@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/scatter.integration.spec-ZPTM3AGQ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/scatter/test/scatter.integration.spec.js"],
+  "sourcesContent": ["import tape from 'tape'\nimport * as helpers from '../../../test/front.helpers.js'\nimport * as d3color from 'd3-color'\nimport * as d3s from 'd3-selection'\nimport {\n\tdetectLst,\n\tdetectStyle,\n\tdetectAttr,\n\tdetectChildAttr,\n\tdetectChildStyle,\n\tdetectGte,\n\tsleep\n} from '../../../test/test.helpers'\nimport { openSummaryPlot, openPlot, getSamplelstTW } from '../../../mass/groups.js'\nimport { mclass } from '#shared/common.js'\nimport {\n\tgetGenesetMutTw,\n\tgetGeneVariantTw,\n\tgetSsgseaTw,\n\tgetScgeneexpTw,\n\tgetScctTw\n} from '../../../test/testdata/data.ts'\n\n/* Tests:\nRender TermdbTest scatter plot and open survival and summary\nRender TermdbTest scatter plot adding age as Z to render a 3D plot\nRender 3D plot with age as Z and showContour set to true to apply contour on 3D plot\ndynamic scatter of agedx & hrtavg\ndynamic scatter of 2-gene expression\ndynamic scatter of 2-ssgsea\ndynamic scatter of 2-dnameth\nInvalid colorTW.id\nInvalid colorTW.term\nInvalid plot name\nTest legend\nRender color groups\nChange symbol and reference size from menu\nChange chart width and height from menu\nCheck/uncheck Show axes from menu\nClick zoom in, zoom out, and reset buttons\nGroups and group menus function\ncolorTW=geneVariant with no groupsetting\ncolorTW=geneVariant gene list\ncolorTW=ssgsea\nsinglecell map\nsinglecell geneexp\n*/\n\nconst runpp = helpers.getRunPp('mass', {\n\tstate: {\n\t\tnav: { activeTab: 1 },\n\t\tvocab: {\n\t\t\tdslabel: 'TermdbTest',\n\t\t\tgenome: 'hg38-test'\n\t\t}\n\t},\n\tdebug: 1\n})\n\nconst state = {\n\tplots: [\n\t\t{\n\t\t\tchartType: 'sampleScatter',\n\t\t\tcolorTW: { id: 'diaggrp' },\n\t\t\tname: 'TermdbTest TSNE'\n\t\t}\n\t]\n}\n\nconst open_state = {\n\tnav: { header_mode: 'hide_search' },\n\tplots: [\n\t\t{\n\t\t\tchartType: 'sampleScatter',\n\t\t\tcolorTW: { id: 'diaggrp' },\n\t\t\tname: 'TermdbTest TSNE'\n\t\t}\n\t]\n}\n\nconst state3D = {\n\tplots: [\n\t\t{\n\t\t\tchartType: 'sampleScatter',\n\t\t\tcolorTW: { id: 'diaggrp' },\n\t\t\tname: 'TermdbTest TSNE',\n\t\t\tterm0: { id: 'agedx', q: { mode: 'continuous' } }\n\t\t}\n\t]\n}\n\nconst stateDynamicScatter = {\n\tplots: [\n\t\t{\n\t\t\tchartType: 'sampleScatter',\n\t\t\tcolorTW: { id: 'diaggrp' },\n\t\t\tterm: { id: 'agedx', q: { mode: 'continuous' } },\n\t\t\tterm2: { id: 'hrtavg', q: { mode: 'continuous' } }\n\t\t}\n\t]\n}\nconst state2geneexp = {\n\tplots: [\n\t\t{\n\t\t\tchartType: 'sampleScatter',\n\t\t\tcolorTW: { id: 'diaggrp' },\n\t\t\tterm: { term: { type: 'geneExpression', gene: 'AKT1' }, q: { mode: 'continuous' } },\n\t\t\tterm2: { term: { type: 'geneExpression', gene: 'TP53' }, q: { mode: 'continuous' } }\n\t\t}\n\t]\n}\nconst state2ssgsea = {\n\tplots: [\n\t\t{\n\t\t\tchartType: 'sampleScatter',\n\t\t\tcolorTW: { id: 'diaggrp' },\n\t\t\tterm: { term: { type: 'ssGSEA', id: 'HALLMARK_ADIPOGENESIS' }, q: { mode: 'continuous' } },\n\t\t\tterm2: { term: { type: 'ssGSEA', id: 'HALLMARK_ALLOGRAFT_REJECTION' }, q: { mode: 'continuous' } }\n\t\t}\n\t]\n}\nconst state2dnameth = {\n\tplots: [\n\t\t{\n\t\t\tchartType: 'sampleScatter',\n\t\t\tcolorTW: { id: 'diaggrp' },\n\t\t\tterm: {\n\t\t\t\tterm: { type: 'dnaMethylation', chr: 'chr17', start: 7673484, stop: 7681953, genomicFeatureType: 'gene' },\n\t\t\t\tq: { mode: 'continuous' }\n\t\t\t},\n\t\t\tterm2: {\n\t\t\t\tterm: { type: 'dnaMethylation', chr: 'chr17', start: 7663195, stop: 7671664, genomicFeatureType: 'gene' },\n\t\t\t\tq: { mode: 'continuous' }\n\t\t\t}\n\t\t}\n\t]\n}\nconst state2scgeneexp = {\n\tplots: [\n\t\t{\n\t\t\tchartType: 'sampleScatter',\n\t\t\tterm: getScgeneexpTw(),\n\t\t\tterm2: getScgeneexpTw('TP53')\n\t\t}\n\t]\n}\n\nconst state3DContour = {\n\tplots: [\n\t\t{\n\t\t\tchartType: 'sampleScatter',\n\t\t\tcolorTW: { id: 'diaggrp' },\n\t\t\tname: 'TermdbTest TSNE',\n\t\t\tterm0: { id: 'agedx', q: { mode: 'continuous' } },\n\t\t\tsettings: { sampleScatter: { showContour: true } }\n\t\t}\n\t]\n}\n\nconst groups = [\n\t{\n\t\tname: 'Test group 1',\n\t\titems: [\n\t\t\t{\n\t\t\t\tsample: '2646',\n\t\t\t\tx: -103.141543,\n\t\t\t\ty: 73.31223702,\n\t\t\t\tsampleId: 41,\n\t\t\t\tcategory_info: {},\n\t\t\t\thidden: {\n\t\t\t\t\tcategory: false\n\t\t\t\t},\n\t\t\t\tcategory: '\"Acute lymphoblastic leukemia\"',\n\t\t\t\tshape: 'Ref'\n\t\t\t},\n\t\t\t{\n\t\t\t\tsample: '2800',\n\t\t\t\tx: -99.20065673,\n\t\t\t\ty: 73.64971694,\n\t\t\t\tsampleId: 52,\n\t\t\t\tcategory_info: {},\n\t\t\t\thidden: {\n\t\t\t\t\tcategory: false\n\t\t\t\t},\n\t\t\t\tcategory: '\"Acute lymphoblastic leukemia\"',\n\t\t\t\tshape: 'Ref'\n\t\t\t}\n\t\t],\n\t\tindex: 1\n\t}\n]\n\nfunction getHolder() {\n\treturn d3s.select('body').append('div')\n}\n\n/**************\n test sections\n***************/\ntape('\\n', function (test) {\n\ttest.comment('-***- plots/sampleScatter -***-')\n\ttest.end()\n})\n\ntape('Render TermdbTest scatter plot and open survival and summary', function (test) {\n\ttest.timeoutAfter(8000)\n\ttest.plan(7)\n\tconst holder = getHolder()\n\trunpp({\n\t\tholder, //Fix for test failing because survival & summary sandboxs are not destroyed.\n\t\tstate,\n\t\tsampleScatter: {\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(scatter) {\n\t\tconst scatterDiv = scatter.Inner.model.charts[0].chartDiv\n\n\t\ttestPlot()\n\t\ttestLegendTitle()\n\t\tconst group = await testCreateGroup()\n\t\tconst tw = getSamplelstTW([group])\n\n\t\tawait testOpenSurvivalPlot()\n\t\tawait testOpenSummaryPlot()\n\n\t\tif (test._ok) holder.remove()\n\t\ttest.end()\n\n\t\tfunction testPlot() {\n\t\t\tconst serieG = scatterDiv.select('.sjpcb-scatter-series')\n\t\t\tconst numSymbols = serieG.selectAll('path').size()\n\t\t\ttest.equal(\n\t\t\t\tnumSymbols,\n\t\t\t\tscatter.Inner.model.charts[0].data.samples.length,\n\t\t\t\t`Should be ${scatter.Inner.model.charts[0].data.samples.length}. Rendered ${numSymbols} symbols.`\n\t\t\t)\n\t\t}\n\n\t\tfunction testLegendTitle() {\n\t\t\tconst g = scatterDiv.select('.sjpcb-scatter-legend')\n\t\t\ttest.true(g != null, 'Should have a legend')\n\t\t\tconst texts = g.selectAll('text[data-testid=\"legendTitle\"]')\n\t\t\ttest.true(\n\t\t\t\ttexts._groups[0][0].innerHTML.startsWith(scatter.Inner.config.colorTW.term.name),\n\t\t\t\t'colorTW legend title made'\n\t\t\t)\n\t\t\ttest.true(\n\t\t\t\ttexts._groups[0][1].innerHTML.startsWith(scatter.Inner.config.shapeTW.term.name),\n\t\t\t\t'shapeTW legend title made'\n\t\t\t)\n\t\t}\n\n\t\tasync function testCreateGroup() {\n\t\t\tconst samples = scatterDiv\n\t\t\t\t.select('.sjpcb-scatter-series')\n\t\t\t\t.selectAll('path')\n\t\t\t\t.nodes()\n\t\t\t\t.filter(p => p.__data__?.category === 'Acute lymphoblastic leukemia')\n\t\t\t\t.map(path => path.__data__)\n\t\t\ttest.equal(samples.length, 36, `Group should have 36 symbols.`)\n\n\t\t\tconst self = scatter.Inner\n\t\t\tconst group = {\n\t\t\t\tname: `Group 1`,\n\t\t\t\titems: samples,\n\t\t\t\tindex: 0\n\t\t\t}\n\t\t\tself.config.groups.push(group)\n\t\t\treturn group\n\t\t}\n\n\t\tasync function testOpenSurvivalPlot() {\n\t\t\tconst plots = scatter.Inner.app.getState().plots\n\t\t\tconst elem = scatter.Inner.app.Inner.dom.plotDiv.node()\n\t\t\tconst preSandboxes = [...elem.querySelectorAll('.sjpp-sandbox')]\n\t\t\tconst sandboxes = await detectLst({\n\t\t\t\telem,\n\t\t\t\tselector: '.sjpp-sandbox',\n\t\t\t\tcount: plots.length + 1,\n\t\t\t\tasync trigger() {\n\t\t\t\t\tconst survivalTerm = await scatter.Inner.app.vocabApi.getterm('efs')\n\t\t\t\t\tawait openPlot('survival', survivalTerm, tw, scatter.Inner.app)\n\t\t\t\t}\n\t\t\t})\n\t\t\tconst newSandbox = sandboxes.find(s => !preSandboxes.includes(s))\n\t\t\ttest.equal(\n\t\t\t\t[...newSandbox.querySelectorAll('.sja_errorbar')].filter(b => b.style.display != 'none').length,\n\t\t\t\t0,\n\t\t\t\t'Should render survival plot without errors\".'\n\t\t\t)\n\t\t}\n\n\t\tasync function testOpenSummaryPlot() {\n\t\t\tconst plots = scatter.Inner.app.getState().plots\n\t\t\tconst elem = scatter.Inner.app.Inner.dom.plotDiv.node()\n\t\t\tconst preSandboxes = [...elem.querySelectorAll('.sjpp-sandbox')]\n\t\t\tconst survivalTerm = await scatter.Inner.app.vocabApi.getterm('efs')\n\t\t\tconst sandboxes = await detectLst({\n\t\t\t\telem,\n\t\t\t\tselector: '.sjpp-sandbox',\n\t\t\t\tcount: plots.length + 1,\n\t\t\t\tasync trigger() {\n\t\t\t\t\tconst genderTerm = await scatter.Inner.app.vocabApi.getterm('sex')\n\t\t\t\t\tawait openSummaryPlot(genderTerm, tw, scatter.Inner.app)\n\t\t\t\t}\n\t\t\t})\n\t\t\tconst newSandbox = sandboxes.find(s => !preSandboxes.includes(s))\n\t\t\ttest.equal(\n\t\t\t\t[...newSandbox.querySelectorAll('.sja_errorbar')].filter(b => b.style.display != 'none').length,\n\t\t\t\t0,\n\t\t\t\t'Should render summary plot without errors\".'\n\t\t\t)\n\t\t}\n\t}\n})\n\ntape('Render TermdbTest scatter plot adding age as Z to render a 3D plot', function (test) {\n\ttest.timeoutAfter(8000)\n\ttest.plan(1)\n\tconst holder = getHolder()\n\trunpp({\n\t\tholder, //Fix for test failing because survival & summary sandboxs are not destroyed.\n\t\tstate: state3D,\n\t\tsampleScatter: {\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(scatter) {\n\t\tconst is3D = scatter.Inner.model.is3D\n\t\tconst scatterDiv = scatter.Inner.model.charts[0].chartDiv\n\t\ttest.true(is3D, 'Should be a 3D scatter plot')\n\t\tif (test._ok) holder.remove()\n\t\ttest.end()\n\t}\n})\n\ntape('Render 3D plot with age as Z and showContour set to true to apply contour on 3D plot', function (test) {\n\ttest.timeoutAfter(8000)\n\ttest.plan(1)\n\tconst holder = getHolder()\n\trunpp({\n\t\tholder, //Fix for test failing because survival & summary sandboxs are not destroyed.\n\t\tstate: state3DContour,\n\t\tsampleScatter: {\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(scatter) {\n\t\tconst chart = scatter.Inner.model.charts[0]\n\t\tawait sleep(1000)\n\t\ttest.true(chart.plane != null, 'Should have a plane with the contour map')\n\t\tif (test._ok) holder.remove()\n\t\ttest.end()\n\t}\n})\n\ntape('dynamic scatter of agedx & hrtavg', function (test) {\n\ttest.timeoutAfter(8000)\n\ttest.plan(2)\n\tconst holder = getHolder()\n\trunpp({\n\t\tholder,\n\t\tstate: stateDynamicScatter,\n\t\tsampleScatter: {\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(scatter) {\n\t\tscatter.on('postRender.test', null)\n\t\tconst chart = scatter.Inner.model.charts[0]\n\t\ttest.true(scatter.Inner.settings.showAxes, 'Dynamic scatter should have axes')\n\t\tscatter.Inner.settings.showContour = true\n\t\tawait scatter.Inner.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: scatter.Inner.id,\n\t\t\tconfig: { settings: { sampleScatter: scatter.Inner.settings } }\n\t\t})\n\t\tconst contourG = scatter.Inner.model.charts[0].chartDiv.select('g[stroke-linejoin=\"round\"]').node()\n\t\ttest.true(\n\t\t\tcontourG != null,\n\t\t\t'Scatter should have contour showing the density of points after selecting show contour'\n\t\t)\n\t\tif (test._ok) holder.remove()\n\t\ttest.end()\n\t}\n})\n\ntape('dynamic scatter of 2-gene expression', function (test) {\n\tconst holder = getHolder()\n\trunpp({\n\t\tholder,\n\t\tstate: state2geneexp,\n\t\tsampleScatter: { callbacks: { 'postRender.test': runTests } }\n\t})\n\tasync function runTests(scatter) {\n\t\tscatter.on('postRender.test', null)\n\t\tconst chart = scatter.Inner.model.charts[0]\n\t\ttest.true(scatter.Inner.settings.showAxes, 'Dynamic scatter should have axes')\n\t\tif (test._ok) holder.remove()\n\t\ttest.end()\n\t}\n})\n\ntape('dynamic scatter of 2-ssgsea', function (test) {\n\tconst holder = getHolder()\n\trunpp({\n\t\tholder,\n\t\tstate: state2ssgsea,\n\t\tsampleScatter: { callbacks: { 'postRender.test': runTests } }\n\t})\n\tasync function runTests(scatter) {\n\t\tscatter.on('postRender.test', null)\n\t\tconst chart = scatter.Inner.model.charts[0]\n\t\ttest.true(scatter.Inner.settings.showAxes, 'Dynamic scatter should have axes')\n\t\tif (test._ok) holder.remove()\n\t\ttest.end()\n\t}\n})\n\ntape('dynamic scatter of 2-dnameth', function (test) {\n\tconst holder = getHolder()\n\trunpp({\n\t\tholder,\n\t\tstate: state2dnameth,\n\t\tsampleScatter: { callbacks: { 'postRender.test': runTests } }\n\t})\n\tasync function runTests(scatter) {\n\t\tscatter.on('postRender.test', null)\n\t\tconst chart = scatter.Inner.model.charts[0]\n\t\ttest.true(scatter.Inner.settings.showAxes, 'Dynamic scatter should have axes')\n\t\tif (test._ok) holder.remove()\n\t\ttest.end()\n\t}\n})\n\ntape('Show tooltip for sample', function (test) {\n\ttest.timeoutAfter(8000)\n\ttest.plan(2)\n\tconst holder = getHolder()\n\trunpp({\n\t\tholder, //Fix for test failing because survival & summary sandboxs are not destroyed.\n\t\tstate,\n\t\tsampleScatter: {\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(scatter) {\n\t\tscatter.on('postRender.test', null)\n\t\tconst chart = scatter.Inner.model.charts[0]\n\t\tconst sample = groups[0].items[0]\n\t\tscatter.Inner.vm.scatterTooltip.showSampleTooltip(sample, 100, 100, chart)\n\t\tconst tooltipDiv = scatter.Inner.view.dom.tooltip.d.node()\n\t\tconst tree = scatter.Inner.vm.scatterTooltip.tree\n\t\tconst parentNode = tree.find(n => n.id == 'Acute lymphoblastic leukemia' && n.samples.length == 3)\n\t\ttest.true(parentNode != null, 'Tooltip should have 3 samples for Acute lymphoblastic leukemia')\n\t\ttest.true(tooltipDiv != null, 'Tooltip should be shown')\n\t\tscatter.Inner.view.dom.tooltip.hide()\n\t\tif (test._ok) holder.remove()\n\t\ttest.end()\n\t}\n})\n\ntape('Test scale dot', function (test) {\n\ttest.timeoutAfter(8000)\n\ttest.plan(2)\n\tconst holder = getHolder()\n\tconst state = {\n\t\tplots: [\n\t\t\t{\n\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\tscaleDotTW: { id: 'agedx', q: { mode: 'continuous' } },\n\t\t\t\tname: 'TermdbTest TSNE'\n\t\t\t}\n\t\t]\n\t}\n\trunpp({\n\t\tholder, //Fix for test failing because survival & summary sandboxs are not destroyed.\n\t\tstate,\n\t\tsampleScatter: {\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(scatter) {\n\t\tscatter.on('postRender.test', null)\n\t\tconst self = scatter.Inner\n\t\tconst chart = scatter.Inner.model.charts[0]\n\t\tconst dots = self.view.dom.mainDiv.selectAll('.sjpcb-scatter-series > path').nodes()\n\t\tconst minSize = (self.settings.minShapeSize * self.zoom) / 3\n\n\t\tconst maxSize = (self.settings.maxShapeSize * self.zoom) / 3 //original icons are scaled to 0.3\n\n\t\ttest.true(\n\t\t\tdots.find(dot => dot.getAttribute('transform').includes(`scale(${minSize})`)) != null,\n\t\t\t`Dots with the minimum size should be found`\n\t\t)\n\t\ttest.true(\n\t\t\tdots.find(dot => dot.getAttribute('transform').includes(`scale(${maxSize})`)) != null,\n\t\t\t`Dots with the maximum size should be found`\n\t\t)\n\t\tif (test._ok) holder.remove()\n\t\ttest.end()\n\t}\n})\n\ntape('Test lasso menus options', function (test) {\n\ttest.timeoutAfter(8000)\n\n\trunpp({\n\t\tstate,\n\t\tsampleScatter: {\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(scatter) {\n\t\tscatter.on('postRender.test', null)\n\n\t\tawait triggerLassoMenu(scatter)\n\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tasync function triggerLassoMenu(scatter) {\n\t\t/* Menu appears in the upper left corner instead of under groups button.\n        This is expected. No x/y coord is provided to orient the menu \n        under the groups button. */\n\t\tconst group = groups[0]\n\t\tscatter.Inner.vm.scatterLasso.showLassoMenu(new PointerEvent('click'), group.items)\n\t\tconst groupsMenu = scatter.Inner.view.dom.tip.d.selectAll('div.sja_menuoption').nodes()\n\t\tconst options = ['List 2 samples', 'Add to a group', 'Add to a group and filter', 'Open sample view']\n\t\tfor (const [i, node] of Object.entries(groupsMenu)) {\n\t\t\tconst option = node.innerText\n\t\t\ttest.equal(option, options[i], `Should display ${option} in the menu`)\n\t\t}\n\t\t//Create group and add checks\n\n\t\tscatter.Inner.vm.scatterLasso.showTable(group, 0, 0, false)\n\t\ttestSampleTable(scatter, group)\n\t\tgroupsMenu[1].click()\n\t\tawait sleep(1000)\n\t\ttest.equal(scatter.Inner.state.groups.length, 1, `Should create a group in mass state`)\n\t\tgroupsMenu[2].click()\n\t\tawait sleep(1000)\n\t\ttest.equal(scatter.Inner.state.groups.length, 2, `Should create another group in mass state`)\n\t\ttest.true(\n\t\t\tscatter.Inner.state.termfilter?.filter?.lst[1]?.lst[0]?.tvs?.term.type == 'samplelst',\n\t\t\t`Should create a samplelst filter in mass state`\n\t\t)\n\t}\n\n\tfunction testSampleTable(scatter, group) {\n\t\tconst samplesRendered = scatter.Inner.view.dom.tip.d.selectAll('.sjpp_row_wrapper > td:nth-child(3)').nodes()\n\t\tconst samples2Check = []\n\t\tfor (const item of samplesRendered) {\n\t\t\tsamples2Check.push(item.innerHTML)\n\t\t}\n\n\t\t//Check every sample in group renders in sample table\n\t\tlet foundSamples = 0\n\t\tfor (const sampleData of group.items) {\n\t\t\tif (samples2Check.some(d => d == sampleData.sample)) ++foundSamples\n\t\t\telse test.fail(`Sample = ${sampleData.sample} is not displayed in sample table`)\n\t\t}\n\t\ttest.equal(samples2Check.length, foundSamples, `Should render all samples for ${group.name}`)\n\n\t\tscatter.Inner.view.dom.tip.hide()\n\t}\n})\n\n// tape('Test continuous mode with age color', function (test) {\n// \ttest.timeoutAfter(8000)\n// \ttest.plan(4)\n// \tconst holder = getHolder()\n// \tconst state = {\n// \t\tplots: [\n// \t\t\t{\n// \t\t\t\tchartType: 'sampleScatter',\n// \t\t\t\tcolorTW: { id: 'agedx', q: { mode: 'continuous' } },\n// \t\t\t\tname: 'TermdbTest TSNE'\n// \t\t\t}\n// \t\t]\n// \t}\n// \trunpp({\n// \t\tholder, //Fix for test failing because survival & summary sandboxs are not destroyed.\n// \t\tstate,\n// \t\tsampleScatter: {\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(scatter) {\n// \t\tscatter.on('postRender.test', null)\n\n// \t\tconst self = scatter.Inner\n// \t\tconst chart = scatter.Inner.model.charts[0]\n// \t\tconst startColor = self.config.startColor[chart.id]\n// \t\tconst stopColor = self.config.stopColor[chart.id]\n// \t\ttest.true(startColor == chart.startRect.style('fill'), `The start color rect should be ${startColor}`)\n// \t\ttest.true(stopColor == chart.stopRect.style('fill'), `The stop color rect should be ${stopColor}`)\n// \t\tlet color = rgb('green').toString()\n// \t\tlet matched = await detectChildAttr({\n// \t\t\telem: scatter.Inner.view.dom.mainDiv.node(),\n// \t\t\tselector: '.sjpcb-scatter-series > path',\n// \t\t\tobserve: {\n// \t\t\t\tattributeFilter: ['fill']\n// \t\t\t},\n// \t\t\ttrigger: () => self.changeGradientColor(chart, 'startColor', chart.startRect, color),\n// \t\t\tmatcher(mutations) {\n// \t\t\t\treturn mutations.filter(m => m.target.getAttribute('fill') == color)\n// \t\t\t}\n// \t\t})\n// \t\ttest.true(matched.length > 0, `Should render at least one sample with start color ${color}`)\n// \t\tcolor = rgb('red').toString()\n// \t\tmatched = await detectChildAttr({\n// \t\t\telem: scatter.Inner.view.dom.mainDiv.node(),\n// \t\t\tselector: '.sjpcb-scatter-series > path',\n// \t\t\tobserve: {\n// \t\t\t\tattributeFilter: ['fill']\n// \t\t\t},\n// \t\t\ttrigger: () => self.changeGradientColor(chart, 'stopColor', chart.stopRect, color),\n// \t\t\tmatcher(mutations) {\n// \t\t\t\treturn mutations.filter(m => m.target.getAttribute('fill') == color)\n// \t\t\t}\n// \t\t})\n// \t\ttest.true(matched.length > 0, `Should render at least one sample with stop color ${color}`)\n// \t\tif (test._ok) holder.remove()\n// \t\ttest.end()\n// \t}\n// })\n\ntape('Invalid colorTW.id', async function (test) {\n\ttest.timeoutAfter(3000)\n\tconst message = `Should display error for colorTW.id not found within dataset`\n\tconst holder = getHolder()\n\tconst id = 'Not real data'\n\n\ttry {\n\t\trunpp({\n\t\t\tholder,\n\t\t\tstate: {\n\t\t\t\tplots: [\n\t\t\t\t\t{\n\t\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\t\tcolorTW: { id },\n\t\t\t\t\t\tname: 'TermdbTest TSNE'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t})\n\n\t\tconst errorbar = await detectGte({ elem: holder.node(), selector: '.sja_errorbar' })\n\t\ttest.equal(errorbar.length, 1, 'Should display only one error message.')\n\t\ttest.ok(\n\t\t\terrorbar[0].innerText.includes(`missing dictionary term for id=${id}`),\n\t\t\t`Should display, \"Error: no term found for ${id} [sampleScatter getPlotConfig()]\".`\n\t\t)\n\t} catch (e) {\n\t\ttest.fail(message + ': ' + e)\n\t}\n\n\tif (test._ok) holder.remove()\n\ttest.end()\n})\n\ntape('Invalid colorTW.term', async function (test) {\n\ttest.timeoutAfter(3000)\n\tconst holder = getHolder()\n\tconst id = 'Not real data'\n\ttry {\n\t\trunpp({\n\t\t\tholder,\n\t\t\tstate: {\n\t\t\t\tplots: [\n\t\t\t\t\t{\n\t\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\t\tcolorTW: { term: { id } },\n\t\t\t\t\t\tname: 'TermdbTest TSNE'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t})\n\t\tconst errorbar = await detectGte({ elem: holder.node(), selector: '.sja_errorbar > div:nth-child(2)' })\n\t\tconst error = 'Error: Error: Type is not defined [sampleScatter getPlotConfig()]'\n\t\ttest.true(errorbar[0].innerText.startsWith(error), `Should display, \"${error}...\".`)\n\t} catch (e) {\n\t\ttest.fail(e)\n\t}\n\n\tif (test._ok) holder.remove()\n\ttest.end()\n})\n\ntape('Invalid plot name', async function (test) {\n\ttest.timeoutAfter(3000)\n\tconst message = `Should display error for invalid plot name`\n\tconst holder = getHolder()\n\n\ttry {\n\t\trunpp({\n\t\t\tholder,\n\t\t\tstate: {\n\t\t\t\tplots: [\n\t\t\t\t\t{\n\t\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\t\tcolorTW: {\n\t\t\t\t\t\t\tid: 'diaggrp'\n\t\t\t\t\t\t},\n\t\t\t\t\t\tname: 'Not real data'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t})\n\t\tconst errorbar = await detectGte({ elem: holder.node(), selector: '.sja_errorbar' })\n\t\ttest.equal(errorbar.length, 1, 'Should display only one error message.')\n\t\ttest.ok(\n\t\t\terrorbar[0].innerText.includes(`plot not found with plotName`),\n\t\t\t'Should display, \"Error: plot not found with plotName: Not real data\".'\n\t\t)\n\t} catch (e) {\n\t\ttest.fail(message + ': ' + e)\n\t}\n\n\tif (test._ok) holder.remove()\n\ttest.end()\n})\n\ntape('Test legend', function (test) {\n\ttest.timeoutAfter(6000) //Fix for breaking on local CI but maynot be necessary for nightly build\n\n\trunpp({\n\t\tstate: structuredClone(state),\n\t\tsampleScatter: {\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(scatter) {\n\t\tscatter.on('postRender.test', null)\n\t\tconst samples = scatter.Inner.model.charts[0].data.samples\n\t\tconst scatterDiv = scatter.Inner.model.charts[0].chartDiv\n\n\t\tawait testHideCategory(scatter, samples)\n\t\tawait testChangeColor(scatter, samples)\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tasync function testHideCategory(scatter, samples) {\n\t\tconst key = 'Acute lymphoblastic leukemia'\n\t\tconst expectedNum = samples.filter(s => s.category === key).length\n\n\t\tconst matched = await detectChildStyle({\n\t\t\telem: scatter.Inner.view.dom.mainDiv.node(),\n\t\t\tselector: '.sjpcb-scatter-series > path',\n\t\t\tstyle: {\n\t\t\t\tfillOpacity: '0'\n\t\t\t},\n\t\t\tcount: expectedNum,\n\t\t\ttrigger: () => {\n\t\t\t\tconst chart = scatter.Inner.model.charts[0]\n\t\t\t\tscatter.Inner.vm.legendvm.legendInteractivity.hideCategory(scatter.Inner.config.colorTW, key, true)\n\t\t\t\tscatter.Inner.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: scatter.Inner.id,\n\t\t\t\t\tconfig: { colorTW: scatter.Inner.config.colorTW }\n\t\t\t\t})\n\t\t\t}\n\t\t\t/* example of a custom matcher, instead of opts.style\n            matcher(mutations, observer) {\n                const hidden = mutations.filter(m => m.target.__data__.category == key && m.target.style.fillOpacity == '0')\n                if (hidden.length >= expectedNum) return hidden.map(d => d.target)\n            }*/\n\t\t})\n\t\ttest.equal(\n\t\t\tmatched.filter(t => t.__data__.category == key).length,\n\t\t\texpectedNum,\n\t\t\t`Should remove all samples with category = ${key}`\n\t\t)\n\t}\n\n\tasync function testChangeColor(scatter, samples) {\n\t\tconst key = 'Wilms tumor'\n\t\tconst color = 'blue'\n\t\tconst expectedColor = d3color.rgb(color).toString()\n\t\tconst expectedNum = samples.filter(s => s.category === key).length\n\t\tconst targets = await detectChildAttr({\n\t\t\telem: scatter.Inner.view.dom.mainDiv.node(),\n\t\t\tselector: '.sjpcb-scatter-series > path',\n\t\t\tobserve: {\n\t\t\t\tattributeFilter: ['fill']\n\t\t\t},\n\t\t\t/* example of opts.attr, instead of opts.matcher()\n            attr: {\n                // key is name of attribute, value can be a string, number, or function\n                fill: value => {\n                    return d3color.rgb(value).toString() === expectedColor\n                }\n            },*/\n\t\t\tcount: expectedNum,\n\t\t\ttrigger: async () => {\n\t\t\t\tscatter.Inner.vm.legendvm.legendInteractivity.changeColor(key, color)\n\t\t\t},\n\t\t\t// example of a custom matcher, instead of opts.attr{}\n\t\t\tmatcher(mutations) {\n\t\t\t\tconst targets = mutations.filter(m => d3color.rgb(m.target.getAttribute('fill')) == expectedColor)\n\t\t\t\tif (targets.length >= expectedNum) return targets.map(d => d.target)\n\t\t\t}\n\t\t})\n\n\t\ttest.equal(targets.length, 2, `Should change the color of the category = ${key} to blue`)\n\t}\n})\n\ntape('Render color groups', 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: 'sampleScatter',\n\t\t\t\t\tcolorTW: {\n\t\t\t\t\t\tid: 'genetic_race',\n\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\tcustomset: {\n\t\t\t\t\t\t\t\tgroups: [\n\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\tname: 'non-Asian Ancestry',\n\t\t\t\t\t\t\t\t\t\ttype: 'values',\n\t\t\t\t\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t\t\t\t\t{ key: 'European Ancestry', label: 'European Ancestry' },\n\t\t\t\t\t\t\t\t\t\t\t{ key: 'African Ancestry', label: 'African Ancestry' },\n\t\t\t\t\t\t\t\t\t\t\t{ key: 'Multi-Ancestry-Admixed', label: 'Multi-Ancestry-Admixed' }\n\t\t\t\t\t\t\t\t\t\t]\n\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\tname: 'Asian Ancestry',\n\t\t\t\t\t\t\t\t\t\ttype: 'values',\n\t\t\t\t\t\t\t\t\t\tvalues: [{ key: 'Asian Ancestry', label: 'Asian Ancestry' }]\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\tname: 'TermdbTest TSNE'\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsampleScatter: {\n\t\t\tcallbacks: { 'postRender.test': runTests }\n\t\t}\n\t})\n\n\tasync function runTests(scatter) {\n\t\tscatter.on('postRender.test', null)\n\n\t\tawait testColorLegend(scatter)\n\t\tawait changeColorGroups(scatter)\n\t\tawait testColorLegend(scatter)\n\t\t// await removeColorGroups(scatter)\n\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tasync function testColorLegend(scatter) {\n\t\tconst legendLabels = await detectGte({\n\t\t\telem: scatter.Inner.model.charts[0].chartDiv.node(),\n\t\t\tselector: 'text[name=\"sjpp-scatter-legend-label\"]'\n\t\t})\n\n\t\tconst groups = []\n\t\tfor (const group of legendLabels) {\n\t\t\tconst label = group.innerHTML.split(',')\n\t\t\tgroups.push({\n\t\t\t\tlabel: label[0],\n\t\t\t\tsamples: label[1].match(/[\\d\\.]+/g)\n\t\t\t})\n\t\t}\n\t\ttest.equal(\n\t\t\tscatter.Inner.model.charts[0].colorLegend.size,\n\t\t\tgroups.length + 1,\n\t\t\t`Legend categories (# = ${groups.length + 1}) should equal size of colorLegend (# = ${\n\t\t\t\tscatter.Inner.model.charts[0].colorLegend.size\n\t\t\t}) `\n\t\t)\n\t\tcompareData2DOMLegend(scatter, groups)\n\t}\n\n\tfunction compareData2DOMLegend(scatter, groups) {\n\t\tfor (const group of groups) {\n\t\t\tconst mapLeg = scatter.Inner.model.charts[0].colorLegend.get(group.label)\n\t\t\ttest.ok(mapLeg, `Should display group custom label = ${group.label} in legend`)\n\t\t\ttest.equal(\n\t\t\t\t`${mapLeg.sampleCount}`,\n\t\t\t\tgroup.samples[0],\n\t\t\t\t`Should show matching n = ${group.samples[0]} for ${group.label}`\n\t\t\t)\n\t\t}\n\t}\n\n\tasync function changeColorGroups(scatter) {\n\t\tscatter.Inner.config.colorTW.q.customset = {\n\t\t\tgroups: [\n\t\t\t\t{\n\t\t\t\t\tname: 'European Ancestryy',\n\t\t\t\t\ttype: 'values',\n\t\t\t\t\tvalues: [{ key: 'European Ancestry', label: 'European Ancestry' }]\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tname: 'non-European Ancestry',\n\t\t\t\t\ttype: 'values',\n\t\t\t\t\tvalues: [\n\t\t\t\t\t\t{ key: 'Asian Ancestry', label: 'Asian Ancestry' },\n\t\t\t\t\t\t{ key: 'African Ancestry', label: 'African Ancestry' },\n\t\t\t\t\t\t{ key: 'Multi-Ancestry-Admixed', label: 'Multi-Ancestry-Admixed' }\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\n\t\tawait scatter.Inner.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: scatter.Inner.id,\n\t\t\tconfig: scatter.Inner.config\n\t\t})\n\t}\n\n\t// async function removeColorGroups(scatter) {\n\t// \tscatter.Inner.config.colorTW.q.groupsetting = { inuse: false }\n\t// \tawait scatter.Inner.app.dispatch({\n\t// \t\ttype: 'plot_edit',\n\t// \t\tid: scatter.Inner.id,\n\t// \t\tconfig: scatter.Inner.config\n\t// \t})\n\t// }\n})\n\ntape('Change symbol and reference size from menu', function (test) {\n\ttest.timeoutAfter(10000)\n\n\trunpp({\n\t\tstate: structuredClone(open_state),\n\t\tsampleScatter: {\n\t\t\tcallbacks: { 'postRender.test': runTests }\n\t\t}\n\t})\n\n\tconst testSymSize = 300\n\tconst testRefSize = 1\n\n\tasync function runTests(scatter) {\n\t\thelpers\n\t\t\t.rideInit({ arg: scatter, bus: scatter, eventType: 'postRender.test' })\n\t\t\t.use(changeSymbolInput)\n\t\t\t.to(testSymbolSize, { wait: 100 })\n\t\t\t.use(changeRefInput, { wait: 100 })\n\t\t\t.to(testRefDotSize, { wait: 300 })\n\t\t\t.done(test)\n\t}\n\tfunction changeSymbolInput(scatter) {\n\t\tconst sizeInput = scatter.Inner.view.dom.controlsHolder\n\t\t\t.selectAll('input')\n\t\t\t.nodes()\n\t\t\t.find(e => e.value == scatter.Inner.settings.size)\n\t\tsizeInput.value = testSymSize\n\t\tsizeInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter' }))\n\t}\n\tfunction testSymbolSize(scatter) {\n\t\t//separate function because wait needed before test to run\n\t\ttest.equal(scatter.Inner.settings.size, testSymSize, `Should change symbol dot size to test value = ${testSymSize}`)\n\t}\n\tfunction changeRefInput(scatter) {\n\t\tconst refInput = scatter.Inner.view.dom.controlsHolder\n\t\t\t.selectAll('input')\n\t\t\t.nodes()\n\t\t\t.find(e => e.value == scatter.Inner.settings.refSize)\n\t\trefInput.value = testRefSize\n\t\trefInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter' }))\n\t}\n\tfunction testRefDotSize(scatter) {\n\t\ttest.equal(\n\t\t\tscatter.Inner.settings.refSize,\n\t\t\ttestRefSize,\n\t\t\t`Should change reference dot size to test value = ${testRefSize}`\n\t\t)\n\t}\n})\n\ntape('Change chart width and height from menu', function (test) {\n\ttest.timeoutAfter(1000)\n\n\trunpp({\n\t\tstate: structuredClone(open_state),\n\t\tsampleScatter: {\n\t\t\tcallbacks: { 'postRender.test': runTests }\n\t\t}\n\t})\n\n\tconst testWidth = 550\n\tconst testHeight = 550\n\n\tasync function runTests(scatter) {\n\t\tscatter.on('postRender.test', null)\n\n\t\tawait testChartSizeChange(scatter)\n\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tasync function testChartSizeChange(scatter) {\n\t\t//Change chart width\n\t\tconst widthInput = scatter.Inner.view.dom.controlsHolder\n\t\t\t.selectAll('input')\n\t\t\t.nodes()\n\t\t\t.find(e => e.value == scatter.Inner.settings.svgw)\n\t\twidthInput.value = testWidth\n\n\t\t//Change chart height\n\t\tconst heightInput = scatter.Inner.view.dom.controlsHolder\n\t\t\t.selectAll('input')\n\t\t\t.nodes()\n\t\t\t.find(e => e.value == scatter.Inner.settings.svgh)\n\t\theightInput.value = testHeight\n\t\t//Detect change in chart height and width\n\t\tawait detectAttr({\n\t\t\ttarget: scatter.Inner.view.dom.mainDiv.select('svg').node(),\n\t\t\tobserve: {\n\t\t\t\tattributeFilter: ['height', 'width']\n\t\t\t},\n\t\t\t// count: 1,\n\t\t\ttrigger() {\n\t\t\t\twidthInput.dispatchEvent(new Event('change'))\n\t\t\t\theightInput.dispatchEvent(new Event('change'))\n\t\t\t}\n\t\t\t// matcher(mutations){\n\t\t\t// \tlet foundH, foundW = 0\n\t\t\t// \tfor (const mut of mutations) {\n\t\t\t// \t\tif (mut.type == 'width') ++foundW\n\t\t\t// \t\tif (mut.type == 'height') ++foundH\n\t\t\t// \t}\n\t\t\t// }\n\t\t})\n\n\t\ttest.equal(\n\t\t\tscatter.Inner.settings.svgw,\n\t\t\ttestWidth,\n\t\t\t`Chart width = ${scatter.Inner.settings.svgw} should be equal to test width = ${testWidth}`\n\t\t)\n\t\ttest.equal(\n\t\t\tscatter.Inner.settings.svgh,\n\t\t\ttestHeight,\n\t\t\t`Chart height = ${scatter.Inner.settings.svgh} should be equal to test height = ${testHeight}`\n\t\t)\n\t}\n})\n\ntape('Check/uncheck Show axes from menu', function (test) {\n\ttest.timeoutAfter(4000)\n\n\trunpp({\n\t\tstate: structuredClone(open_state),\n\t\tsampleScatter: {\n\t\t\tcallbacks: { 'postRender.test': runTests }\n\t\t}\n\t})\n\n\tasync function runTests(scatter) {\n\t\tscatter.on('postRender.test', null)\n\n\t\tawait showAxes(scatter, true)\n\t\tawait showAxes(scatter, false)\n\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tasync function showAxes(scatter, isvisible) {\n\t\tconst opacity = isvisible ? 1 : 0\n\n\t\tconst axesDiv = await detectStyle({\n\t\t\ttarget: scatter.Inner.view.dom.mainDiv.node().querySelector('.sjpcb-scatter-axis'),\n\t\t\tstyle: {\n\t\t\t\topacity: `${opacity}`\n\t\t\t},\n\t\t\ttrigger() {\n\t\t\t\tconst axesCheckbox = scatter.Inner.view.dom.controlsHolder.select('input[data-testid=\"showAxes\"]')\n\t\t\t\taxesCheckbox.property('checked', isvisible)\n\t\t\t\taxesCheckbox.node().dispatchEvent(new Event('change'))\n\t\t\t}\n\t\t})\n\t\tconst axesStyle = getComputedStyle(axesDiv[0])\n\t\ttest.equal(axesStyle.opacity, `${opacity}`, `Should ${isvisible ? 'show' : 'hide'} axes`)\n\t}\n})\n\ntape('Click zoom in, zoom out, and reset buttons', function (test) {\n\ttest.timeoutAfter(10000)\n\n\trunpp({\n\t\tstate: structuredClone(state),\n\t\tsampleScatter: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tasync function runTests(scatter) {\n\t\tscatter.on('postRender.test', null)\n\n\t\tawait testZoomIn(scatter)\n\t\tawait testReset(scatter)\n\t\tawait testZoomOut(scatter)\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n\n\tasync function testZoomIn(scatter) {\n\t\tconst zoomin_bt = scatter.Inner.view.dom.toolsDiv.node().querySelector('div[name=\"sjpp-zoom-in-btn\"]')\n\t\tconst m = await detectTransform(scatter, zoomin_bt, 1.2)\n\t\ttest.ok(m != null, `Plot should zoom in`)\n\t}\n\n\tasync function testReset(scatter) {\n\t\tconst reset_bt = scatter.Inner.view.dom.toolsDiv.node().querySelector('div[name=\"sjpp-reset-btn\"]')\n\t\tconst m = await detectTransform(scatter, reset_bt, 1)\n\t\ttest.ok(m != null, `Plot should reset`)\n\t}\n\n\tasync function testZoomOut(scatter) {\n\t\tconst zoomout_bt = scatter.Inner.view.dom.toolsDiv.node().querySelector('div[name=\"sjpp-zoom-out-btn\"]')\n\t\tconst m = await detectTransform(scatter, zoomout_bt, 0.8)\n\t\ttest.ok(m != null, `Plot should zoom out`)\n\t}\n\n\tasync function detectTransform(scatter, btn, scale) {\n\t\tconst target = await detectAttr({\n\t\t\ttarget: scatter.Inner.view.dom.mainDiv.node().querySelector('.sjpcb-scatter-series'),\n\t\t\tobserve: {\n\t\t\t\tsubtree: true,\n\t\t\t\tcharacterData: true,\n\t\t\t\tattributeFilter: ['transform']\n\t\t\t},\n\t\t\tcount: 1,\n\t\t\ttrigger() {\n\t\t\t\tbtn.click()\n\t\t\t},\n\t\t\tmatcher(mutations) {\n\t\t\t\tfor (const m of mutations) {\n\t\t\t\t\tif (m.attributeName == 'transform' && m.target.attributes[1].value.includes(`scale(${scale})`)) return m\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\t\treturn target\n\t}\n\n\t//Add tests for changes in axes\n})\n\ntape('colorTW=geneVariant with no groupsetting', function (test) {\n\ttest.timeoutAfter(6000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tname: 'TermdbTest TSNE',\n\t\t\t\t\tcolorTW: { term: { gene: 'TP53', name: 'TP53', type: 'geneVariant' } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsampleScatter: { callbacks: { 'postRender.test': runTests } }\n\t})\n\tasync function runTests(scatter) {\n\t\tconst dots = scatter.Inner.view.dom.mainDiv.selectAll('.sjpcb-scatter-series > path').nodes()\n\t\ttest.true(\n\t\t\tdots.find(dot => dot.getAttribute('fill') == mclass['M'].color),\n\t\t\t'At least a sample with MISSENSE color was expected'\n\t\t)\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('colorTW=geneVariant with groupsetting', function (test) {\n\ttest.timeoutAfter(6000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tname: 'TermdbTest TSNE',\n\t\t\t\t\tcolorTW: getGeneVariantTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsampleScatter: { callbacks: { 'postRender.test': runTests } }\n\t})\n\tasync function runTests(scatter) {\n\t\tconst dots = scatter.Inner.view.dom.mainDiv.selectAll('.sjpcb-scatter-series > path').nodes()\n\t\tconst lab = 'TP53 SNV/indel Mutated (somatic)'\n\t\ttest.true(\n\t\t\tdots.find(d => d.__data__.category == lab),\n\t\t\t`A dot with category=${lab}`\n\t\t)\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('colorTW=geneVariant with gene list', function (test) {\n\ttest.timeoutAfter(6000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tname: 'TermdbTest TSNE',\n\t\t\t\t\tcolorTW: getGenesetMutTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsampleScatter: { callbacks: { 'postRender.test': runTests } }\n\t})\n\tasync function runTests(scatter) {\n\t\tconst dots = scatter.Inner.view.dom.mainDiv.selectAll('.sjpcb-scatter-series > path').nodes()\n\t\tconst lab = 'TP53, KRAS, AKT1, BCR SNV/indel Mutated (somatic)'\n\t\ttest.true(\n\t\t\tdots.find(d => d.__data__.category == lab),\n\t\t\t`A dot with category=${lab}`\n\t\t)\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('colorTW=ssgsea', function (test) {\n\ttest.timeoutAfter(6000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tname: 'TermdbTest TSNE',\n\t\t\t\t\tcolorTW: getSsgseaTw()\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsampleScatter: { callbacks: { 'postRender.test': runTests } }\n\t})\n\tasync function runTests(scatter) {\n\t\tconst dots = scatter.Inner.view.dom.mainDiv.selectAll('.sjpcb-scatter-series > path').nodes()\n\t\ttest.true(\n\t\t\tdots.find(d => Number.isFinite(d.__data__.category)),\n\t\t\t`A dot with category=number`\n\t\t)\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('singlecell map', function (test) {\n\ttest.timeoutAfter(6000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'sampleScatter',\n\t\t\t\t\tcolorTW: getScctTw(),\n\t\t\t\t\tsingleCellPlot: { name: 'UMAP', sample: { sID: '1_patient' } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsampleScatter: { callbacks: { 'postRender.test': runTests } }\n\t})\n\tasync function runTests(scatter) {\n\t\tconst dots = scatter.Inner.view.dom.mainDiv.selectAll('.sjpcb-scatter-series > path').nodes()\n\t\ttest.true(dots.length, 'some dots are loaded from singlecell map')\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('singlecell geneexp', function (test) {\n\trunpp({\n\t\tstate: state2scgeneexp,\n\t\tsampleScatter: { callbacks: { 'postRender.test': runTests } }\n\t})\n\tasync function runTests(scatter) {\n\t\tconst dots = scatter.Inner.view.dom.mainDiv.selectAll('.sjpcb-scatter-series > path').nodes()\n\t\ttest.true(dots.length, 'some dots are loaded from singlecell map')\n\t\tif (test._ok) scatter.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('Disco plot and lollipop', test => {\n\ttest.timeoutAfter(2000)\n\tconst holder = getHolder()\n\n\trunpp({\n\t\tholder,\n\t\tstate: state2ssgsea,\n\t\tsampleScatter: { callbacks: { 'postRender.test': runTests } }\n\t})\n\n\tasync function runTests(scatter) {\n\t\tscatter.on('postRender.test', null)\n\t\tconst sampleWithMutDataFile = scatter.Inner.dom.mainDiv\n\t\t\t.select('.sjpcb-scatter-series')\n\t\t\t.selectAll('path')\n\t\t\t.filter(d => d.sample === '3416')\n\t\t\t.node()\n\t\tconst box = sampleWithMutDataFile.getBoundingClientRect()\n\t\tsampleWithMutDataFile.dispatchEvent(\n\t\t\tnew MouseEvent('click', {\n\t\t\t\tbubbles: true,\n\t\t\t\tclientX: box.x + box.width / 2,\n\t\t\t\tclientY: box.y + box.height / 2\n\t\t\t})\n\t\t)\n\t\tconst chordTexts = await detectGte({\n\t\t\telem: holder.node(),\n\t\t\tselector: '.chord-text',\n\t\t\tcount: 1,\n\t\t\ttrigger: () => {\n\t\t\t\tscatter.Inner.dom.tooltip.d\n\t\t\t\t\t.selectAll('button')\n\t\t\t\t\t.filter(function () {\n\t\t\t\t\t\treturn this.innerHTML == 'Disco'\n\t\t\t\t\t})\n\t\t\t\t\t.node()\n\t\t\t\t\t.click()\n\t\t\t}\n\t\t})\n\t\tconst label = [...chordTexts].find(c => c.__data__?.text === 'TP53')\n\n\t\tif (!label) {\n\t\t\ttest.failt('must have a TP53 gene label')\n\t\t} else {\n\t\t\tconst trackLabelsG = await detectGte({\n\t\t\t\telem: holder.node(),\n\t\t\t\tselector: '[data-testid=\"sja_sample_menu_opener\"]',\n\t\t\t\tcount: 2,\n\t\t\t\ttrigger: () => {\n\t\t\t\t\tlabel.dispatchEvent(new MouseEvent('click'))\n\t\t\t\t}\n\t\t\t})\n\n\t\t\tawait sleep(500)\n\t\t\tconst trackLabels = [...trackLabelsG[0].querySelectorAll('text')]\n\t\t\ttest.equal(\n\t\t\t\ttrackLabels.filter(t => t.innerHTML.includes('unknown data source')).length,\n\t\t\t\t0,\n\t\t\t\t'must not have an error after clicking a Disco plot gene label to launch a genome browser track'\n\t\t\t)\n\t\t\tif (test._ok) holder.remove()\n\t\t\ttest.end()\n\t\t}\n\t}\n})\n"],
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+  "names": ["tape", "group", "state", "targets", "groups"]
+}

package/dist/selectGenomeWithTklst-3RLZFW62.js

@@ -0,0 +1,132 @@
+import {
+  addGeneSearchbox,
+  first_genetrack_tolist
+} from "./chunk-YWUVCXFS.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-3QBZ2Y77.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-6ZCHECOT.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import {
+  contigNameNoChr2
+} from "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+
+// src/selectGenomeWithTklst.js
+var tip = new Menu({ padding: "" });
+var variantFlankingSize = 60;
+async function init(arg, holder, genomes) {
+  holder.style("margin", "40px 20px 20px 20px");
+  const formdiv = holder.append("div");
+  formdiv.append("p").text("To launch view, press ENTER at gene search.").style("opacity", 0.3);
+  const blockholder = holder.append("div");
+  const genomeselect = addGenomeSelect(formdiv, genomes).on("change", makeGeneSearch);
+  let coordInput, genome;
+  const geneInputSpan = formdiv.append("span").style("margin-left", "10px");
+  const submitBtn = formdiv.append("button").style("display", "none").style("margin-top", "20px").style("padding", "10px 15px").style("border-radius", "30px").text("Launch ProteinPaint").on("click", submit);
+  makeGeneSearch();
+  function makeGeneSearch() {
+    geneInputSpan.selectAll("*").remove();
+    const s = genomeselect.node();
+    genome = genomes[s.options[s.selectedIndex].innerHTML];
+    const opt = {
+      genome,
+      tip,
+      row: geneInputSpan,
+      allowVariant: true,
+      /* only show submit button if valid coord is found
+      this is deal with a defect with genesearch.js
+      that pasting coordinate in <input> without hitting enter
+      will not trigger coord parsing
+      */
+      callback: () => submitBtn.style("display", "block")
+    };
+    coordInput = addGeneSearchbox(opt);
+  }
+  async function submit() {
+    try {
+      formdiv.remove();
+      const par = {
+        nobox: 1,
+        genome,
+        holder: blockholder,
+        tklst: arg.selectGenomeWithTklst
+      };
+      const ci = coordInput;
+      if (ci.chr) {
+        const [nocount, hascount] = contigNameNoChr2(genome, [ci.chr]);
+        if (nocount + hascount == 0) throw "Invalid chromosome name: " + ci.chr;
+        const chr = nocount ? "chr" + ci.chr : ci.chr;
+        if (Number.isInteger(ci.pos)) {
+          if (!ci.ref) throw "Reference allele missing from variant string";
+          if (!ci.alt) throw "Alternative allele missing from variant string";
+          par.chr = chr;
+          par.start = ci.pos - variantFlankingSize;
+          par.stop = ci.pos + variantFlankingSize;
+          for (const tk of par.tklst) {
+            if (tk.type == "bam") {
+              tk.variants = [
+                {
+                  chr,
+                  pos: ci.pos - 1,
+                  // convert 1-based to 0-based
+                  ref: ci.ref,
+                  alt: ci.alt
+                }
+              ];
+            }
+          }
+        } else {
+          if (!Number.isInteger(ci.start) || !Number.isInteger(ci.stop)) throw "non-integer start/stop";
+          par.chr = chr;
+          par.start = ci.start;
+          par.stop = ci.stop;
+        }
+      } else {
+        const d = genome.defaultcoord;
+        par.chr = d.chr;
+        par.start = d.start;
+        par.stop = d.stop;
+      }
+      first_genetrack_tolist(genome, par.tklst);
+      const _ = await import("./block-IGBB4BJH.js");
+      new _.Block(par);
+    } catch (e) {
+      window.alert(e.message || e);
+    }
+  }
+}
+function addGenomeSelect(div, genomes) {
+  const select = div.append("select");
+  for (const gn in genomes) {
+    select.append("option").text(gn);
+  }
+  return select;
+}
+export {
+  init
+};
+//# sourceMappingURL=selectGenomeWithTklst-3RLZFW62.js.map

package/dist/singleCellCellType-3LQJXS7H.js

@@ -0,0 +1,36 @@
+import {
+  SearchHandler
+} from "./chunk-PZ3KIUWJ.js";
+import "./chunk-YWUVCXFS.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-3QBZ2Y77.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-6ZCHECOT.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  SearchHandler
+};
+//# sourceMappingURL=singleCellCellType-3LQJXS7H.js.map

package/dist/singleCellCellType.unit.spec-UJM72SP4.js

@@ -0,0 +1,158 @@
+import {
+  SearchHandler
+} from "./chunk-PZ3KIUWJ.js";
+import {
+  require_tape
+} from "./chunk-QWOE5YTB.js";
+import "./chunk-YWUVCXFS.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-3QBZ2Y77.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-6ZCHECOT.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import {
+  SINGLECELL_CELLTYPE
+} from "./chunk-EGWVYY7K.js";
+import {
+  TermTypeGroups
+} from "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// termdb/handlers/test/singleCellCellType.unit.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+function getHolder() {
+  return select_default("body").append("div");
+}
+function getUsecase(plotName = "Plot A") {
+  return {
+    target: "sampleScatter",
+    detail: "term",
+    specialCase: {
+      config: { name: plotName }
+    }
+  };
+}
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- termdb/handlers/singleCellCellType -***-");
+  test.end();
+});
+(0, import_tape.default)("validateOpts() should require callback, termType2terms, and specialCase.config.name", (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  test.throws(
+    () => handler.validateOpts({
+      holder,
+      app: { vocabApi: { termdbConfig: { termType2terms: {} } } },
+      usecase: getUsecase("Plot A")
+    }),
+    /callback is required/,
+    "Should throw when callback is missing"
+  );
+  test.throws(
+    () => handler.validateOpts({
+      holder,
+      callback: () => {
+      },
+      app: { vocabApi: { termdbConfig: {} } },
+      usecase: getUsecase("Plot A")
+    }),
+    /termType2terms is required in termdbConfig for singleCellCellType handler/,
+    "Should throw when termType2terms is missing"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("init() should render only terms matching usecase plot and call callback on click", async (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  let selectedTerm;
+  const scctTerms = [
+    { id: "t1", name: "Myeloid", type: SINGLECELL_CELLTYPE, plot: "Plot A" },
+    { id: "t2", name: "Lymphoid", type: SINGLECELL_CELLTYPE, plot: "Plot A" },
+    { id: "t3", name: "Nonmatching", type: SINGLECELL_CELLTYPE, plot: "Plot B" }
+  ];
+  await handler.init({
+    holder,
+    callback: (t) => {
+      selectedTerm = t;
+    },
+    app: {
+      vocabApi: {
+        termdbConfig: {
+          termType2terms: {
+            [TermTypeGroups.SINGLECELL_CELLTYPE]: scctTerms
+          }
+        }
+      }
+    },
+    usecase: getUsecase("Plot A")
+  });
+  const labels = holder.selectAll(".termlabel");
+  test.equal(labels.size(), 2, "Should render only two matching terms for Plot A");
+  test.deepEqual(
+    labels.nodes().map((n) => n.textContent),
+    ["Myeloid", "Lymphoid"],
+    "Should render labels in the filtered order"
+  );
+  const firstLabel = labels.nodes()[0];
+  firstLabel.click();
+  test.equal(selectedTerm?.id, "t1", "Should pass clicked term object to callback");
+  test.equal(selectedTerm?.type, SINGLECELL_CELLTYPE, "Callback term type should be singleCellCellType");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("init() should render sayerror when termType2terms key is missing for singleCellCellType", async (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  await handler.init({
+    holder,
+    callback: () => {
+    },
+    app: {
+      vocabApi: {
+        termdbConfig: {
+          termType2terms: {
+            [TermTypeGroups.DICTIONARY_VARIABLES]: []
+          }
+        }
+      }
+    },
+    usecase: getUsecase("Plot A")
+  });
+  const errorDiv = holder.select(".sja_errorbar").node();
+  test.ok(errorDiv, "Should render an error message when singleCellCellType terms are missing");
+  test.ok(
+    holder.text().includes(
+      `termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`
+    ),
+    "Should show expected configuration error text"
+  );
+  test.equal(holder.selectAll(".termlabel").size(), 0, "Should not render term labels when config is missing");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+//# sourceMappingURL=singleCellCellType.unit.spec-UJM72SP4.js.map

package/dist/singleCellGeneExpression-JOWJWPIQ.js

@@ -0,0 +1,36 @@
+import {
+  SearchHandler
+} from "./chunk-MVCGSYS2.js";
+import "./chunk-YWUVCXFS.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-3QBZ2Y77.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-G6O3URDN.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-KWM6B3NL.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-6ZCHECOT.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-2K5DSRBJ.js";
+import "./chunk-X4NI4JLQ.js";
+import "./chunk-L4QG7XZE.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-UWYCEYML.js";
+import "./chunk-7UHUOC6F.js";
+import "./chunk-ZYY54HBU.js";
+import "./chunk-EGWVYY7K.js";
+import "./chunk-AMYSEKPF.js";
+import "./chunk-TV74I3Y5.js";
+import "./chunk-KSGA62R2.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-TOU7EVFQ.js";
+import "./chunk-OAWQ6LOO.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  SearchHandler
+};
+//# sourceMappingURL=singleCellGeneExpression-JOWJWPIQ.js.map