@sjcrh/proteinpaint-client 2.207.0 → 2.207.1

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

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/survival/test/survival.integration.spec.js", "../test/testdata/data.ts"],
+  "sourcesContent": ["import tape from 'tape'\nimport { termjson } from '#test/testdata/termjson.ts'\nimport * as helpers from '#test/front.helpers.js'\nimport { detectGte, sleep } from '#test/test.helpers.js'\nimport { getAgeCollectionFractionTw } from '#test/testdata/data.ts'\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\tsurvival term as term1, term2 = termCollection fraction\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, 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\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\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\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\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(1)\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\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 = 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\ntape('survival term as term1, term2 = termCollection fraction', 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: getAgeCollectionFractionTw()\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(\n\t\t\tsurvival.Inner.state.config.term2.type,\n\t\t\t'TermCollectionTWFraction',\n\t\t\t'term2 should be a fraction termCollection tw'\n\t\t)\n\t\ttest.equal(\n\t\t\tsurvivalDiv && survivalDiv.selectAll('.sjpp-survival-series').size(),\n\t\t\t2,\n\t\t\t'should render 1 surv series g per fraction bin'\n\t\t)\n\t\ttest.deepEqual(\n\t\t\tsurvival.Inner.refs.orderedKeys.series,\n\t\t\t['<0.8', '>0.8'],\n\t\t\t'should order the series by the fraction bins'\n\t\t)\n\n\t\tif (test._ok) survival.Inner.app.destroy()\n\t\ttest.end()\n\t}\n})\n", "import * as tt from '#types'\nimport { scTestSample } from '#shared/testData'\n/* \nexports a set of functions, each returns a TermdbTest-based term/tw/tvs that is complex and lengthy\nthat are used in unit/integration tests so to simplify test and avoid code duplication\n\nfunctions could accept parameters to return customized objects\n\n::NOTE::\n\nif some data contents needs to be changed, better off creating a new function and avoid changing existing one, as multiple tests may be coded against that data\n*/\n\nexport function getSamplelstTw() {\n\tconst values = [\n\t\t{\n\t\t\tsampleId: 42,\n\t\t\tsample: '2660'\n\t\t},\n\t\t{\n\t\t\tsampleId: 44,\n\t\t\tsample: '2688'\n\t\t},\n\t\t{\n\t\t\tsampleId: 45,\n\t\t\tsample: '2702'\n\t\t},\n\t\t{\n\t\t\tsampleId: 46,\n\t\t\tsample: '2716'\n\t\t},\n\t\t{\n\t\t\tsampleId: 59,\n\t\t\tsample: '2898'\n\t\t},\n\t\t{\n\t\t\tsampleId: 60,\n\t\t\tsample: '2912'\n\t\t},\n\t\t{\n\t\t\tsampleId: 67,\n\t\t\tsample: '3010'\n\t\t},\n\t\t{\n\t\t\tsampleId: 68,\n\t\t\tsample: '3024'\n\t\t},\n\t\t{\n\t\t\tsampleId: 69,\n\t\t\tsample: '3038'\n\t\t},\n\t\t{\n\t\t\tsampleId: 70,\n\t\t\tsample: '3052'\n\t\t},\n\t\t{\n\t\t\tsampleId: 73,\n\t\t\tsample: '3094'\n\t\t},\n\t\t{\n\t\t\tsampleId: 79,\n\t\t\tsample: '3178'\n\t\t},\n\t\t{\n\t\t\tsampleId: 80,\n\t\t\tsample: '3192'\n\t\t}\n\t]\n\treturn {\n\t\tterm: {\n\t\t\tname: 'termdbtest samplelst',\n\t\t\ttype: 'samplelst',\n\t\t\tvalues: {\n\t\t\t\t'Group 1': {\n\t\t\t\t\tkey: 'Group 1',\n\t\t\t\t\tlabel: 'Group 1',\n\t\t\t\t\tlist: values\n\t\t\t\t},\n\t\t\t\t'Not in Group 1': {\n\t\t\t\t\tkey: 'Not in Group 1',\n\t\t\t\t\tlabel: 'Not in Group 1',\n\t\t\t\t\tlist: values\n\t\t\t\t}\n\t\t\t}\n\t\t},\n\t\tq: {\n\t\t\tmode: 'discrete',\n\t\t\tgroups: [\n\t\t\t\t{\n\t\t\t\t\tname: 'Group 1',\n\t\t\t\t\tin: true,\n\t\t\t\t\tvalues\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tname: 'Not in Group 1',\n\t\t\t\t\tin: false,\n\t\t\t\t\tvalues\n\t\t\t\t}\n\t\t\t],\n\t\t\tisAtomic: true\n\t\t}\n\t}\n}\n\nexport function getCategoryGroupsetting() {\n\treturn {\n\t\tid: 'diaggrp',\n\t\tq: {\n\t\t\ttype: 'custom-groupset',\n\t\t\tcustomset: {\n\t\t\t\tname: 'A versus B',\n\t\t\t\tgroups: [\n\t\t\t\t\t{\n\t\t\t\t\t\tname: 'Test A',\n\t\t\t\t\t\ttype: 'values',\n\t\t\t\t\t\tvalues: [{ key: 'Acute lymphoblastic leukemia' }, { key: 'Wilms tumor' }]\n\t\t\t\t\t},\n\t\t\t\t\t{\n\t\t\t\t\t\tname: 'Test B',\n\t\t\t\t\t\ttype: 'values',\n\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t{ key: 'Central nervous system (CNS)' },\n\t\t\t\t\t\t\t{ key: 'Acute myeloid leukemia' },\n\t\t\t\t\t\t\t{ key: 'Non-Hodgkin lymphoma' }\n\t\t\t\t\t\t]\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function getGenesetMutTw() {\n\treturn {\n\t\tterm: {\n\t\t\tgenes: [\n\t\t\t\t{ kind: 'gene', gene: 'TP53', type: 'geneVariant' },\n\t\t\t\t{ kind: 'gene', gene: 'KRAS', type: 'geneVariant' },\n\t\t\t\t{ kind: 'gene', gene: 'AKT1', type: 'geneVariant' },\n\t\t\t\t{ kind: 'gene', gene: 'BCR', type: 'geneVariant' }\n\t\t\t],\n\t\t\ttype: 'geneVariant'\n\t\t},\n\t\tq: { type: 'predefined-groupset' }\n\t}\n}\n\nexport function getGeneVariantTw(position = false) {\n\treturn {\n\t\tterm: {\n\t\t\tgenes: [\n\t\t\t\tposition\n\t\t\t\t\t? { kind: 'coord', chr: 'chr12', start: 25205246, stop: 25250936, name: 'KRASregion', type: 'geneVariant' }\n\t\t\t\t\t: { kind: 'gene', gene: 'TP53', type: 'geneVariant' }\n\t\t\t],\n\t\t\ttype: 'geneVariant'\n\t\t},\n\t\tq: { type: 'predefined-groupset', predefined_groupset_idx: 0, hiddenValues: {} }\n\t}\n}\n\nexport function getSsgseaTw(isBin = false) {\n\treturn {\n\t\tterm: { id: 'HALLMARK_ADIPOGENESIS', type: 'ssGSEA', name: 'HALLMARK_ADIPOGENESIS' },\n\t\tq: isBin\n\t\t\t? {\n\t\t\t\t\ttype: 'regular-bin',\n\t\t\t\t\tstartinclusive: true,\n\t\t\t\t\tbin_size: 0.2,\n\t\t\t\t\tfirst_bin: { stop: -0.4 },\n\t\t\t\t\tlast_bin: { start: 0.8 },\n\t\t\t\t\tmode: 'discrete'\n\t\t\t  }\n\t\t\t: { mode: 'continuous' }\n\t}\n}\n\nexport function getFilter_agedx(start = 10) {\n\treturn {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: 'and',\n\t\tlst: [\n\t\t\t{\n\t\t\t\ttag: 'filterUiRoot',\n\t\t\t\ttype: 'tvslst',\n\t\t\t\tjoin: '',\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\tterm: { id: 'agedx', type: 'float', name: 'Age of diagnosis' },\n\t\t\t\t\t\t\tranges: [\n\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\tstart,\n\t\t\t\t\t\t\t\t\tstartinclusive: false,\n\t\t\t\t\t\t\t\t\tstartunbounded: false,\n\t\t\t\t\t\t\t\t\tstop: 16,\n\t\t\t\t\t\t\t\t\tstopinclusive: false,\n\t\t\t\t\t\t\t\t\tstopunbounded: false\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\ttype: 'tvs'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t]\n\t}\n}\nexport function getFilter_male() {\n\treturn {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: 'and',\n\t\tlst: [\n\t\t\t{\n\t\t\t\ttag: 'filterUiRoot',\n\t\t\t\ttype: 'tvslst',\n\t\t\t\tjoin: '',\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\tterm: { id: 'sex' },\n\t\t\t\t\t\t\tvalues: [{ key: '1', label: 'Male' }]\n\t\t\t\t\t\t},\n\t\t\t\t\t\ttype: 'tvs'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t]\n\t}\n}\nexport function getFilter_Hodgkin() {\n\treturn {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: 'and',\n\t\tlst: [\n\t\t\t{\n\t\t\t\ttag: 'filterUiRoot',\n\t\t\t\ttype: 'tvslst',\n\t\t\t\tjoin: '',\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\tterm: { id: 'diaggrp', type: 'categorical', name: 'diaggrp' },\n\t\t\t\t\t\t\tvalues: [{ key: 'Hodgkin lymphoma', name: 'Hodgkin' }]\n\t\t\t\t\t\t},\n\t\t\t\t\t\ttype: 'tvs'\n\t\t\t\t\t}\n\t\t\t\t]\n\t\t\t}\n\t\t]\n\t}\n}\nexport function getFilter_genemutationset(isnot = false) {\n\treturn {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin: 'and',\n\t\tlst: [\n\t\t\t{\n\t\t\t\ttag: 'cohortFilter',\n\t\t\t\ttype: 'tvs',\n\t\t\t\ttvs: { term: { id: 'subcohort', type: 'multivalue' }, values: [{ key: 'ABC', label: 'ABC' }] }\n\t\t\t},\n\t\t\t{\n\t\t\t\ttype: 'tvslst',\n\t\t\t\tin: true,\n\t\t\t\tjoin: '',\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\tid: 'snvindel_somatic',\n\t\t\t\t\t\t\t\tquery: 'snvindel',\n\t\t\t\t\t\t\t\tname: 'SNV/indel (somatic)',\n\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\ttype: 'dtsnvindel',\n\t\t\t\t\t\t\t\tdt: 1,\n\t\t\t\t\t\t\t\tvalues: { M: { label: 'MISSENSE' }, F: { label: 'FRAMESHIFT' }, WT: { label: 'Wildtype' } },\n\t\t\t\t\t\t\t\tname_noOrigin: 'SNV/indel',\n\t\t\t\t\t\t\t\torigin: 'somatic',\n\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\tid: 'HALLMARK_ADIPOGENESIS',\n\t\t\t\t\t\t\t\t\tname: 'HALLMARK_ADIPOGENESIS',\n\t\t\t\t\t\t\t\t\tgenes: [\n\t\t\t\t\t\t\t\t\t\t{ kind: 'gene', id: 'TP53', gene: 'TP53', name: 'TP53', type: 'geneVariant' },\n\t\t\t\t\t\t\t\t\t\t{ kind: 'gene', id: 'AKT1', gene: 'AKT1', name: 'AKT1', type: 'geneVariant' },\n\t\t\t\t\t\t\t\t\t\t{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' },\n\t\t\t\t\t\t\t\t\t\t{ kind: 'gene', id: 'BCR', gene: 'BCR', name: 'BCR', type: 'geneVariant' }\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\tvalues: [\n\t\t\t\t\t\t\t\t{ key: 'M', label: 'MISSENSE', value: 'M', bar_width_frac: null },\n\t\t\t\t\t\t\t\t{ key: 'F', label: 'FRAMESHIFT', value: 'F', bar_width_frac: null }\n\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\tisnot,\n\t\t\t\t\t\t\tgenotype: 'variant',\n\t\t\t\t\t\t\tmcount: 'any'\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t],\n\t\t\t\ttag: 'filterUiRoot'\n\t\t\t}\n\t\t]\n\t}\n}\n\n// for ds using categorical cnv, e.g. gdc or mb\n// TODO shrink size!\n// uses kras which exists in tdbtest, and may be used in integration test\nexport function getCnv_categorical() {\n\treturn {\n\t\tterm: {\n\t\t\ttype: 'geneVariant',\n\t\t\tchildTerms: [\n\t\t\t\t{\n\t\t\t\t\tid: 'snvindel',\n\t\t\t\t\tquery: 'snvindel',\n\t\t\t\t\tname: 'SNV/indel',\n\t\t\t\t\tparent_id: null,\n\t\t\t\t\tisleaf: true,\n\t\t\t\t\ttype: 'dtsnvindel',\n\t\t\t\t\tdt: 1,\n\t\t\t\t\tvalues: {\n\t\t\t\t\t\tM: { key: 'M', label: 'MISSENSE' },\n\t\t\t\t\t\tS: { key: 'S', label: 'SILENT' },\n\t\t\t\t\t\tIntron: { key: 'Intron', label: 'INTRON' },\n\t\t\t\t\t\tD: { key: 'D', label: 'PROTEINDEL' }\n\t\t\t\t\t},\n\t\t\t\t\tname_noOrigin: 'SNV/indel',\n\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t}\n\t\t\t\t},\n\t\t\t\t{\n\t\t\t\t\tid: 'cnv',\n\t\t\t\t\tquery: 'cnv',\n\t\t\t\t\tname: 'CNV',\n\t\t\t\t\tparent_id: null,\n\t\t\t\t\tisleaf: true,\n\t\t\t\t\ttype: 'dtcnv',\n\t\t\t\t\tdt: 4,\n\t\t\t\t\tvalues: {\n\t\t\t\t\t\tCNV_amplification: { key: 'CNV_amplification', label: 'Amplification' },\n\t\t\t\t\t\tCNV_amp: { key: 'CNV_amp', label: 'Gain' },\n\t\t\t\t\t\tCNV_loss: { key: 'CNV_loss', label: 'Heterozygous Deletion' }\n\t\t\t\t\t},\n\t\t\t\t\tname_noOrigin: 'CNV',\n\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t],\n\t\t\tid: 'KRAS',\n\t\t\tname: 'KRAS',\n\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }],\n\t\t\tgroupsetting: {\n\t\t\t\tdisabled: false,\n\t\t\t\tlst: [\n\t\t\t\t\t{\n\t\t\t\t\t\tname: 'SNV/indel',\n\t\t\t\t\t\tdt: 1,\n\t\t\t\t\t\tgroups: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS SNV/indel Mutated',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'snvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'snvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'SNV/indel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtsnvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 1,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tM: { key: 'M', label: 'MISSENSE' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tS: { key: 'S', label: 'SILENT' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tIntron: { key: 'Intron', label: 'INTRON' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tD: { key: 'D', label: 'PROTEINDEL' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'SNV/indel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t\t\t\t\t\t\t{ key: 'M', label: 'MISSENSE', value: 'M' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t{ key: 'S', label: 'SILENT', value: 'S' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t{ key: 'Intron', label: 'INTRON', value: 'Intron' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t{ key: 'D', label: 'PROTEINDEL', value: 'D' }\n\t\t\t\t\t\t\t\t\t\t\t\t],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'variant',\n\t\t\t\t\t\t\t\t\t\t\t\tmcount: 'any',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\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},\n\t\t\t\t\t\t\t\tcolor: '#e75480'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS SNV/indel Wildtype',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'snvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'snvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'SNV/indel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtsnvindel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 1,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tM: { key: 'M', label: 'MISSENSE' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tS: { key: 'S', label: 'SILENT' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tIntron: { key: 'Intron', label: 'INTRON' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tD: { key: 'D', label: 'PROTEINDEL' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'SNV/indel',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'wt',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\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},\n\t\t\t\t\t\t\t\tcolor: '#D3D3D3'\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\t{\n\t\t\t\t\t\tname: 'CNV',\n\t\t\t\t\t\tdt: 4,\n\t\t\t\t\t\tgroups: [\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS CNV Amplification',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtcnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 4,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amplification: { key: 'CNV_amplification', label: 'Amplification' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amp: { key: 'CNV_amp', label: 'Gain' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_loss: { key: 'CNV_loss', label: 'Heterozygous Deletion' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [{ key: 'CNV_amplification', label: 'Amplification', value: 'CNV_amplification' }],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'variant',\n\t\t\t\t\t\t\t\t\t\t\t\tmcount: 'any',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\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},\n\t\t\t\t\t\t\t\tcolor: '#ff0000'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS CNV Gain',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtcnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 4,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amplification: { key: 'CNV_amplification', label: 'Amplification' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amp: { key: 'CNV_amp', label: 'Gain' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_loss: { key: 'CNV_loss', label: 'Heterozygous Deletion' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [{ key: 'CNV_amp', label: 'Gain', value: 'CNV_amp' }],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'variant',\n\t\t\t\t\t\t\t\t\t\t\t\tmcount: 'any',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\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},\n\t\t\t\t\t\t\t\tcolor: '#e9a3c9'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS CNV Heterozygous Deletion',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtcnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 4,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amplification: { key: 'CNV_amplification', label: 'Amplification' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amp: { key: 'CNV_amp', label: 'Gain' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_loss: { key: 'CNV_loss', label: 'Heterozygous Deletion' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [{ key: 'CNV_loss', label: 'Heterozygous Deletion', value: 'CNV_loss' }],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'variant',\n\t\t\t\t\t\t\t\t\t\t\t\tmcount: 'any',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\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},\n\t\t\t\t\t\t\t\tcolor: '#a1d76a'\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tname: 'KRAS CNV Wildtype',\n\t\t\t\t\t\t\t\ttype: 'filter',\n\t\t\t\t\t\t\t\tfilter: {\n\t\t\t\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\t\t\t\tin: true,\n\t\t\t\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\t\t\t\tlst: [\n\t\t\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\t\t\t\t\t\t\ttvs: {\n\t\t\t\t\t\t\t\t\t\t\t\tterm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tquery: 'cnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparent_id: null,\n\t\t\t\t\t\t\t\t\t\t\t\t\tisleaf: true,\n\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'dtcnv',\n\t\t\t\t\t\t\t\t\t\t\t\t\tdt: 4,\n\t\t\t\t\t\t\t\t\t\t\t\t\tvalues: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amplification: { key: 'CNV_amplification', label: 'Amplification' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_amp: { key: 'CNV_amp', label: 'Gain' },\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tCNV_loss: { key: 'CNV_loss', label: 'Heterozygous Deletion' }\n\t\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\t\tname_noOrigin: 'CNV',\n\t\t\t\t\t\t\t\t\t\t\t\t\tparentTerm: {\n\t\t\t\t\t\t\t\t\t\t\t\t\t\ttype: 'geneVariant',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tid: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tname: 'KRAS',\n\t\t\t\t\t\t\t\t\t\t\t\t\t\tgenes: [{ kind: 'gene', id: 'KRAS', gene: 'KRAS', name: 'KRAS', type: 'geneVariant' }]\n\t\t\t\t\t\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t\t\t\t\t\tvalues: [],\n\t\t\t\t\t\t\t\t\t\t\t\tgenotype: 'wt',\n\t\t\t\t\t\t\t\t\t\t\t\texcludeGeneName: true\n\t\t\t\t\t\t\t\t\t\t\t}\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},\n\t\t\t\t\t\t\t\tcolor: '#D3D3D3'\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\tq: { type: 'predefined-groupset', predefined_groupset_idx: 1, cnvMaxLength: 2000000, hiddenValues: {} }\n\t}\n}\n\nexport function getScgeneexpTw(gene = 'KRAS') {\n\treturn {\n\t\tterm: {\n\t\t\ttype: tt.SINGLECELL_GENE_EXPRESSION,\n\t\t\tid: gene,\n\t\t\tgene,\n\t\t\tname: gene,\n\t\t\tsample: {\n\t\t\t\tsID: scTestSample\n\t\t\t}\n\t\t},\n\t\tq: {\n\t\t\tmode: 'continuous'\n\t\t}\n\t}\n}\nexport function getScctTw() {\n\treturn {\n\t\tterm: {\n\t\t\ttype: tt.SINGLECELL_CELLTYPE,\n\t\t\tid: 'CellType',\n\t\t\tname: 'Cell Type',\n\t\t\tsample: {\n\t\t\t\tsID: scTestSample\n\t\t\t},\n\t\t\tplot: 'UMAP',\n\t\t\tcolorBy: 'CellType',\n\t\t\tvalues: {\n\t\t\t\tT_NK: {\n\t\t\t\t\tkey: 'T_NK',\n\t\t\t\t\tvalue: 'T_NK'\n\t\t\t\t},\n\t\t\t\tBlast: {\n\t\t\t\t\tkey: 'Blast',\n\t\t\t\t\tvalue: 'Blast'\n\t\t\t\t},\n\t\t\t\tMonocyte: {\n\t\t\t\t\tkey: 'Monocyte',\n\t\t\t\t\tvalue: 'Monocyte'\n\t\t\t\t}\n\t\t\t},\n\t\t\tgroupsetting: {\n\t\t\t\tdisabled: false\n\t\t\t}\n\t\t}\n\t}\n}\n/** TODO: Pseudobulk data is not enabled in TermdbTest!!\n * Do not use until data is available. Capturing structure for\n * clarity during development. */\nexport function getPseudobulkTW(nameId = 'Blast') {\n\treturn {\n\t\tterm: {\n\t\t\ttype: tt.PSEUDOBULK,\n\t\t\tassay: 'geneExpression',\n\t\t\tmemberId: 'CellType',\n\t\t\tname: nameId,\n\t\t\tid: nameId\n\t\t}\n\t}\n}\nexport function getPseudobulkTermCollection(termIds = ['Blast', 'Monocyte', 'T_NK']) {\n\tconst termlst = termIds.map(id => getPseudobulkTW(id).term)\n\n\treturn {\n\t\ttype: 'TermCollectionTWCont',\n\t\tterm: {\n\t\t\ttype: tt.TERM_COLLECTION,\n\t\t\tmemberType: 'numeric',\n\t\t\tid: 'test',\n\t\t\tname: 'Test pseudobulk term collection',\n\t\t\ttermIds,\n\t\t\ttermlst,\n\t\t\tisCustom: true\n\t\t},\n\t\tq: {\n\t\t\tmode: 'continuous',\n\t\t\ttype: 'values',\n\t\t\tlst: []\n\t\t}\n\t}\n}\n\n////////////// following are gdc-specific! may move to separate file\n\nexport function getGdcDiseaseGroupsetting() {\n\treturn {\n\t\tterm: { type: 'categorical', id: 'case.disease_type' },\n\t\tq: {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'custom-groupset',\n\t\t\thiddenValues: {},\n\t\t\tcustomset: {\n\t\t\t\tgroups: [\n\t\t\t\t\t{ name: 'Excluded categories', type: 'values', uncomputable: true, values: [] },\n\t\t\t\t\t{\n\t\t\t\t\t\tname: 'Group Mix',\n\t\t\t\t\t\ttype: 'values',\n\t\t\t\t\t\tuncomputable: false,\n\t\t\t\t\t\tvalues: [\n\t\t\t\t\t\t\t{ key: 'Ductal and Lobular Neoplasms', label: 'Ductal and Lobular Neoplasms', samplecount: 2829 },\n\t\t\t\t\t\t\t{ key: 'Complex Epithelial Neoplasms', label: 'Complex Epithelial Neoplasms', samplecount: 69 },\n\t\t\t\t\t\t\t{ key: 'Not Applicable', label: 'Not Applicable', samplecount: 9 },\n\t\t\t\t\t\t\t{ key: 'Epithelial Neoplasms, NOS', label: 'Epithelial Neoplasms, NOS', samplecount: 1221 },\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tkey: 'Cystic, Mucinous and Serous Neoplasms',\n\t\t\t\t\t\t\t\tlabel: 'Cystic, Mucinous and Serous Neoplasms',\n\t\t\t\t\t\t\t\tsamplecount: 17\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tkey: 'Adnexal and Skin Appendage Neoplasms',\n\t\t\t\t\t\t\t\tlabel: 'Adnexal and Skin Appendage Neoplasms',\n\t\t\t\t\t\t\t\tsamplecount: 1\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{ key: 'Adenomas and Adenocarcinomas', label: 'Adenomas and Adenocarcinomas', samplecount: 18 },\n\t\t\t\t\t\t\t{ key: 'Squamous Cell Neoplasms', label: 'Squamous Cell Neoplasms', samplecount: 3 },\n\t\t\t\t\t\t\t{ key: 'Nevi and Melanomas', label: 'Nevi and Melanomas', samplecount: 7 },\n\t\t\t\t\t\t\t{ key: 'Basal Cell Neoplasms', label: 'Basal Cell Neoplasms', samplecount: 1 },\n\t\t\t\t\t\t\t{ key: 'Fibroepithelial Neoplasms', label: 'Fibroepithelial Neoplasms', samplecount: 2 },\n\t\t\t\t\t\t\t{ key: 'Neoplasms, NOS', label: 'Neoplasms, NOS', samplecount: 1547 },\n\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\tkey: 'Soft Tissue Tumors and Sarcomas, NOS',\n\t\t\t\t\t\t\t\tlabel: 'Soft Tissue Tumors and Sarcomas, NOS',\n\t\t\t\t\t\t\t\tsamplecount: 30\n\t\t\t\t\t\t\t},\n\t\t\t\t\t\t\t{ key: 'Not Reported', label: 'Not Reported', samplecount: 34 },\n\t\t\t\t\t\t\t{ key: 'Meningiomas', label: 'Meningiomas', samplecount: 29 },\n\t\t\t\t\t\t\t{ key: 'Mature B-Cell Lymphomas', label: 'Mature B-Cell Lymphomas', samplecount: 3 },\n\t\t\t\t\t\t\t{ key: 'Lymphoid Leukemias' },\n\t\t\t\t\t\t\t{ key: 'Myeloid Leukemias' },\n\t\t\t\t\t\t\t{ key: 'Acute Lymphoblastic Leukemia' },\n\t\t\t\t\t\t\t{ key: 'Neuroepitheliomatous Neoplasms' },\n\t\t\t\t\t\t\t{ key: 'Complex Mixed and Stromal Neoplasms' }\n\t\t\t\t\t\t]\n\t\t\t\t\t},\n\t\t\t\t\t{ name: 'Group Brain', type: 'values', uncomputable: false, values: [{ key: 'Gliomas', label: 'Gliomas' }] }\n\t\t\t\t]\n\t\t\t}\n\t\t}\n\t}\n}\n\nexport function getCategoricalTermcollectionTw() {\n\treturn {\n\t\ttype: 'TermCollectionTWQual',\n\t\tterm: { type: 'termCollection', name: 'Assay Availability' }\n\t}\n}\n\nexport function getAgeCollectionFractionTw() {\n\treturn {\n\t\ttype: 'TermCollectionTWFraction',\n\t\tterm: {\n\t\t\ttype: 'termCollection',\n\t\t\ttermIds: ['agedx', 'a_death', 'a_ndi', 'agelastvisit'],\n\t\t\tname: 'Fake Collection 1', // NOTE this name must match with the termCollection entry in termdbtest\n\t\t\tmemberType: 'numeric'\n\t\t},\n\t\tq: {\n\t\t\tmode: 'discrete',\n\t\t\tnumerators: ['a_death'],\n\t\t\tdenominators: ['agedx', 'a_death'],\n\t\t\ttype: 'custom-bin',\n\t\t\tlst: [\n\t\t\t\t{ startunbounded: true, stop: 0.8, label: '<0.8' },\n\t\t\t\t{ stopunbounded: true, start: 0.8, label: '>0.8' }\n\t\t\t]\n\t\t}\n\t}\n}\nexport function getIsoformExpCollectionFractionTw() {\n\treturn {\n\t\ttype: 'TermCollectionTWFraction',\n\t\tterm: {\n\t\t\ttype: 'termCollection',\n\t\t\tisCustom: true,\n\t\t\tmemberType: 'numeric',\n\t\t\tname: 'KRAS Isoforms (TPM)',\n\t\t\ttermlst: [\n\t\t\t\t{ id: 'ENST00000256078', name: 'ENST00000256078', type: 'isoformExpression', isoform: 'ENST00000256078' },\n\t\t\t\t{ id: 'ENST00000311936', name: 'ENST00000311936', type: 'isoformExpression', isoform: 'ENST00000311936' }\n\t\t\t]\n\t\t},\n\t\tq: {\n\t\t\tmode: 'discrete',\n\t\t\ttype: 'custom-bin',\n\t\t\tlst: [\n\t\t\t\t{ startunbounded: true, stop: 0.1, startinclusive: false, stopinclusive: true, label: 'low0.1' },\n\t\t\t\t{ start: 0.1, startinclusive: false, stopinclusive: false, stopunbounded: true, label: 'high0.1' }\n\t\t\t],\n\t\t\tdenominators: ['ENST00000256078', 'ENST00000311936'],\n\t\t\tnumerators: ['ENST00000256078']\n\t\t}\n\t}\n}\n"],
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