@sjcrh/proteinpaint-client 2.196.0 → 2.197.0

package/dist/cuminc.integration.spec-MSAWDLD7.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/test/cuminc.integration.spec.js"],
+  "sourcesContent": ["import tape from 'tape'\nimport * as helpers from '../../test/front.helpers.js'\nimport { termjson } from '../../test/testdata/termjson'\nimport { select, selectAll } from 'd3-selection'\nimport { detectOne, detectGte } from '../../test/test.helpers.js'\n\n/*\nTests:\n\tbasic cuminc\n\tterm1=Cardiovascular System, filter=ALL\n\tterm1=Cardiovascular System, term2=agedx\n\tterm1=Cardiovascular System, term0=sex\n\tterm1 = Cardiovascular System, term2 = agedx, numeric regular bins\n\tterm1 = Cardiovascular System, term0 = agedx, numeric regular bins ** skipped, see note in runTests()\n\tterm1 = Cardiovascular System, term2 = agedx, numeric custom bins\n\tterm1 = Cardiovascular System, term0 = agedx, numeric custom bins\n\thidden uncomputable\n\tskipped series\n\tterm1 = Cardiovascular System, term2 = samplelst\n\nTODOs: \n\tTest tipline functionality and rendering\n\tTest overlay and divide by rendering\n */\n\n/*************************\n reusable helper functions\n**************************/\n\nconst runpp = helpers.getRunPp('mass', {\n\tstate: {\n\t\tnav: {\n\t\t\theader_mode: 'hide_search',\n\t\t\tactiveTab: 1\n\t\t},\n\t\tdslabel: 'TermdbTest',\n\t\tgenome: 'hg38-test'\n\t},\n\tdebug: 1\n})\n\n/**************\n test sections\n ***************/\n\ntape('\\n', function (test) {\n\ttest.comment('-***- plots/cuminc -***-')\n\ttest.end()\n})\n\ntape('term1=Cardiac dysrhythmia', function (test) {\n\ttest.timeoutAfter(10000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\tterm: { id: 'Cardiac dysrhythmia' },\n\t\t\t\t\tsettings: { cuminc: { minSampleSize: 1, minAtRisk: 0 } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tcuminc: {\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(cuminc) {\n\t\tconst cumincDiv = cuminc.Inner.dom.chartsDiv\n\n\t\t//Test all dom elements present\n\t\ttest.equal(cumincDiv && cumincDiv.selectAll('.sjpcb-cuminc-series').size(), 1, 'should render 1 cuminc series g')\n\t\ttest.equal(\n\t\t\tcumincDiv && cumincDiv.selectAll('.sjpcb-cuminc-series path').size(),\n\t\t\t2,\n\t\t\t'should render 2 cuminc series paths for estimate line and 95% CI area'\n\t\t)\n\t\ttest.equal(cumincDiv.selectAll('.sjpcb-cuminc-title').size(), 1, `Should render title above chart`)\n\t\ttest.equal(cumincDiv.selectAll('.sjpp-cuminc-atrisk').size(), 1, `Should render 'Number at risk' table below chart`)\n\n\t\tif (test._ok) cuminc.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=Cardiovascular System, filter=ALL', function (test) {\n\t// this test breaks due to the \"missing minSampleSize\" err\n\ttest.timeoutAfter(10000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\tterm: { id: 'Cardiovascular System' },\n\t\t\t\t\tsettings: { cuminc: { minSampleSize: 1, minAtRisk: 0 } }\n\t\t\t\t}\n\t\t\t],\n\t\t\ttermfilter: {\n\t\t\t\tfilter: {\n\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\tjoin: '',\n\t\t\t\t\tin: true,\n\t\t\t\t\tlst: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\tterm: { id: 'diaggrp' },\n\t\t\t\t\t\t\t\tvalues: [{ key: 'Acute lymphoblastic leukemia', label: 'Acute lymphoblastic leukemia' }]\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\tcuminc: {\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(plot) {\n\t\tconst div = plot.Inner.dom.chartsDiv\n\t\ttest.equal(div.selectAll('.sjpcb-cuminc-series').size(), 1, 'should render 1 cuminc series <g>')\n\t\ttest.equal(\n\t\t\tdiv.selectAll('.sjpcb-cuminc-series path').size(),\n\t\t\t2,\n\t\t\t'should render 2 cuminc series paths for estimate line and 95% CI area'\n\t\t)\n\n\t\tif (test._ok) plot.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=Cardiovascular System, term2=agedx', function (test) {\n\ttest.timeoutAfter(10000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\tterm: { id: 'Cardiovascular System' },\n\t\t\t\t\tterm2: { id: 'agedx' },\n\t\t\t\t\tsettings: { cuminc: { minSampleSize: 1, minAtRisk: 0 } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tcuminc: {\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(cuminc) {\n\t\tconst div = cuminc.Inner.dom.chartsDiv\n\t\ttest.equal(div.selectAll('.sjpcb-cuminc-series').size(), 2, 'should render 2 cuminc series <g>')\n\t\ttest.equal(\n\t\t\tdiv.selectAll('.sjpcb-cuminc-series path').size(),\n\t\t\t4,\n\t\t\t'should render 4 cuminc series paths for estimate line and 95% CI area'\n\t\t)\n\n\t\tconst legend = div.selectAll('.pp-cuminc-chartLegends').node()\n\t\ttest.ok(legend, `Should render chart legend`)\n\t\t//Exclude table header and tick values\n\t\tconst numRiskRowLabels = div.selectAll('[data-testid=\"sjpp-atrisk-seriesId\"]').nodes()\n\n\t\t//Test legend and risk table match legend data\n\t\tfor (const [i, d] of legend.__data__.visibleSerieses.entries()) {\n\t\t\tif (cuminc.Inner.legendData[0].items[i].seriesId != d.seriesId)\n\t\t\t\ttest.fail(\n\t\t\t\t\t`Missing or mismatched series found in legend, series = '${cuminc.Inner.legendData[0].items[i].seriesId}'`\n\t\t\t\t)\n\t\t\telse if (numRiskRowLabels[i].__data__.seriesId != d.seriesId)\n\t\t\t\ttest.fail(\n\t\t\t\t\t`Missing or mismatched series found in 'Number at risk' table, series = '${numRiskRowLabels[i].__data__.seriesId}'`\n\t\t\t\t)\n\t\t\telse test.pass(`Should display series = '${d.seriesId}' in both legend and 'Number at risk' table`)\n\t\t}\n\n\t\tif (test._ok) cuminc.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1=Cardiovascular System, term0=sex', test => {\n\ttest.timeoutAfter(5000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\tterm: { id: 'Cardiovascular System' },\n\t\t\t\t\tterm0: { id: 'sex' },\n\t\t\t\t\tsettings: { cuminc: { minSampleSize: 1, minAtRisk: 0 } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tcuminc: {\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(cuminc) {\n\t\tcuminc.on('postRender.test', null)\n\n\t\tconst cumincDiv = cuminc.Inner.dom.chartsDiv\n\t\tconst term0Values = cuminc.Inner.config.term0.term.values\n\n\t\t//Test all dom elements present\n\t\ttest.equal(\n\t\t\tcumincDiv.selectAll('.pp-cuminc-chart').size(),\n\t\t\tObject.keys(term0Values).length,\n\t\t\t`Should render ${Object.keys(term0Values).length} cuminc charts`\n\t\t)\n\t\ttest.equal(\n\t\t\tcumincDiv.selectAll('.sjpp-cuminc-atrisk').size(),\n\t\t\tObject.keys(term0Values).length,\n\t\t\t`Should render 'Number at risk' tables below chart`\n\t\t)\n\n\t\tconst titleNodes = cumincDiv.selectAll('.sjpcb-cuminc-title').nodes()\n\t\tfor (const v of Object.values(term0Values)) {\n\t\t\tif (!titleNodes.some(d => d.innerText == v.label)) test.fail(`Missing title for term0 value = ${v.label}`)\n\t\t}\n\n\t\tif (test._ok) cuminc.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1 = Cardiovascular System, term2 = agedx, numeric regular bins', test => {\n\ttest.timeoutAfter(10000)\n\tconst testBinSize = 5\n\tconst testStop = 5\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\tterm: { id: 'Cardiovascular System' },\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tid: 'agedx',\n\t\t\t\t\t\tname: 'Age (years) at Cancer Diagnosis',\n\t\t\t\t\t\ttype: 'float',\n\t\t\t\t\t\tbins: {\n\t\t\t\t\t\t\tdefault: {\n\t\t\t\t\t\t\t\ttype: 'regular-bin',\n\t\t\t\t\t\t\t\tbin_size: testBinSize,\n\t\t\t\t\t\t\t\tstartinclusive: true,\n\t\t\t\t\t\t\t\tfirst_bin: {\n\t\t\t\t\t\t\t\t\tstartunbounded: true,\n\t\t\t\t\t\t\t\t\tstop: testStop\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\tlabel_offset: 1\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\tcuminc: { minSampleSize: 1, minAtRisk: 0 }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tcuminc: {\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(cuminc) {\n\t\tcuminc.on('postRender.test', null)\n\n\t\tconst div = cuminc.Inner.dom.chartsDiv\n\n\t\t//Test data correctly appears\n\t\ttest.equal(cuminc.Inner.config.term2.q.type, 'regular-bin', `Should correctly pass 'regular-bin' to config`)\n\t\ttest.equal(\n\t\t\tcuminc.Inner.config.term2.q.bin_size,\n\t\t\ttestBinSize,\n\t\t\t`Should correctly pass q.bin_size = ${testBinSize} to config`\n\t\t)\n\t\ttest.equal(\n\t\t\tcuminc.Inner.config.term2.q.first_bin.stop,\n\t\t\ttestStop,\n\t\t\t`Should correctly pass q.first_bin.stop = ${testStop} to config`\n\t\t)\n\n\t\t//***Test q.bin_size and q.first_bin.stop changes are applied\n\t\tconst config = structuredClone(cuminc.Inner.config)\n\t\tconst expectedCount = cuminc.Inner.uniqueSeriesIds.size\n\n\t\t//Plot\n\t\tconst cumincCurves = await detectGte({\n\t\t\telem: div.node(),\n\t\t\tselector: '.sjpcb-cuminc-series',\n\t\t\tcount: expectedCount,\n\t\t\tasync trigger() {\n\t\t\t\tconfig.term2.q.bin_size = 3\n\t\t\t\tconfig.term2.q.first_bin.stop = 1\n\t\t\t\tawait cuminc.Inner.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: cuminc.Inner.id,\n\t\t\t\t\tconfig\n\t\t\t\t})\n\t\t\t},\n\t\t\tmatcher(mutations) {\n\t\t\t\tconst changedSeries = mutations.filter(\n\t\t\t\t\tm => m.previousSibling != null && cuminc.Inner.uniqueSeriesIds.has(m.target.__data__.seriesId)\n\t\t\t\t)\n\t\t\t\tif (changedSeries.length >= expectedCount) return changedSeries.map(d => d.target)\n\t\t\t}\n\t\t})\n\n\t\ttest.equal(cumincCurves.length, expectedCount, `Should update ${expectedCount} curves in plot`)\n\n\t\t//Number at risk table\n\t\tconst numRiskRowLabels = div.selectAll('[data-testid=\"sjpp-atrisk-seriesId\"]').nodes()\n\t\tconst foundNewLabels = numRiskRowLabels.filter(l => cuminc.Inner.uniqueSeriesIds.has(l.__data__.seriesId))\n\t\ttest.equal(foundNewLabels.length, expectedCount, `Should update ${expectedCount} labels in Number at risk table`)\n\n\t\tif (test._ok) cuminc.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\n//No assertions written for this test\ntape.skip('term1 = Cardiovascular System, term0 = agedx, numeric regular bins', test => {\n\ttest.timeoutAfter(5000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\tterm: { id: 'Cardiovascular System' },\n\t\t\t\t\tterm0: {\n\t\t\t\t\t\tid: 'agedx',\n\t\t\t\t\t\tterm: {\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\tlabel_offset: 1\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\tname: 'Age (years) at Cancer Diagnosis',\n\t\t\t\t\t\t\tid: 'agedx'\n\t\t\t\t\t\t\t// isleaf: true,\n\t\t\t\t\t\t\t// values: {},\n\t\t\t\t\t\t\t// included_types: [\n\t\t\t\t\t\t\t// \t'float'\n\t\t\t\t\t\t\t// ],\n\t\t\t\t\t\t\t// child_types: []\n\t\t\t\t\t\t},\n\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\tisAtomic: true,\n\t\t\t\t\t\t\tmode: 'discrete',\n\t\t\t\t\t\t\ttype: 'regular-bin'\n\t\t\t\t\t\t\t// type: 'custom-bin',\n\t\t\t\t\t\t\t// lst: [\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: 8.164619357749999,\n\t\t\t\t\t\t\t// \t\tstopinclusive: false,\n\t\t\t\t\t\t\t// \t\tlabel: '<8.164619357749999'\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: 8.164619357749999,\n\t\t\t\t\t\t\t// \t\tstartinclusive: true,\n\t\t\t\t\t\t\t// \t\tstopunbounded: true,\n\t\t\t\t\t\t\t// \t\tlabel: '\u22658.164619357749999'\n\t\t\t\t\t\t\t// \t}\n\t\t\t\t\t\t\t// ],\n\t\t\t\t\t\t\t// hiddenValues: {}\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\tcuminc: { minSampleSize: 1, minAtRisk: 0 },\n\t\t\t\t\t\tcontrols: {\n\t\t\t\t\t\t\tterm0: { id: 'agedx', term: termjson['agedx'] }\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\tcuminc: {\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(cuminc) {\n\t\tcuminc.on('postRender.test', null)\n\n\t\t//TODO: Need data in TermdbTest to process\n\n\t\t// if (test._ok) cuminc.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1 = Cardiovascular System, term2 = agedx, numeric custom bins', test => {\n\ttest.timeoutAfter(10000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\tterm: { id: 'Cardiovascular System' },\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tid: 'agedx',\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{ startunbounded: true, stop: 7, stopinclusive: false, label: '<7' },\n\t\t\t\t\t\t\t\t{ startinclusive: true, stopinclusive: true, start: 7, stop: 12, label: '7 to 12' },\n\t\t\t\t\t\t\t\t{ start: 12, startinclusive: false, stopunbounded: true, label: '>12' }\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\tsettings: {\n\t\t\t\t\t\tcuminc: { minSampleSize: 1, minAtRisk: 0 }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tcuminc: {\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(cuminc) {\n\t\tcuminc.on('postRender.test', null)\n\n\t\tconst inner = cuminc.Inner\n\t\tconst div = inner.dom.chartsDiv\n\n\t\t//Test data correctly appears\n\t\ttest.equal(inner?.config.term2.q.type, 'custom-bin', `Should correctly pass 'custom-bin' to config`)\n\n\t\t//Test overlay changes are applied\n\t\tconst config = structuredClone(cuminc.Inner.config)\n\t\tconst expectedCount = cuminc.Inner.uniqueSeriesIds.size\n\n\t\t//Plot\n\t\tconst cumincCurves = await detectGte({\n\t\t\telem: div.node(),\n\t\t\tselector: '.sjpcb-cuminc-series',\n\t\t\tcount: expectedCount,\n\t\t\tasync trigger() {\n\t\t\t\tconfig.term2.q.lst[2] = { startinclusive: true, stopinclusive: true, start: 12, stop: 15, label: '12 to 15' }\n\t\t\t\tconfig.term2.q.lst.push({ start: 15, startinclusive: false, stopunbounded: true, label: '>15' })\n\t\t\t\tawait cuminc.Inner.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: inner.id,\n\t\t\t\t\tconfig\n\t\t\t\t})\n\t\t\t},\n\t\t\tmatcher(mutations) {\n\t\t\t\tconst changedSeries = mutations.filter(\n\t\t\t\t\tm => m.previousSibling != null && inner.uniqueSeriesIds.has(m.target.__data__.seriesId)\n\t\t\t\t)\n\t\t\t\tif (changedSeries.length >= expectedCount) return changedSeries.map(d => d.target)\n\t\t\t}\n\t\t})\n\n\t\ttest.equal(cumincCurves.length, expectedCount, `Should update ${expectedCount} curves in plot`)\n\n\t\t//Number at risk table\n\t\tconst numRiskRowLabels = div.selectAll('[data-testid=\"sjpp-atrisk-seriesId\"]').nodes()\n\t\tconst foundNewLabels = numRiskRowLabels.filter(l => inner.uniqueSeriesIds.has(l.__data__.seriesId))\n\t\ttest.equal(foundNewLabels.length, expectedCount, `Should update ${expectedCount} labels in Number at risk table`)\n\n\t\tif (test._ok) inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('term1 = Cardiovascular System, term0 = agedx, numeric custom bins', test => {\n\ttest.timeoutAfter(10000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\tterm: { id: 'Cardiovascular System' },\n\t\t\t\t\tterm0: {\n\t\t\t\t\t\tid: 'agedx',\n\t\t\t\t\t\tterm: {\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\tlabel_offset: 1\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\tname: 'Age (years) at Cancer Diagnosis',\n\t\t\t\t\t\t\tid: 'agedx'\n\t\t\t\t\t\t},\n\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\tisAtomic: true,\n\t\t\t\t\t\t\tmode: 'discrete',\n\t\t\t\t\t\t\ttype: 'custom-bin',\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: 12,\n\t\t\t\t\t\t\t\t\tstopinclusive: false,\n\t\t\t\t\t\t\t\t\tlabel: '<12'\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: 12,\n\t\t\t\t\t\t\t\t\tstartinclusive: true,\n\t\t\t\t\t\t\t\t\tstopunbounded: true,\n\t\t\t\t\t\t\t\t\tlabel: '\u226512'\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\thiddenValues: {}\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\tcuminc: { minSampleSize: 1, minAtRisk: 0 }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tcuminc: {\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(cuminc) {\n\t\tcuminc.on('postRender.test', null)\n\t\tconst inner = cuminc.Inner\n\t\tconst div = cuminc.Inner.dom.chartsDiv\n\n\t\t//Test data correctly appears\n\t\ttest.equal(inner.config.term0.q.type, 'custom-bin', `Should correctly pass 'custom-bin' to config`)\n\n\t\t//***Test divide by changes are applied\n\t\tconst config = structuredClone(inner.config)\n\n\t\t//Plot\n\t\tconst chartIds2Check = new Set()\n\t\tconst cumincCurves = await detectGte({\n\t\t\ttarget: div.node(),\n\t\t\tselector: 'g.sjpcb-cuminc-mainG',\n\t\t\tasync trigger() {\n\t\t\t\tconfig.term0.q.lst[0] = { startunbounded: true, stop: 15, stopinclusive: false, label: '<15' }\n\t\t\t\tconfig.term0.q.lst[1] = { start: 15, startinclusive: false, stopunbounded: true, label: '>15' }\n\t\t\t\tconfig.term0.q.lst.forEach(d => chartIds2Check.add(d.label))\n\t\t\t\tawait inner.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: inner.id,\n\t\t\t\t\tconfig\n\t\t\t\t})\n\t\t\t},\n\t\t\tmatcher(mutations) {\n\t\t\t\tconst changedSeries = mutations.filter(\n\t\t\t\t\tm => m.attributeName == 'transform' && chartIds2Check.has(m.target.__data__.chartId)\n\t\t\t\t)\n\t\t\t\tif (changedSeries.length >= chartIds2Check.size) return changedSeries.map(d => d.target)\n\t\t\t}\n\t\t})\n\n\t\ttest.equal(cumincCurves.length, chartIds2Check.size, `Should update ${chartIds2Check.size} plots`)\n\n\t\tif (test._ok) inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('skipped series', function (test) {\n\ttest.timeoutAfter(10000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\tterm: { id: 'Cardiovascular System' },\n\t\t\t\t\tterm2: { id: 'genetic_race' },\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\tcuminc: { minSampleSize: 10, minAtRisk: 0 }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tcuminc: {\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(cuminc) {\n\t\tconst skippedDivs = cuminc.Inner.dom.chartsDiv\n\t\t\t.select('.pp-cuminc-chartLegends')\n\t\t\t.selectAll('.pp-cuminc-chartLegends-skipped')\n\n\t\t// db rebuilt on 8/30/23 no longer shows Asian skipped for \"No event\"\n\t\t//test.equal(skippedDivs && skippedDivs.size(), 2, 'should render 2 skipped series')\n\t\ttest.equal(skippedDivs && skippedDivs.size(), 1, 'should render 1 skipped series')\n\n\t\tif (test._ok) cuminc.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape.skip('term1 = Cardiovascular System, term2 = samplelst', function (test) {\n\ttest.timeoutAfter(5000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'cuminc',\n\t\t\t\t\tterm: { id: 'Cardiovascular System' },\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\tname: 'Samplelst term',\n\t\t\t\t\t\t\ttype: 'samplelst',\n\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t'Group 1': {\n\t\t\t\t\t\t\t\t\tkey: 'Group 1',\n\t\t\t\t\t\t\t\t\tlabel: 'Test 1',\n\t\t\t\t\t\t\t\t\tinuse: false,\n\t\t\t\t\t\t\t\t\tlist: [\n\t\t\t\t\t\t\t\t\t\t{ sampleId: 1, sample: 1 },\n\t\t\t\t\t\t\t\t\t\t{ sampleId: 2, sample: 2 }\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\t'Group 2': {\n\t\t\t\t\t\t\t\t\tkey: 'Group 2',\n\t\t\t\t\t\t\t\t\tlabel: 'Test 2',\n\t\t\t\t\t\t\t\t\tinuse: false,\n\t\t\t\t\t\t\t\t\tlist: [\n\t\t\t\t\t\t\t\t\t\t{ sampleId: 3, sample: 3 },\n\t\t\t\t\t\t\t\t\t\t{ sampleId: 4, sample: 4 },\n\t\t\t\t\t\t\t\t\t\t{ sampleId: 5, sample: 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\t'Group 3': { key: 'Group 3', label: 'Test 3', inuse: false, list: [{ sampleId: 6, sample: 6 }] }\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t},\n\t\t\t\t\t\tq: {\n\t\t\t\t\t\t\tgroups: [\n\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\tname: 'Group 1',\n\t\t\t\t\t\t\t\t\tin: false,\n\t\t\t\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t\t\t\t{ sampleId: 1, sample: 1 },\n\t\t\t\t\t\t\t\t\t\t{ sampleId: 2, sample: 2 }\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\t{\n\t\t\t\t\t\t\t\t\tname: 'Group 2',\n\t\t\t\t\t\t\t\t\tin: false,\n\t\t\t\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t\t\t\t{ sampleId: 3, sample: 3 },\n\t\t\t\t\t\t\t\t\t\t{ sampleId: 4, sample: 4 },\n\t\t\t\t\t\t\t\t\t\t{ sampleId: 5, sample: 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\t{\n\t\t\t\t\t\t\t\t\tname: 'Group 3',\n\t\t\t\t\t\t\t\t\tin: false,\n\t\t\t\t\t\t\t\t\tvalues: [{ sampleId: 6, sample: 6 }]\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\tsettings: {\n\t\t\t\t\t\tcuminc: { minSampleSize: 1, minAtRisk: 0 }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tcuminc: {\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(cuminc) {\n\t\tcuminc.on('postRender.test', null)\n\n\t\tconst valKeys = Object.keys(cuminc.Inner.config.term2.term.values)\n\t\tconst uniqueSeriesIds = Array.from(cuminc.Inner.uniqueSeriesIds)\n\t\ttest.equal(JSON.stringify(valKeys), JSON.stringify(uniqueSeriesIds), `Should create custom groups`)\n\n\t\tlet numGrpLabelFails = 0\n\t\tconst numRiskRowLabels = cuminc.Inner.dom.chartsDiv\n\t\t\t.selectAll('.sjpp-cuminc-atrisk text')\n\t\t\t.nodes()\n\t\t\t.filter(d => !d.__data__?.tickVal && d.className.animVal != 'sjpp-atrisk-title')\n\n\t\tfor (const grp of Object.values(cuminc.Inner.config.term2.term.values)) {\n\t\t\tconst findGrpLabel = numRiskRowLabels.some(d => d.__data__.seriesId == grp.key && d.innerHTML == grp.label)\n\t\t\tif (!findGrpLabel) {\n\t\t\t\ttest.fail(`Missing group in 'Number at risk' table: group = ${grp.key}, label = ${grp.label}`)\n\t\t\t\t++numGrpLabelFails\n\t\t\t}\n\t\t}\n\t\tif (numGrpLabelFails == 0) test.pass(`All custom groups display`)\n\n\t\tif (test._ok) cuminc.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n"],
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+  "names": ["tape"]
+}

package/dist/customdata.inputui-YU4IQJOV.js

@@ -0,0 +1,289 @@
+import {
+  mclasscolor2table
+} from "./chunk-JHZK6IDA.js";
+import {
+  aa2gmcoord,
+  rna2gmcoord
+} from "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-FYY3T565.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-7Z6E3NA5.js";
+import "./chunk-V2ET64EJ.js";
+import {
+  dofetch3
+} from "./chunk-5ERYRSVV.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-23AEAG37.js";
+import "./chunk-M2PPUO4E.js";
+import {
+  dtcnv,
+  dtfusionrna,
+  dtsnvindel,
+  mclass,
+  mclasscnvgain,
+  mclasscnvloss,
+  mclassfusionrna
+} from "./chunk-ZRSJVACE.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// mds3/customdata.inputui.js
+function customdata_inputui_default(block) {
+  if (!block.usegm) {
+    return;
+  }
+  const div = block.tip.d.append("div").style("margin", "20px");
+  div.append("p").text(`Add mutation and/or fusion to show over ${block.usegm.name} ${block.usegm.isoform}`);
+  const textarea2 = div.append("textarea").attr("cols", "50").attr("rows", "5").property("placeholder", "Enter data");
+  textarea2.node().focus();
+  const nameinput = div.append("div").append("input").attr("type", "text").style("width", "130px").property("placeholder", "Dataset name");
+  const row = div.append("div").style("margin-top", "5px");
+  const select = row.append("select");
+  select.append("option").text("Codon position");
+  select.append("option").text("RNA position");
+  select.append("option").text("Genomic position");
+  row.append("button").style("margin-left", "5px").text("Submit").on("click", async () => {
+    const v = textarea2.property("value");
+    if (v == "") return;
+    says.style("display", "none");
+    const selecti = select.node().selectedIndex, mlst = [], bad = [];
+    for (const line0 of v.trim().split("\n")) {
+      const line = line0.trim();
+      if (!line) continue;
+      const l = line.split(line.includes("	") ? "	" : line.includes(",") ? "," : " ");
+      try {
+        if (l.length == 3 || l.length == 4) {
+          if (Number.isFinite(Number(l[2]))) {
+            parseCnv(l, mlst, selecti, block);
+          } else {
+            parseMutation(l, mlst, selecti, block);
+          }
+          continue;
+        }
+        if (l.length == 6 || l.length == 7) {
+          await parseFusion(l, mlst, selecti, block);
+          continue;
+        }
+        throw `Line="${l}" does not match the mutation, fusion, or cnv format. Please review.`;
+      } catch (e) {
+        bad.push(line + ": " + (e.message || e));
+      }
+    }
+    if (mlst.find((m) => m.sample) && mlst.find((m) => !m.sample)) {
+      bad.push("sample name is provided for some but not all variants");
+    }
+    if (bad.length) {
+      says.style("display", "block").text("Rejected: " + bad.join("\n"));
+    }
+    if (mlst.length == 0) return;
+    const tk = block.block_addtk_template({
+      type: "mds3",
+      name: nameinput.property("value") || "Custom data",
+      iscustom: true,
+      custom_variants: mlst
+    });
+    block.tk_load(tk);
+  });
+  row.append("button").text("Clear").style("margin-left", "5px").on("click", () => {
+    textarea2.property("value", "");
+    nameinput.property("value", "");
+  });
+  const says = div.append("div").style("display", "none", "margin-top", "20px");
+  printHelp(div);
+}
+function parseMutation(l, mlst, selecti, block) {
+  const _class = l[2].trim();
+  if (!mclass[_class]) throw `Invalid mutation class=${_class}`;
+  const m = {
+    class: _class,
+    dt: dtsnvindel,
+    isoform: block.usegm.isoform,
+    mname: l[0].trim()
+  };
+  if (!m.mname) throw "missing mutation name";
+  const o = parsePositionFromGm(selecti, l[1].trim(), block.usegm);
+  m.chr = o[0];
+  m.pos = o[1];
+  if (l[3]) m.sample = l[3];
+  mlst.push(m);
+}
+async function parseFusion(l, mlst, selecti, block) {
+  const m = {
+    class: mclassfusionrna,
+    dt: dtfusionrna
+    // compute and assign gene1/2, chr1/2, pos1/2
+  };
+  if (l[6]) m.sample = l[6];
+  const [gene1, isoform1, pos1, gene2, isoform2, pos2] = l;
+  if (!gene1) throw "gene1 is missing";
+  if (!gene2) throw "gene2 is missing";
+  if (!isoform1) throw "isoform1 is missing";
+  if (!isoform2) throw "isoform2 is missing";
+  if (!pos1) throw "pos1 is missing";
+  if (!pos2) throw "pos2 is missing";
+  {
+    const d = await dofetch3("genelookup", { body: { deep: 1, genome: block.genome.name, input: gene1 } });
+    if (d.error) throw "invalid gene1";
+    const gm = d.gmlst.find((i) => i.isoform == isoform1);
+    if (!gm) throw "invalid isoform1";
+    m.gene1 = gene1;
+    m.chr1 = gm.chr;
+    const o = parsePositionFromGm(selecti, pos1, gm);
+    m.pos1 = o[1];
+    m.strand1 = gm.strand;
+    m.isoform1 = isoform1;
+  }
+  {
+    const d = await dofetch3("genelookup", { body: { deep: 1, genome: block.genome.name, input: gene2 } });
+    if (d.error) throw "invalid gene2";
+    const gm = d.gmlst.find((i) => i.isoform == isoform2);
+    if (!gm) throw "invalid isoform2";
+    m.gene2 = gene2;
+    m.chr2 = gm.chr;
+    const o = parsePositionFromGm(selecti, pos2, gm);
+    m.pos2 = o[1];
+    m.strand2 = gm.strand;
+    m.isoform2 = isoform2;
+  }
+  mlst.push(m);
+}
+function parseCnv(l, mlst, selecti, block) {
+  const value = Number(l[2].trim());
+  if (!Number.isFinite(value)) throw "CNV value is not number";
+  const m = {
+    chr: block.usegm.chr,
+    dt: dtcnv,
+    value,
+    class: value > 0 ? mclasscnvgain : mclasscnvloss
+  };
+  if (l[3]) m.sample = l[3];
+  const a = parsePositionFromGm(selecti, l[0].trim(), block.usegm), b = parsePositionFromGm(selecti, l[1].trim(), block.usegm);
+  m.start = Math.min(a[1], b[1]);
+  m.stop = Math.max(a[1], b[1]);
+  mlst.push(m);
+}
+function parsePositionFromGm(selecti, str, gm) {
+  const value = parseInputPosition(str, gm.chr);
+  if (!Number.isInteger(value)) throw "position is not integer";
+  if (selecti == 0) {
+    const p = aa2gmcoord(value, gm);
+    if (p == null) throw "cannot convert codon to genomic position";
+    return [gm.chr, p];
+  }
+  if (selecti == 1) {
+    const p = rna2gmcoord(value, gm);
+    if (p == null) throw "cannot convert RNA position to genomic position";
+    return [gm.chr, p];
+  }
+  if (selecti == 2) {
+    return [gm.chr, value - 1];
+  }
+  throw "unknown selection";
+}
+function parseInputPosition(str, chr) {
+  let value;
+  if (str.includes(":")) {
+    const tmp = str.split(":");
+    if (tmp[0] != chr) throw `Included chromosome=${tmp[0]} does not match current chromosome position=${chr}`;
+    value = Number(tmp[1]);
+  } else {
+    value = Number(str);
+  }
+  return value;
+}
+function printHelp(div) {
+  {
+    const [label, infodiv] = makeHelpDiv(div);
+    label.text("Mutation format: mutation name, position, class, sample");
+    infodiv.html(
+      `One mutation per line. Fields are joined by tab, comma or space. Please do not use both comma and space as separator.
+		<ol>
+			<li>Mutation name, can be any string</li>
+			<li>Mutation position</li>
+			<li>Mutation class code</li>
+			<li>Optional sample name</li>
+		</ol>
+		Position types:
+		<ul><li>Codon position: integer, 1-based (do not use for noncoding gene)</li>
+		<li>RNA position: integer, 1-based, beginning from transcription start site</li>
+		<li>Genomic position: integer, 1-based coordinate</li></ul>`
+    );
+    mclasscolor2table(infodiv.append("table").style("margin-top", "3px"), true);
+  }
+  {
+    const [label, infodiv] = makeHelpDiv(div);
+    label.text("SV/fusion format: gene1, isoform1, position1, gene2, isoform2, position2, sample");
+    infodiv.html(
+      `Limited to two-gene fusion products. One product per line.
+			Fields are joined by tab, comma or space. Please do not use both comma and space as separator.
+		<ol><li>N-term gene symbol</li>
+		<li>N-term gene isoform</li>
+		<li>N-term gene break-end position</li>
+		<li>C-term gene symbol</li>
+		<li>C-term gene isoform</li>
+		<li>C-term gene break-end position</li>
+		<li>Optional sample name</li>
+		</ol>
+		Break-end position types:
+		<ul><li>Codon position: integer, 1-based</li>
+		<li>RNA position: integer, 1-based, beginning from transcription start site</li>
+		<li>Genomic position: 1-based coordinate</li></ul>
+		Either one of the isoforms must be already displayed.`
+    );
+  }
+  {
+    const [label, infodiv] = makeHelpDiv(div);
+    label.text("CNV format: segment start, segment stop, CNV value, sample");
+    infodiv.html(
+      `One CNV segment per line. Fields are joined by tab, comma or space. Please do not use both comma and space as separator.
+		<ol>
+			<li>Segment start position</li>
+			<li>Segment stop position</li>
+			<li>Copy number change value, positive value for gain, negative value for loss. Do not use 0</li>
+			<li>Optional sample name</li>
+		</ol>
+		Position types:
+		<ul><li>Codon position: integer, 1-based (do not use for noncoding gene)</li>
+		<li>RNA position: integer, 1-based, beginning from transcription start site</li>
+		<li>Genomic position: integer, 1-based coordinate</li></ul>`
+    );
+  }
+}
+function makeHelpDiv(div) {
+  const p = div.append("p");
+  const label = p.append("span").style("opacity", 0.6);
+  p.append("span").attr("class", "sja_clbtext").style("margin-left", "10px").text("Show details").on("click", (event) => {
+    const show = infodiv.style("display") == "none";
+    infodiv.style("display", show ? "" : "none");
+    event.target.innerHTML = show ? "Hide details" : "Show details";
+  });
+  const infodiv = div.append("div").style("display", "none").style("margin-left", "20px").style("padding-left", "10px").style("border-left", "solid 1px black").style("color", "#858585");
+  return [label, infodiv];
+}
+export {
+  customdata_inputui_default as default,
+  parseCnv,
+  parseFusion,
+  parseInputPosition,
+  parseMutation,
+  parsePositionFromGm
+};
+//# sourceMappingURL=customdata.inputui-YU4IQJOV.js.map