {\n\ttest.timeoutAfter(3000)\n\trunpp({\n\t\tstate: {\n\t\t\tnav: {\n\t\t\t\theader_mode: 'hide_search'\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: 'violin',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'aaclassic_5',\n\t\t\t\t\t\tisAtomic: true,\n\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\tmode: 'continuous'\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\tviolin: {\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(violin) {\n\t\tconst legendDiv = violin.Inner.dom.legendDiv\n\t\tviolin.on('postRender.test', null)\n\n\t\tawait testUncomputableCategories(violin, legendDiv)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tasync function testUncomputableCategories(violin, legendDiv) {\n\t\tconst keys = Object.keys(violin.Inner.data.uncomputableValues)\n\t\tconst categories = await detectGte({ elem: legendDiv.node(), selector: '.legend-row', count: 9 })\n\t\ttest.ok(categories, 'Uncomputable categories exist')\n\n\t\tconst uncomputableLegend = categories.filter(c => keys.find(k => c.__data__.text.startsWith(k)))\n\n\t\ttest.equal(keys.length, uncomputableLegend.length, 'should have the correct number of uncomputable legend entries')\n\t\ttest.equal(\n\t\t\tuncomputableLegend\n\t\t\t\t.find(c => c.__data__.text.startsWith(keys[0]))\n\t\t\t\t?.__data__.text.split(',')\n\t\t\t\t.pop(),\n\t\t\t' n = ' + violin.Inner.data.uncomputableValues[keys[0]],\n\t\t\t`Uncomputable category '${keys[0]}' rendered with the correct count`\n\t\t)\n\t\ttest.equal(\n\t\t\tuncomputableLegend\n\t\t\t\t.find(c => c.__data__.text.startsWith(keys[1]))\n\t\t\t\t?.__data__.text.split(',')\n\t\t\t\t.pop(),\n\t\t\t' n = ' + violin.Inner.data.uncomputableValues[keys[1]],\n\t\t\t`Uncomputable category '${keys[1]}' rendered with the correct count`\n\t\t)\n\t}\n})\n\ntape('Load linear regression-violin UI', 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: 'regression',\n\t\t\t\t\thasUnsubmittedEdits: true,\n\t\t\t\t\tregressionType: 'linear',\n\t\t\t\t\toutcome: {\n\t\t\t\t\t\tid: 'hrtavg',\n\t\t\t\t\t\tisAtomic: true\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tregression: {\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(regression) {\n\t\tregression.on('postRender.test', null)\n\t\t// point to outcome tw holder and avoid searching whole regression ui, in case later input terms are also added\n\t\tawait testViolinByCount(test, regression.Inner.inputs.outcome.dom.holder, 1)\n\t\tif (test._ok) regression.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('Test violin render with term1=singleCellExpression, term2=singleCellCellType', 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\tterm: getScgeneexpTw(),\n\t\t\t\t\tterm2: getScctTw()\n\t\t\t\t}\n\t\t\t],\n\t\t\tvocab: {\n\t\t\t\tgenome: 'hg38-test',\n\t\t\t\tdslabel: 'TermdbTest'\n\t\t\t}\n\t\t},\n\t\tviolin: {\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(violin) {\n\t\tviolin.on('postRender.test', null)\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 3)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 3)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\ntape('Test violin rendering with term1=dnameth, term2=geneExp', function (test) {\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: 'violin',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\ttype: 'dnaMethylation',\n\t\t\t\t\t\t\tchr: 'chr17',\n\t\t\t\t\t\t\tstart: 7673484,\n\t\t\t\t\t\t\tstop: 7681953,\n\t\t\t\t\t\t\tgenomicFeatureType: 'promoter'\n\t\t\t\t\t\t},\n\t\t\t\t\t\tq: { mode: 'continuous' }\n\t\t\t\t\t},\n\t\t\t\t\tterm2: { term: { gene: 'TP53', name: 'TP53', type: 'geneExpression' } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tviolin: { callbacks: { 'postRender.test': runTests } }\n\t})\n\tasync function runTests(violin) {\n\t\tconst violinDiv = violin.Inner.dom.violinDiv\n\t\tawait testViolinByCount(test, violinDiv, 4)\n\t\tawait testLabelHoverClick(test, violin, violinDiv, 8)\n\t\tif (test._ok) violin.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\n/*************************\n reusable helper functions\n**************************/\n\nconst runpp = getRunPp('mass', {\n\tstate: {\n\t\tnav: { activeTab: 1 },\n\t\tvocab: { dslabel: 'TermdbTest', genome: 'hg38-test' }\n\t},\n\tdebug: 1\n})\nconst open_state = {\n\tchartType: 'summary',\n\tchildType: 'violin',\n\tterm: {\n\t\tid: 'agedx',\n\t\tq: { mode: 'continuous' }\n\t},\n\tterm2: { id: 'sex' }\n}\n\n// detect given number of violin labels\n// use the first label to test mouseover menu and click menu options\nasync function testLabelHoverClick(test, violin, violinDiv, labelcount) {\n\tconst labs = await detectLst({\n\t\telem: violinDiv.node(),\n\t\tselector: '[data-testid=\"sjpp-violin-label\"]',\n\t\tcount: labelcount\n\t})\n\ttest.ok(labs, `Detected ${labelcount} violin labels`)\n\t// this test just work without term0 and can be generalized\n\tfor (let i = 0; i < labelcount; i++) {\n\t\tconst n = violin.Inner.data.charts[''].plots[i].values.length\n\t\ttest.ok(labs[i].innerHTML.endsWith('n=' + n), `violin #${i} label text ends with \"n=${n}\"`)\n\t}\n\n\t// test mouseover\n\tlabs[0].dispatchEvent(new Event('mouseover'), { bubbles: true })\n\t{\n\t\tconst tip = violin.Inner.dom.hovertip\n\t\tawait whenVisible(tip.d)\n\t\tconst table = await detectOne({ elem: tip.dnode, selector: '[data-testid=\"sja_simpletable\"]' })\n\t\ttest.pass('summary stat table found in hover tooltip')\n\t\ttip.hide()\n\t}\n\n\tlabs[0].dispatchEvent(new Event('click'), { bubbles: true })\n\tconst tip = violin.Inner.dom.clicktip\n\tif (!violin.Inner.state.config.term2 || violin.Inner.state.config.term2.term.type == SINGLECELL_CELLTYPE) {\n\t\t/* by design, menu won't show:\n\t\t- if no term2\n\t\t- if term2 is singleCellCellType\n\t\t*/\n\t\ttest.equal(tip.d.style('display'), 'none', 'Clicked on first label and app.tip will not show')\n\t\t//await whenHidden(tip.d) // this breaks\n\t} else {\n\t\t// has term2, click label will show menu and test this menu\n\t\tawait whenVisible(tip.d)\n\t\ttest.pass('Clicked on first label and app.tip will show')\n\t\tawait detectOne({ elem: tip.dnode, selector: '[data-testid=\"sjpp-violinLabOpt-addf\"]' })\n\t\ttest.pass('Add filter option is in menu')\n\t\tawait detectOne({ elem: tip.dnode, selector: '[data-testid=\"sjpp-violinLabOpt-hide\"]' })\n\t\ttest.pass('Hide option is in menu')\n\t\t// option \"List sample\" is conditional; lacks way to test different conditions\n\t\tconst lab = await detectOne({ elem: tip.dnode, selector: '[data-testid=\"sjpp-violinLabOpt-list\"]' })\n\t\ttest.pass('List option is in menu')\n\t\t// click to load samples and display in table\n\t\tawait whenVisible(violin.Inner.dom.sampletabletip.d)\n\t\tlab.dispatchEvent(new Event('click'))\n\t\tawait detectOne({ elem: violin.Inner.dom.sampletabletip.dnode, selector: '[data-testid=\"sjpp-listsampletable\"]' })\n\t\ttest.pass('Tip with sample table displayed after clicking \"List sample\"')\n\t\tviolin.Inner.dom.sampletabletip.hide()\n\t\ttip.hide()\n\t}\n}\n", "import { detectLst } from '../../test/test.helpers'\n\n/*\ncommon helpers for various charts\n\nfile is named \"spec\" to bypass \"Inner\" usage scan\n*/\n\n// detect given number of violin plots; each violin has two path.sjpp-vp-path, thus *2!!\nexport async function testViolinByCount(test: any, div: any, count: number): Promise<void> {\n\tconst groups = await detectLst({ elem: div.node(), selector: 'path.sjpp-vp-path', count: count * 2 })\n\ttest.ok(groups, `Detected ${count} violin <path class=sjpp-vp-path>`)\n}\n\nexport async function testSurvivalByCount(test: any, survival: any, count: number) {\n\tconst survivalDiv = survival.Inner.dom.chartsDiv\n\tconst series = await detectLst({ elem: survivalDiv.node(), selector: 'g.sjpp-survival-series', count })\n\ttest.ok(series, `should render ${count} survival series <g>`)\n}\n\nexport function testScatter(test: any, scatter: any, plotCount: number) {\n\ttest.equal(scatter.Inner.model.charts.length, plotCount, `should render ${plotCount} scatter plots`)\n\tfor (let i = 0; i < scatter.Inner.model.charts.length; i++) {\n\t\tconst chart = scatter.Inner.model.charts[i]\n\t\tconst scatterDiv = chart.chartDiv\n\t\tconst serieG = scatterDiv.select('.sjpcb-scatter-series')\n\t\tconst numSymbols = serieG.selectAll('path').size()\n\t\ttest.equal(\n\t\t\tnumSymbols,\n\t\t\tchart.data.samples.length,\n\t\t\t`In ${i}th plot, should be ${chart.data.samples.length}. Rendered ${numSymbols} symbols.`\n\t\t)\n\t}\n}\n"],
+  "mappings": 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+  "names": ["tape", "tip"]
+}

package/dist/violin.interactivity-STOCZMVN.js

@@ -0,0 +1,38 @@
+import {
+  setInteractivity
+} from "./chunk-D565DNJD.js";
+import "./chunk-TKW5TW4Z.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-3SHZTAGF.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OTTMHVYH.js";
+import "./chunk-GNS6CQMA.js";
+import "./chunk-JVPWIVDT.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-7JRDJNLR.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-MPSLUEI4.js";
+import "./chunk-6PNPHACF.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-BZTWTH4Y.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  setInteractivity
+};
+//# sourceMappingURL=violin.interactivity-STOCZMVN.js.map

package/dist/violin.renderer-MKDTJ3EX.js

@@ -0,0 +1,40 @@
+import {
+  createNumericScale,
+  setViolinRenderer
+} from "./chunk-B7VDZ6VF.js";
+import "./chunk-TKW5TW4Z.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-3SHZTAGF.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OTTMHVYH.js";
+import "./chunk-GNS6CQMA.js";
+import "./chunk-JVPWIVDT.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-7JRDJNLR.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-MPSLUEI4.js";
+import "./chunk-6PNPHACF.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-BZTWTH4Y.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  createNumericScale,
+  setViolinRenderer as default
+};
+//# sourceMappingURL=violin.renderer-MKDTJ3EX.js.map

package/dist/violin.renderer-MKDTJ3EX.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": [],
+  "sourcesContent": [],
+  "mappings": "",
+  "names": []
+}

package/dist/vocabulary-4IHU6DNN.js

@@ -0,0 +1,41 @@
+import {
+  getVocabFromSamplesArray,
+  q_to_param,
+  vocabInit
+} from "./chunk-TKW5TW4Z.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-3SHZTAGF.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-OTTMHVYH.js";
+import "./chunk-GNS6CQMA.js";
+import "./chunk-JVPWIVDT.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-7JRDJNLR.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-MPSLUEI4.js";
+import "./chunk-6PNPHACF.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-BZTWTH4Y.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  getVocabFromSamplesArray,
+  q_to_param,
+  vocabInit
+};
+//# sourceMappingURL=vocabulary-4IHU6DNN.js.map

package/dist/vocabulary-4IHU6DNN.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": [],
+  "sourcesContent": [],
+  "mappings": "",
+  "names": []
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-client",
-  "version": "2.198.0",
+  "version": "2.200.0",
   "description": "a genomics visualization tool for exploring a cohort's genotype and phenotype data",
   "type": "module",
   "main": "dist/app.js",
@@ -50,14 +50,11 @@
   "license": "SEE LICENSE IN ./LICENSE",
   "devDependencies": {
     "@babel/core": "^7.9.6",
-    "@babel/plugin-proposal-class-properties": "^7.18.6",
-    "@babel/plugin-proposal-object-rest-spread": "^7.20.7",
-    "@babel/plugin-syntax-dynamic-import": "^7.8.3",
     "@babel/plugin-transform-runtime": "^7.9.6",
     "@babel/preset-env": "^7.9.6",
     "@babel/preset-typescript": "^7.21.4",
-    "@sjcrh/proteinpaint-shared": "2.198.0",
-    "@sjcrh/proteinpaint-types": "2.198.0",
+    "@sjcrh/proteinpaint-shared": "2.200.0",
+    "@sjcrh/proteinpaint-types": "2.200.0",
     "@types/d3": "^7.4.3",
     "@types/ol-ext": "npm:@siedlerchr/types-ol-ext@^3.4.0",
     "@types/openseadragon": "^3.0.10",