@sjcrh/proteinpaint-client 2.196.0 → 2.197.0

package/dist/survival.integration.spec-KVXHHAA3.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/survival/test/survival.integration.spec.js"],
+  "sourcesContent": ["import tape from 'tape'\nimport { termjson } from '#test/testdata/termjson.ts'\nimport * as helpers from '#test/front.helpers.js'\nimport { detectGte, Locator, sleep } from '#test/test.helpers.js'\n\n/*\nTests:\n\tsurvival term as term1\n\tsurvival term as term1, with categorical overlay\n\tsurvival term as term1, with numeric overlay\n\tsurvival term as term1, with condition overlay (some samples have missing values)\n\tsurvival term as overlay\n\tsurvival term as term1, with categorical divide by\n\tsurvival term as term1, with numeric divide by\n\tsurvival term as term1, with condition divide by (some samples have missing values)\n\tsurvival term as term1, term2 = genetic_race, categorical groupsetting\n\tsurvival term as term1, term0 = genetic_race, categorical groupsetting\n\tsurvival term as term1, term2 = agedx, regular bins\n\tsurvival term as term1, term2 = agedx, custom bins\n\tsurvival term as term1, term0 = agedx, custom bins\n\tsurvival term as term1, term2 = geneVariant\n\tsurvival term as term1, term2 = geneExpression\n\tsurvival term as term1, term2 = ssGSEA\n\tsurvival term as term1, term2 = isoformExpression\n\tsurvival term as term1, term2 = dnaMethylation\n */\n\n/*************************\n reusable helper functions\n**************************/\n\nconst runpp = helpers.getRunPp('mass', {\n\tstate: {\n\t\tnav: {\n\t\t\tactiveTab: 1\n\t\t},\n\t\tdslabel: 'TermdbTest',\n\t\tgenome: 'hg38-test'\n\t},\n\tdebug: 1\n})\n\n/**************\n test sections\n***************/\ntape('\\n', function (test) {\n\ttest.comment('-***- plots/survival -***-')\n\ttest.end()\n})\n\ntape('survival term as term1', 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: 'survival',\n\t\t\t\t\tterm: {\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\tsurvival: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet survivalDiv\n\tasync function runTests(survival) {\n\t\tsurvivalDiv = survival.Inner.dom.chartsDiv\n\t\ttest.equal(survivalDiv && survivalDiv.selectAll('.sjpp-survival-series').size(), 1, 'should render 1 surv series g')\n\t\t// please advice if to remove below tests using \"circle\" which is no longered rendered\n\t\ttest.equal(\n\t\t\tsurvivalDiv && survivalDiv.selectAll('.sjpp-survival-censored-x').size(),\n\t\t\t10,\n\t\t\t'should render 10 survival censored symbols'\n\t\t)\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, with categorical overlay', 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: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tid: 'diaggrp'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet survivalDiv\n\tasync function runTests(survival) {\n\t\tsurvivalDiv = survival.Inner.dom.chartsDiv\n\t\ttest.equal(survivalDiv && survivalDiv.selectAll('.sjpp-survival-series').size(), 7, 'should render 7 surv series g')\n\t\ttest.equal(\n\t\t\tsurvivalDiv && survivalDiv.selectAll('.sjpp-survival-censored-x').size(),\n\t\t\t10,\n\t\t\t'should render 9 survival censored symbols'\n\t\t)\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, with numeric overlay', 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: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tid: 'agedx'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet survivalDiv\n\tasync function runTests(survival) {\n\t\tsurvivalDiv = survival.Inner.dom.chartsDiv\n\t\ttest.equal(survivalDiv && survivalDiv.selectAll('.sjpp-survival-series').size(), 2, 'should render 2 surv series g')\n\t\ttest.equal(\n\t\t\tsurvivalDiv && survivalDiv.selectAll('.sjpp-survival-censored-x').size(),\n\t\t\t10,\n\t\t\t'should render 10 survival censored symbols'\n\t\t)\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, with condition overlay (some samples have missing values)', 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: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tid: 'Auditory System'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet survivalDiv\n\tasync function runTests(survival) {\n\t\tsurvivalDiv = survival.Inner.dom.chartsDiv\n\t\ttest.equal(survivalDiv && survivalDiv.selectAll('.sjpp-survival-series').size(), 5, 'should render 5 surv series g')\n\t\ttest.equal(\n\t\t\tsurvivalDiv && survivalDiv.selectAll('.sjpp-survival-censored-x').size(),\n\t\t\t3,\n\t\t\t'should render 3 survival censored symbols'\n\t\t)\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as overlay', 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: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'diaggrp'\n\t\t\t\t\t},\n\t\t\t\t\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\tsurvival: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet survivalDiv\n\tasync function runTests(survival) {\n\t\tsurvivalDiv = survival.Inner.dom.chartsDiv\n\t\ttest.equal(survivalDiv && survivalDiv.selectAll('.sjpp-survival-series').size(), 7, 'should render 7 surv series g')\n\t\ttest.equal(\n\t\t\tsurvivalDiv && survivalDiv.selectAll('.sjpp-survival-censored-x').size(),\n\t\t\t10,\n\t\t\t'should render 10 survival censored symbols'\n\t\t)\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, with categorical divide by', 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: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\n\t\t\t\t\tterm0: {\n\t\t\t\t\t\tid: 'genetic_race'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\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(survival) {\n\t\tconst inner = survival.Inner\n\t\tconst survivalDiv = inner.dom.chartsDiv\n\t\tconst term0Values = inner.state.config.term0.term.values\n\n\t\t//Test all dom elements present\n\t\ttest.equal(survivalDiv.selectAll('.pp-survival-chart').size(), 3, `Should render 3 survival charts`)\n\n\t\ttest.equal(\n\t\t\tsurvivalDiv.selectAll('.sjpp-survival-atrisk').size(),\n\t\t\t3,\n\t\t\t`Should render 'Number at risk' tables below each chart`\n\t\t)\n\n\t\tconst term0Labels = Object.values(term0Values).map(v => v.label)\n\t\tconst titleNodes = survivalDiv.selectAll('.sjpp-survival-title').nodes()\n\t\tfor (const d of titleNodes) {\n\t\t\tif (!term0Labels.includes(d.innerText)) test.fail(`Unexpected title: ${d.innerText}`)\n\t\t}\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, with numeric divide by', 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: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\n\t\t\t\t\tterm0: {\n\t\t\t\t\t\tid: 'agedx'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\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(survival) {\n\t\tconst inner = survival.Inner\n\t\tconst survivalDiv = inner.dom.chartsDiv\n\n\t\t//Test all dom elements present\n\t\ttest.equal(survivalDiv.selectAll('.pp-survival-chart').size(), 2, `Should render 2 survival charts`)\n\n\t\ttest.equal(\n\t\t\tsurvivalDiv.selectAll('.sjpp-survival-atrisk').size(),\n\t\t\t2,\n\t\t\t`Should render 'Number at risk' tables below each chart`\n\t\t)\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, with condition divide by (some samples have missing values)', 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: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\n\t\t\t\t\tterm0: {\n\t\t\t\t\t\tid: 'Auditory System'\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\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(survival) {\n\t\tconst inner = survival.Inner\n\t\tconst survivalDiv = inner.dom.chartsDiv\n\t\tconst term0Values = inner.state.config.term0.term.values\n\n\t\t//Test all dom elements present\n\t\ttest.equal(survivalDiv.selectAll('.pp-survival-chart').size(), 5, `Should render 5 survival charts`)\n\n\t\ttest.equal(\n\t\t\tsurvivalDiv.selectAll('.sjpp-survival-atrisk').size(),\n\t\t\t5,\n\t\t\t`Should render 'Number at risk' tables below each chart`\n\t\t)\n\n\t\tconst term0Labels = Object.values(term0Values).map(v => v.label)\n\t\tconst titleNodes = survivalDiv.selectAll('.sjpp-survival-title').nodes()\n\t\tfor (const d of titleNodes) {\n\t\t\tif (!term0Labels.includes(d.innerText)) test.fail(`Unexpected title: ${d.innerText}`)\n\t\t}\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, term2 = genetic_race, categorical groupsetting', function (test) {\n\ttest.timeoutAfter(3000)\n\n\tconst groups = [\n\t\t{\n\t\t\tname: 'non-Asian Ancestry',\n\t\t\ttype: 'values',\n\t\t\tvalues: [\n\t\t\t\t{ key: 'European Ancestry', label: 'European Ancestry' },\n\t\t\t\t{ key: 'African Ancestry', label: 'African Ancestry' },\n\t\t\t\t{ key: 'Multi-Ancestry-Admixed', label: 'Multi-Ancestry-Admixed' }\n\t\t\t]\n\t\t},\n\t\t{\n\t\t\tname: 'Asian Ancestry',\n\t\t\ttype: 'values',\n\t\t\tvalues: [{ key: 'Asian Ancestry', label: 'Asian Ancestry' }]\n\t\t}\n\t]\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\n\t\t\t\t\tterm2: {\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}\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\tsurvival: {\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(survival) {\n\t\tsurvival.on('postRender.test', null)\n\n\t\tconst inner = survival.Inner\n\t\tconst config = inner.state.config\n\n\t\ttest.equal(\n\t\t\tJSON.stringify(config.term2.q.customset.groups),\n\t\t\tJSON.stringify(groups),\n\t\t\t`Should correctly pass customset groups for term2`\n\t\t)\n\n\t\tconst numOfTerms = Object.keys(inner.term2toColor).length\n\t\ttest.equal(\n\t\t\tinner.dom.chartsDiv.selectAll('.sjpp-survival-series').size(),\n\t\t\tnumOfTerms,\n\t\t\t`Should render ${numOfTerms} surv series g`\n\t\t)\n\n\t\tconst censoredSym = inner.currData.filter(d => d.ncensor)\n\t\ttest.equal(\n\t\t\tinner.dom.chartsDiv.selectAll('.sjpp-survival-censored-x').size(),\n\t\t\tcensoredSym.length,\n\t\t\t`should render ${censoredSym.length} survival censored symbols`\n\t\t)\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, term0 = genetic_race, categorical groupsetting', function (test) {\n\ttest.timeoutAfter(10000)\n\n\tconst groups = [\n\t\t{\n\t\t\tname: 'non-Asian Ancestry',\n\t\t\ttype: 'values',\n\t\t\tvalues: [\n\t\t\t\t{ key: 'European Ancestry', label: 'European Ancestry' },\n\t\t\t\t{ key: 'African Ancestry', label: 'African Ancestry' },\n\t\t\t\t{ key: 'Multi-Ancestry-Admixed', label: 'Multi-Ancestry-Admixed' }\n\t\t\t]\n\t\t},\n\t\t{\n\t\t\tname: 'Asian Ancestry',\n\t\t\ttype: 'values',\n\t\t\tvalues: [{ key: 'Asian Ancestry', label: 'Asian Ancestry' }]\n\t\t}\n\t]\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\n\t\t\t\t\tterm0: {\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}\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\tsurvival: {\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(survival) {\n\t\tsurvival.on('postRender.test', null)\n\n\t\tconst inner = survival.Inner\n\t\tconst config = inner.state.config\n\t\tconst term0Values = config.term0.term.values\n\n\t\ttest.equal(\n\t\t\tJSON.stringify(config.term0.q.customset.groups),\n\t\t\tJSON.stringify(groups),\n\t\t\t`Should correctly pass customset groups for term0`\n\t\t)\n\n\t\t//Test all dom elements present\n\t\tconst termNum = inner.serverData.refs.orderedKeys.chart\n\t\ttest.equal(\n\t\t\tinner.dom.chartsDiv.selectAll('.pp-survival-chart').size(),\n\t\t\ttermNum.length,\n\t\t\t`Should render ${termNum.length} survival charts`\n\t\t)\n\n\t\ttest.equal(\n\t\t\tinner.dom.chartsDiv.selectAll('.sjpp-survival-atrisk').size(),\n\t\t\ttermNum.length,\n\t\t\t`Should render 'Number at risk' tables below each chart`\n\t\t)\n\n\t\tconst titleNodes = inner.dom.chartsDiv.selectAll('.sjpp-survival-title').nodes()\n\t\ttermNum.forEach(v => {\n\t\t\tif (!titleNodes.some(d => d.innerText == v)) test.fail(`Missing title for term0 value = ${v}`)\n\t\t})\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, term2 = agedx, regular bins', function (test) {\n\ttest.timeoutAfter(10000)\n\ttest.plan(4)\n\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: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\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}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\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(survival) {\n\t\tsurvival.on('postRender.test', null)\n\n\t\t//Test data correctly appears\n\t\ttest.equal(survival.Inner.state.config.term2.q.type, 'regular-bin', `Should correctly pass 'regular-bin' to config`)\n\t\ttest.equal(\n\t\t\tsurvival.Inner.state.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\tsurvival.Inner.state.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 newStop = 1\n\t\t// Create a copy of the state config to modify, otherwise\n\t\t// a dispatch may not propagate to this survival component instance\n\t\t// since the state would just equal itself (nothing has changed so no need to rerender),\n\t\t// whereas a modified copy will not equal the original state\n\t\tconst config = structuredClone(survival.Inner.state.config)\n\t\tconst expectedCount = 8\n\t\tconst survCurves = await detectGte({\n\t\t\telem: survival.Inner.dom.chartsDiv.node(),\n\t\t\tselector: '.sjpp-survival-series',\n\t\t\tcount: expectedCount,\n\t\t\tasync trigger() {\n\t\t\t\t// this modifies the copy\n\t\t\t\tconfig.term2.q.bin_size = 3\n\t\t\t\tconfig.term2.q.first_bin.stop = newStop\n\t\t\t\tsurvival.Inner.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: survival.Inner.id,\n\t\t\t\t\tconfig\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\n\t\ttest.equal(survCurves.length, expectedCount, `Should display the correct bin size = ${expectedCount}`)\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, term2 = agedx, custom bins', function (test) {\n\ttest.timeoutAfter(10000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\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\tsurvival: {}\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\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(survival) {\n\t\tsurvival.on('postRender.test', null)\n\n\t\tconst inner = survival.Inner\n\t\tconst config = inner.state.config\n\n\t\t//Test data correctly appears\n\t\ttest.equal(config.term2.q.type, 'custom-bin', `Should correctly pass 'custom-bin' to config`)\n\n\t\t// Create a copy of the state config to modify, otherwise\n\t\t// a dispatch may not propagate to this survival component instance\n\t\t// since the state would just equal itself (nothing has changed so no need to rerender),\n\t\t// whereas a modified copy will not equal the original state\n\t\tconst config2 = structuredClone(config)\n\t\tconst expectedCount = 3\n\n\t\tconst survCurves = await detectGte({\n\t\t\telem: survival.Inner.dom.chartsDiv.node(),\n\t\t\tselector: '.sjpp-survival-series',\n\t\t\tcount: expectedCount,\n\t\t\tasync trigger() {\n\t\t\t\t//Test overlay bin changes are applied\n\t\t\t\tconfig2.term2.q.lst[2] = { startinclusive: true, stopinclusive: true, start: 12, stop: 15, label: '12 to 15' }\n\t\t\t\tconfig2.term2.q.lst.push({ start: 15, startinclusive: false, stopunbounded: true, label: '>15' })\n\t\t\t\tinner.app.dispatch({\n\t\t\t\t\ttype: 'plot_edit',\n\t\t\t\t\tid: inner.id,\n\t\t\t\t\tconfig: config2\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\n\t\ttest.equal(survCurves.length, expectedCount, `Should display the correct num of bins = ${expectedCount}`)\n\n\t\tif (test._ok) inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, term0 = agedx, custom bins', function (test) {\n\ttest.timeoutAfter(20000)\n\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\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}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\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(survival) {\n\t\tsurvival.on('postRender.test', null)\n\n\t\tconst inner = survival.Inner\n\t\tconst config = inner.state.config\n\n\t\t//Test data correctly appears\n\t\ttest.equal(config.term0.q.type, 'custom-bin', `Should correctly pass 'custom-bin' to config`)\n\n\t\t// Create a copy of the state config to modify, otherwise\n\t\t// a dispatch may not propagate to this survival component instance\n\t\t// since the state would just equal itself (nothing has changed so no need to rerender),\n\t\t// whereas a modified copy will not equal the original state\n\t\tconst config2 = structuredClone(config)\n\t\tconst expectedCount = 3\n\n\t\tconst survCurves = await detectGte({\n\t\t\telem: survival.Inner.dom.chartsDiv.node(),\n\t\t\tselector: '.sjpp-survival-series',\n\t\t\tcount: expectedCount,\n\t\t\tasync trigger() {\n\t\t\t\t//Test overlay bin changes are applied\n\t\t\t\tconfig2.term0.q.lst = [\n\t\t\t\t\t{ startunbounded: true, stop: 5, stopinclusive: false, label: '<5' },\n\t\t\t\t\t{ start: 5, stop: 8, startinclusive: true, stopinclusive: false, label: '5 to <8' },\n\t\t\t\t\t{ start: 8, startinclusive: true, stopunbounded: true, label: '>=8' }\n\t\t\t\t]\n\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: config2\n\t\t\t\t})\n\t\t\t}\n\t\t})\n\t\ttest.equal(survCurves.length, expectedCount, `Should display the correct num of bins = ${expectedCount}`)\n\n\t\tif (test._ok) inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, term2 = geneVariant', function (test) {\n\ttest.timeoutAfter(5000)\n\ttest.plan(4)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\tterm: {\n\t\t\t\t\t\tid: 'efs'\n\t\t\t\t\t},\n\t\t\t\t\tterm2: { term: { type: 'geneVariant', gene: 'TP53' } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet survivalDiv\n\tasync function runTests(survival) {\n\t\tsurvival.on('postRender.test', null)\n\t\tconst { chartsDiv, legendTip } = survival.Inner.dom\n\t\tsurvivalDiv = chartsDiv\n\t\ttest.equal(survivalDiv && survivalDiv.selectAll('.sjpp-survival-series').size(), 2, 'should render 2 surv series g')\n\t\ttest.equal(\n\t\t\tsurvivalDiv && survivalDiv.selectAll('.sjpp-survival-censored-x').size(),\n\t\t\t10,\n\t\t\t'should render 10 survival censored symbols'\n\t\t)\n\n\t\tconst atRiskLegend0 = await Locator.init(survivalDiv.node()).find(`[data-testid='sjpp-atrisk-seriesId']`).click(0)\n\t\t// NOTE: simulated color picker click leads to error \"A user gesture is required to show the color picker\"\n\t\t// directly call color change instead of simulated clicks\n\t\tconst colorInput = await Locator.init(legendTip.d).shows('input[type=\"color\"]').get(0)\n\t\tcolorInput.value = '#0000ff'\n\t\tcolorInput.dispatchEvent(new Event('change', { cancelable: true }))\n\t\tlegendTip.hide()\n\t\tawait sleep(100) // todo: use improved Locator methods to avoid using sleep()\n\t\ttest.equal(atRiskLegend0?.parentNode?.getAttribute('fill'), 'rgb(0, 0, 255)', 'should change the series color')\n\n\t\tawait survival.Inner.app.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: survival.id,\n\t\t\tconfig: {\n\t\t\t\tsettings: {\n\t\t\t\t\tsurvival: {\n\t\t\t\t\t\tatRiskVisible: false\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t})\n\n\t\tawait sleep(100) // todo: use improved Locator methods to avoid using sleep()\n\t\ttest.equal(\n\t\t\tsurvivalDiv.selectAll('.sjpp-atrisk-title').size(),\n\t\t\t0,\n\t\t\t'should hide at-risk legend when settings.survival.atRiskVisible is false'\n\t\t)\n\t\tif (test._ok) {\n\t\t\tsurvival.Inner.app.destroy()\n\t\t\tlegendTip.hide()\n\t\t}\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, term2 = geneExpression', function (test) {\n\ttest.timeoutAfter(8000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\tterm: { id: 'efs' },\n\t\t\t\t\tterm2: { term: { type: 'geneExpression', gene: 'TP53' } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet survivalDiv\n\tasync function runTests(survival) {\n\t\tsurvivalDiv = survival.Inner.dom.chartsDiv\n\t\ttest.equal(survivalDiv && survivalDiv.selectAll('.sjpp-survival-series').size(), 2, 'should render 2 surv series g')\n\t\ttest.equal(\n\t\t\tsurvivalDiv && survivalDiv.selectAll('.sjpp-survival-censored-x').size(),\n\t\t\t10,\n\t\t\t'should render 10 survival censored symbols'\n\t\t)\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, term2 = ssGSEA', function (test) {\n\ttest.timeoutAfter(8000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\tterm: { id: 'efs' },\n\t\t\t\t\tterm2: { term: { type: 'ssGSEA', id: 'HALLMARK_ADIPOGENESIS' } }\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet survivalDiv\n\tasync function runTests(survival) {\n\t\tsurvivalDiv = survival.Inner.dom.chartsDiv\n\t\ttest.equal(survival.Inner.state.config.term2.q.mode, 'discrete', 'term2 ssGSEA should default to discrete mode')\n\t\ttest.equal(survival.Inner.state.config.term2.q.type, 'custom-bin', 'term2 ssGSEA should default to custom bins')\n\t\ttest.equal(survivalDiv && survivalDiv.selectAll('.sjpp-survival-series').size(), 2, 'should render 2 surv series g')\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\ntape('survival term as term1, term2 = isoformExpression', function (test) {\n\ttest.timeoutAfter(8000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\tterm: { id: 'efs' },\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tterm: { isoform: 'ENST00000269305', gene: 'TP53', name: 'ENST00000269305 TPM', type: 'isoformExpression' }\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tsurvival: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet survivalDiv\n\tasync function runTests(survival) {\n\t\tsurvivalDiv = survival.Inner.dom.chartsDiv\n\t\ttest.equal(survival.Inner.state.config.term2.q.mode, 'discrete', 'term2 should default to discrete mode')\n\t\ttest.equal(survival.Inner.state.config.term2.q.type, 'custom-bin', 'term2 should default to custom bins')\n\t\ttest.equal(survivalDiv && survivalDiv.selectAll('.sjpp-survival-series').size(), 2, 'should render 2 surv series g')\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n\ntape('survival term as term1, term2 = dnaMethylation', function (test) {\n\ttest.timeoutAfter(8000)\n\trunpp({\n\t\tstate: {\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'survival',\n\t\t\t\t\tterm: { id: 'efs' },\n\t\t\t\t\tterm2: {\n\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\tchr: 'chr17',\n\t\t\t\t\t\t\tstart: 7661778,\n\t\t\t\t\t\t\tstop: 7687537,\n\t\t\t\t\t\t\ttype: 'dnaMethylation',\n\t\t\t\t\t\t\tunit: 'Average Beta Value',\n\t\t\t\t\t\t\tgenomicFeatureType: 'region',\n\t\t\t\t\t\t\tname: 'chr17:7661778-7687537 Average Beta Value'\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\tsurvival: {\n\t\t\tcallbacks: {\n\t\t\t\t'postRender.test': runTests\n\t\t\t}\n\t\t}\n\t})\n\n\tlet survivalDiv\n\tasync function runTests(survival) {\n\t\tsurvivalDiv = survival.Inner.dom.chartsDiv\n\t\ttest.equal(survival.Inner.state.config.term2.q.mode, 'discrete', 'term2 should default to discrete mode')\n\t\ttest.equal(survival.Inner.state.config.term2.q.type, 'custom-bin', 'term2 should default to custom bins')\n\t\ttest.equal(survivalDiv && survivalDiv.selectAll('.sjpp-survival-series').size(), 2, 'should render 2 surv series g')\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n"],
+  "mappings": 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+}