@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/hierCluster.integration.spec-AF4L3YT6.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/matrix/test/hierCluster.integration.spec.js"],
-  "sourcesContent": ["import tape from 'tape'\nimport * as helpers from '#test/front.helpers.js'\nimport { sleep, detectOne, detectGte, detectLst, detectAttr } from '#test/test.helpers.js'\nimport { select } from 'd3-selection'\nimport { appInit } from '#plots/plot.app.js'\nimport { fillTermWrapper } from '#termsetting'\nimport { TermTypes } from '#shared/terms.js'\n/**************\n test sections\n\nbasic render\nfilter\navoid race condition\ndendrogram click\n\n***************/\n\ntape('\\n', function (test) {\n\ttest.comment('-***- plots/hierCluster.js -***-')\n\ttest.end()\n})\n\ntape('basic render', async test => {\n\ttest.timeoutAfter(4000)\n\tconst { app, hc } = await getHierClusterApp({ terms: getGenes() })\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 4, 'should render 4 gene rows')\n\ttest.equal(hc.dom.sampleLabelG.selectAll('.sjpp-matrix-label').size(), 60, 'should render 60 sample columns') // update \"60\" when data changes\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('filter', async test => {\n\ttest.timeoutAfter(4000)\n\tconst { app, hc } = await getHierClusterApp({\n\t\tterms: getGenes(),\n\t\tfilter: {\n\t\t\ttype: 'tvslst',\n\t\t\tjoin: '',\n\t\t\tin: true,\n\t\t\tlst: [{ type: 'tvs', tvs: { term: { id: 'diaggrp' }, values: [{ key: 'Acute lymphoblastic leukemia' }] } }]\n\t\t}\n\t})\n\ttest.equal(hc.dom.sampleLabelG.selectAll('.sjpp-matrix-label').size(), 36, 'should render 36 sample columns') // update \"36\" when data changes\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('avoid race condition - specified gene list', async test => {\n\t// !!!\n\t// to allow an app or chart code to fail due to race condition,\n\t// hardcode a constant value or comment out the ++ for the sequenceID\n\t// in rx/src/StoreApi.write()\n\t// !!!\n\ttest.timeoutAfter(4000)\n\ttest.plan(4)\n\tconst { app, hc } = await getHierClusterApp({ terms: getGenes() })\n\tconst termgroups = structuredClone(hc.config.termgroups)\n\tconst lst = await Promise.all([\n\t\tfillTermWrapper({ term: { gene: 'KRAS', name: 'KRAS', type: 'geneExpression' } }, app.vocabApi),\n\t\tfillTermWrapper({ term: { gene: 'AKT1', name: 'AKT1', type: 'geneExpression' } }, app.vocabApi),\n\t\tfillTermWrapper({ term: { gene: 'TP53', name: 'TP53', type: 'geneExpression' } }, app.vocabApi),\n\t\tfillTermWrapper({ term: { gene: 'BCR', name: 'BCR', type: 'geneExpression' } }, app.vocabApi)\n\t])\n\ttermgroups[0].lst = lst\n\tconst responseDelay = 250\n\thc.origRequestData = hc.requestData\n\thc.requestData = async () => {\n\t\tconst lst = hc.config.termgroups[0].lst\n\t\tconst data = await hc.origRequestData({})\n\t\tif (lst.length === 3) return data\n\t\t// artificially delay response to first request, to simulate a race condition\n\t\t// do this after the network request, so that this.api.getAbortSignal() in hc.requestData()\n\t\t// will generate the correct signal based on the order of dispatch/sequenceId\n\t\tawait sleep(250)\n\t\treturn data\n\t}\n\n\tconst prom = {}\n\tconst postRenderTest = new Promise(resolve => {\n\t\tprom.resolve = resolve\n\t})\n\tapp.on('postRender.test1', () => {\n\t\tapp.on('postRender.test1', null)\n\t\tprom.resolve()\n\t})\n\n\tawait Promise.all([\n\t\tapp.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: hc.id,\n\t\t\tconfig: { termgroups }\n\t\t}),\n\t\t(async () => {\n\t\t\tawait sleep(0)\n\t\t\tconst termgroups = structuredClone(hc.config.termgroups)\n\t\t\ttermgroups[0].lst = lst.slice(0, 3)\n\t\t\tawait app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: hc.id,\n\t\t\t\tconfig: { termgroups }\n\t\t\t})\n\t\t})()\n\t])\n\n\tawait postRenderTest\n\tawait sleep(responseDelay + 500)\n\t// run tests after the delayed response, as part of simulating the race condition\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 gene rows')\n\tconst rects = hc.dom.seriesesG.selectAll('.sjpp-mass-series-g rect')\n\tconst hits = rects.filter(d => d.key !== 'BCR' && d.value.class != 'WT' && d.value.class != 'Blank')\n\ttest.equal(\n\t\trects.size(),\n\t\t180,\n\t\t'should have the expected total number of matrix cell rects, inlcuding WT and not tested'\n\t)\n\ttest.equal(hits.size(), 180, 'should have the expected number of matrix cell rects with hits')\n\ttest.equal(\n\t\tapp.Inner.dom.holder\n\t\t\t.selectAll('.sja_errorbar')\n\t\t\t.filter(function () {\n\t\t\t\treturn this.style.display != 'none'\n\t\t\t})\n\t\t\t.size(),\n\t\t0,\n\t\t'should not display errors'\n\t)\n\tif (test._ok) app.destroy()\n})\n\ntape('avoid race condition - reused fetch response cache', async test => {\n\t// !!!\n\t// to allow an app or chart code to fail due to race condition,\n\t// hardcode a constant value or comment out the ++ for the sequenceID\n\t// in rx/src/StoreApi.write()\n\t// !!!\n\ttest.timeoutAfter(4000)\n\ttest.plan(4)\n\t// the same terms lst as the previous tape() test above will trigger the reuse of cached fetch response\n\tconst { app, hc } = await getHierClusterApp({ terms: getGenes() })\n\tconst termgroups = structuredClone(hc.config.termgroups)\n\tconst responseDelay = 250\n\thc.origRequestData = hc.requestData\n\thc.requestData = async () => {\n\t\tconst lst = hc.config.termgroups[0].lst\n\t\tconst data = await hc.origRequestData({})\n\t\tif (lst.length === 3) return data\n\t\treturn data\n\t\t// artificially delay response to first request, to simulate a race condition\n\t\tawait sleep(responseDelay)\n\t\treturn data\n\t}\n\n\tconst prom = {}\n\tconst postRenderTest = new Promise(resolve => {\n\t\tprom.resolve = resolve\n\t})\n\tapp.on('postRender.test1', () => {\n\t\tapp.on('postRender.test1', null)\n\t\tprom.resolve()\n\t})\n\n\tawait Promise.all([\n\t\tapp.dispatch({\n\t\t\ttype: 'plot_edit',\n\t\t\tid: hc.id,\n\t\t\tconfig: { termgroups }\n\t\t}),\n\t\t(async () => {\n\t\t\t// sleep() >1 second will not cause an error when reusing a cached fetch response;\n\t\t\t// sleep(0) below is worst case for testing\n\t\t\tawait sleep(0)\n\t\t\tconst _termgroups = structuredClone(termgroups)\n\t\t\t_termgroups[0].lst = _termgroups[0].lst.slice(0, 3)\n\t\t\tawait app.dispatch({\n\t\t\t\ttype: 'plot_edit',\n\t\t\t\tid: hc.id,\n\t\t\t\tconfig: { termgroups: _termgroups }\n\t\t\t})\n\t\t})()\n\t])\n\n\tawait postRenderTest\n\tawait sleep(responseDelay + 500)\n\t// run tests after the delayed response, as part of simulating the race condition\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 gene rows')\n\tconst rects = hc.dom.seriesesG.selectAll('.sjpp-mass-series-g rect')\n\tconst hits = rects.filter(d => d.key !== 'BCR' && d.value.class != 'WT' && d.value.class != 'Blank')\n\ttest.equal(\n\t\trects.size(),\n\t\t180,\n\t\t'should have the expected total number of matrix cell rects, inlcuding WT and not tested'\n\t)\n\ttest.equal(hits.size(), 180, 'should have the expected number of matrix cell rects with hits')\n\ttest.equal(\n\t\tapp.Inner.dom.holder\n\t\t\t.selectAll('.sja_errorbar')\n\t\t\t.filter(function () {\n\t\t\t\treturn this.style.display != 'none'\n\t\t\t})\n\t\t\t.size(),\n\t\t0,\n\t\t'should not display errors'\n\t)\n\tif (test._ok) app.destroy()\n})\n\ntape('dendrogram click', async function (test) {\n\ttest.timeoutAfter(5000)\n\ttest.plan(3)\n\n\tlet numRenders = 0\n\tconst { app, hc } = await getHierClusterApp({ terms: getGenes() })\n\n\tconst img = await detectOne({ elem: hc.dom.topDendrogram.node(), selector: 'image' })\n\tconst svgBox = hc.dom.svg.node().getBoundingClientRect()\n\tconst imgBox = img.getBBox()\n\t// helper to see onscreen the x, y position of the click\n\t// select('body')\n\t// \t.append('div')\n\t// \t.style('position', 'absolute')\n\t// \t.style('top', svgBox.y + imgBox.y + imgBox.height/2)\n\t// \t.style('left', svgBox.x + hc.dimensions.xOffset + imgBox.x + imgBox.width/2)\n\t// \t.style('width', '5px').style('height', '5px')\n\t// \t.style('background-color', '#00f')\n\n\timg.dispatchEvent(\n\t\tnew MouseEvent('click', {\n\t\t\t//'view': window,\n\t\t\tbubbles: true,\n\t\t\tcancelable: true,\n\t\t\tclientX: svgBox.x + hc.dimensions.xOffset + imgBox.x + imgBox.width / 2,\n\t\t\tclientY: svgBox.y + imgBox.y + imgBox.height / 2\n\t\t})\n\t)\n\n\t// not able to nail down all the expected dataURI strings based on env\n\t// const dataUriEnd = hc.dom.topDendrogram.select('image')?.attr('href').slice(-60) || ''\n\t// const expectedUriEnd =\n\t// \twindow.devicePixelRatio === 1 && window.navigator.userAgent.includes('Electron')\n\t// \t\t? `VXLf89aL9WK9WC/DBawX62X4bDm168v/A9duR9df7eS8AAAAAElFTkSuQmCC`\n\t// \t\t: window.devicePixelRatio === 1\n\t// \t\t? `IyHnD+cP5w/nj/4CjhfHS/9qObXnl/8PkgA61yIPYtsAAAAASUVORK5CYII=`\n\t// \t\t: window.navigator.userAgent?.includes(`Electron`) // headless test\n\t// \t\t? `PgFeeOlp0S+88MJLnwAvvPS06Je9vfwCG6yWyx1uowQAAAAASUVORK5CYII=` // retina screen, headless\n\t// \t\t: `8NLTol944YWXPgFeeOlp0S+88HK+lx/PjoLLYOCCJQAAAABJRU5ErkJggg==` // retina screen\n\t//\n\t// test.equal(dataUriEnd, expectedUriEnd, `should rerender with the expected dataURI after a dendrogram click`)\n\n\ttest.deepEqual(\n\t\thc.clickedClusterIds,\n\t\t[\n\t\t\t46, 54, 37, 28, 27, 51, 53, 44, 49, 25, 34, 11, 20, 41, 45, 29, 33, 17, 15, 2, 38, 42, 30, 36, 22, 9, 14, 3, 4,\n\t\t\t31, 13, 26, 1, 16, 8, 10, 5, 6, 7, 23, 47, 48, 35, 43, 21, 32, 18, 24, 56\n\t\t],\n\t\t`should give the expected clickedClusterIds`\n\t)\n\n\ttest.deepEqual(\n\t\t['Zoom in', 'List 50 samples'],\n\t\t[...hc.dom.dendroClickMenu.d.node().querySelectorAll('.sja_menuoption')].map(elem => elem.__data__.label),\n\t\t'should show the expected menu options on dendrogram click'\n\t)\n\n\thc.dom.dendroClickMenu.d.node().querySelector('.sja_menuoption').parentNode.lastChild.click()\n\tawait sleep(5)\n\ttest.equal(\n\t\thc.dom.dendroClickMenu.d.node().querySelectorAll('.sjpp_row_wrapper').length,\n\t\t50,\n\t\t'should list the expected number of samples'\n\t)\n\tif (test._ok) {\n\t\thc.dom.dendroClickMenu.clear().hide()\n\t\tapp.destroy()\n\t}\n})\n\ntape('numeric dictionary terms (float)', async function (test) {\n\t// dictionary numeric terms cluster as their underlying type ('float'), not a synthetic dataType\n\t// leave it here in case it's used later: bins:{ default:{\"type\": \"regular-bin\", \"startinclusive\": true, \"bin_size\": 0.1, \"first_bin\": { \"stop\": 0.1 }, \"last_bin\": { \"start\": 0.7 }} }\n\tconst terms = [\n\t\t{\n\t\t\tid: 'aaclassic_5', // tw.id must be provided\n\t\t\tterm: { id: 'aaclassic_5', name: 'a1', type: 'float' }, // requires {id,name,type}; term.name doesn't need to be real, unique name works\n\t\t\tq: { mode: 'continuous' } // set to continuous to avoid validating tw.term.bins\n\t\t},\n\t\t{ id: 'hrtavg', term: { id: 'hrtavg', name: 'a2', type: 'float' }, q: { mode: 'continuous' } },\n\t\t{ id: 'agedx', term: { id: 'agedx', name: 'a3', type: 'float' }, q: { mode: 'continuous' } }\n\t]\n\tconst { app, hc } = await getHierClusterApp({ terms, dataType: 'float', termGroupName: 'Numeric Dictionary Terms' })\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 rows')\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('isoform expression cluster', async function (test) {\n\ttest.timeoutAfter(4000)\n\tconst terms = [\n\t\t{\n\t\t\tterm: { isoform: 'ENST00000370314', name: 'ENST00000370314', type: 'isoformExpression' }\n\t\t},\n\t\t{\n\t\t\tterm: { isoform: 'ENST00000361510', name: 'ENST00000361510', type: 'isoformExpression' }\n\t\t},\n\t\t{\n\t\t\tterm: { isoform: 'ENST00000229281', name: 'ENST00000229281', type: 'isoformExpression' }\n\t\t}\n\t]\n\tconst { app, hc } = await getHierClusterApp({\n\t\tterms,\n\t\tdataType: 'isoformExpression',\n\t\ttermGroupName: 'Isoform Expression'\n\t})\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 isoform rows')\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('ssGSEA cluster', async function (test) {\n\ttest.timeoutAfter(4000)\n\tconst terms = [\n\t\t{ term: { id: 'HALLMARK_ADIPOGENESIS', name: 'HALLMARK_ADIPOGENESIS', type: 'ssGSEA' } },\n\t\t{\n\t\t\tterm: { id: 'HALLMARK_ALLOGRAFT_REJECTION', name: 'HALLMARK_ALLOGRAFT_REJECTION', type: 'ssGSEA' }\n\t\t},\n\t\t{\n\t\t\tterm: { id: 'HALLMARK_ANDROGEN_RESPONSE', name: 'HALLMARK_ANDROGEN_RESPONSE', type: 'ssGSEA' }\n\t\t}\n\t]\n\tconst { app, hc } = await getHierClusterApp({\n\t\tterms,\n\t\tdataType: 'ssGSEA',\n\t\ttermGroupName: 'Gene Set Enrichment (ssGSEA)'\n\t})\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 ssGSEA rows')\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('dnaMethylation cluster', async function (test) {\n\ttest.timeoutAfter(4000)\n\tconst terms = [\n\t\t{\n\t\t\tterm: { type: 'dnaMethylation', chr: 'chr17', start: 7673484, stop: 7681953, genomicFeatureType: 'gene' }\n\t\t},\n\t\t{\n\t\t\tterm: { type: 'dnaMethylation', chr: 'chr17', start: 7663195, stop: 7671664, genomicFeatureType: 'gene' }\n\t\t},\n\t\t{\n\t\t\tterm: { type: 'dnaMethylation', chr: 'chr17', start: 7673484, stop: 7681953, genomicFeatureType: 'promoter' }\n\t\t}\n\t]\n\tconst { app, hc } = await getHierClusterApp({ terms, dataType: 'dnaMethylation', termGroupName: 'DNA Methylation' })\n\ttest.equal(hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(), 3, 'should render 3 methylation rows')\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('cluster rejects a non-continuous term mode', async function (test) {\n\ttest.timeoutAfter(4000)\n\t// the client does not gate q.mode, so a discrete-mode term reaches the cluster route, which rejects\n\t// the whole request; the plot then renders no rows. (an incompatible term TYPE is instead caught\n\t// client-side by canTermBeInHierGrp before any request, so it can't be exercised through this path.)\n\tconst terms = [\n\t\t{ term: { gene: 'AKT1', name: 'AKT1', type: 'geneExpression' }, q: { mode: 'discrete' } },\n\t\t{ term: { gene: 'TP53', name: 'TP53', type: 'geneExpression' }, q: { mode: 'continuous' } },\n\t\t{ term: { gene: 'BCR', name: 'BCR', type: 'geneExpression' }, q: { mode: 'continuous' } }\n\t]\n\tconst { app, hc } = await getHierClusterApp({ terms, dataType: 'geneExpression' })\n\ttest.equal(\n\t\thc.dom.termLabelG.selectAll('.sjpp-matrix-label').size(),\n\t\t0,\n\t\t'should render no rows when a term is not in continuous mode'\n\t)\n\tif (test._ok) app.destroy()\n\ttest.end()\n})\n\ntape('cluster rejects incompatible numeric types', async function (test) {\n\ttest.timeoutAfter(4000)\n\t// geneExpression and a float dictionary term are both numeric but cannot be clustered together;\n\t// canTermBeInHierGrp throws in getPlotConfig (client-side) before any server request is made\n\tconst terms = [\n\t\t{ term: { gene: 'AKT1', name: 'AKT1', type: 'geneExpression' }, q: { mode: 'continuous' } },\n\t\t{ term: { gene: 'TP53', name: 'TP53', type: 'geneExpression' }, q: { mode: 'continuous' } },\n\t\t{ term: { id: 'agedx', name: 'agedx', type: 'float' }, q: { mode: 'continuous' } }\n\t]\n\tlet rejected = false\n\ttry {\n\t\tconst { app, hc } = await getHierClusterApp({ terms, dataType: 'geneExpression' })\n\t\t// if it didn't throw, the incompatible mix must have prevented any rows from rendering\n\t\trejected = hc.dom.termLabelG.selectAll('.sjpp-matrix-label').size() === 0\n\t\tif (app) app.destroy()\n\t} catch (e) {\n\t\trejected = true\n\t}\n\ttest.ok(rejected, 'should reject a cluster mixing geneExpression and float terms')\n\ttest.end()\n})\n\n/*************************\n reusable helper functions\n**************************/\n\nasync function getHierClusterApp(_opts = {}) {\n\tconst holder = select('body').append('div')\n\tconst defaults = {\n\t\tdebug: true,\n\t\tholder,\n\t\tgenome: 'hg38-test',\n\t\tstate: {\n\t\t\tgenome: 'hg38-test',\n\t\t\tdslabel: 'TermdbTest',\n\t\t\ttermfilter: { filter0: _opts.filter0 },\n\t\t\tplots: [\n\t\t\t\t{\n\t\t\t\t\tchartType: 'hierCluster',\n\t\t\t\t\tdataType: _opts.dataType || TermTypes.GENE_EXPRESSION,\n\t\t\t\t\tsettings: {\n\t\t\t\t\t\thierCluster: {\n\t\t\t\t\t\t\ttermGroupName: _opts.termGroupName || 'Gene Expression (CGC genes only)'\n\t\t\t\t\t\t},\n\t\t\t\t\t\tmatrix: {\n\t\t\t\t\t\t\t// the matrix autocomputes the colw based on available screen width,\n\t\t\t\t\t\t\t// need to set an exact screen width for consistent tests using getBBox()\n\t\t\t\t\t\t\tavailContentWidth: 1200\n\t\t\t\t\t\t}\n\t\t\t\t\t},\n\t\t\t\t\t// force empty termgroups, genes since the instance requestData() will not have expression data,\n\t\t\t\t\t// and will cause a non-trival error if using the actual requestData(), which will be mocked below\n\t\t\t\t\ttermgroups: [], // _opts.termgroups || [],\n\t\t\t\t\t// !!! there will be an initial load error since this is an empty geneset,\n\t\t\t\t\t// !!! but will be ignored since it's not relevant to this test\n\t\t\t\t\tterms: _opts.terms || [],\n\t\t\t\t\tfilter: _opts.filter\n\t\t\t\t}\n\t\t\t]\n\t\t},\n\t\tapp: {\n\t\t\tfeatures: ['recover'],\n\t\t\tcallbacks: _opts?.app?.callbacks || {}\n\t\t},\n\t\trecover: {\n\t\t\tundoHtml: 'Undo',\n\t\t\tredoHtml: 'Redo',\n\t\t\tresetHtml: 'Restore',\n\t\t\tadjustTrackedState(state) {\n\t\t\t\tconst s = structuredClone(state)\n\t\t\t\tdelete s.termfilter.filter0\n\t\t\t\treturn s\n\t\t\t}\n\t\t},\n\t\thierCluster: _opts?.hierCluster || {}\n\t}\n\n\tconst opts = Object.assign(defaults, _opts)\n\tconst app = await appInit(opts)\n\t// dismiss the benign initial load error if present; guard the call since some error bars end in a\n\t// text node (no .click), e.g. the server error from the non-continuous-mode / no-data cluster tests\n\tholder.select('.sja_errorbar').node()?.lastChild?.click?.()\n\tconst hc = Object.values(app.Inner.components.plots).find(\n\t\tp => p.type == 'hierCluster' || p.chartType == 'hierCluster'\n\t).Inner\n\treturn { app, hc }\n}\nfunction getGenes() {\n\t// return a copy for each test, to avoid unexpected changes in reusing scoped variables\n\treturn [\n\t\t{ gene: 'AKT1', type: 'geneExpression' },\n\t\t{ gene: 'TP53', type: 'geneExpression' },\n\t\t{ gene: 'BCR', type: 'geneExpression' },\n\t\t{ gene: 'KRAS', type: 'geneExpression' }\n\t]\n}\n"],
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-  "names": ["tape", "lst", "termgroups"]
-}

package/dist/hierCluster.interactivity-RPY74PK6.js

@@ -1,54 +0,0 @@
-import {
-  addSelectedRowsOptions,
-  addSelectedSamplesOptions,
-  getAllChildrenClusterIds,
-  getClusterFromLeftDendrogram,
-  getClusterFromTopDendrogram,
-  setClusteringBtn,
-  showTable4selectedRows,
-  showTable4selectedSamples,
-  triggerZoomBranch
-} from "./chunk-L7IRWUKT.js";
-import "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.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";
-export {
-  addSelectedRowsOptions,
-  addSelectedSamplesOptions,
-  getAllChildrenClusterIds,
-  getClusterFromLeftDendrogram,
-  getClusterFromTopDendrogram,
-  setClusteringBtn,
-  showTable4selectedRows,
-  showTable4selectedSamples,
-  triggerZoomBranch
-};
-//# sourceMappingURL=hierCluster.interactivity-RPY74PK6.js.map

package/dist/hierCluster.renderers-LOKHZ3V2.js

@@ -1,21 +0,0 @@
-import {
-  maySetSandboxHeader,
-  plotDendrogramHclust,
-  renderImage
-} from "./chunk-2MG6XE6R.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  maySetSandboxHeader,
-  plotDendrogramHclust,
-  renderImage
-};
-//# sourceMappingURL=hierCluster.renderers-LOKHZ3V2.js.map

package/dist/imagePlot-BBEXA754.js

@@ -1,163 +0,0 @@
-import {
-  PlotBase,
-  controlsInit
-} from "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import {
-  dofetch3
-} from "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.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";
-
-// plots/imagePlot.ts
-var ImagePlot = class _ImagePlot extends PlotBase {
-  static {
-    this.type = "imagePlot";
-  }
-  constructor(opts, api) {
-    super(opts, api);
-    this.opts = opts;
-    this.api = api;
-    this.type = _ImagePlot.type;
-    if (this.opts?.header) {
-      if (this.opts?.headerText)
-        this.opts.header.append("span").style("padding-right", "5px").text(this.opts.headerText);
-      this.opts.header.append("span").text("IMAGE PLOT").style("font-size", "0.7em").style("opacity", 0.6);
-    }
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      config,
-      termfilter: appState.termfilter,
-      vocab: appState.vocab
-    };
-  }
-  async init(appState) {
-    const config = this.getState(appState).config;
-    const holder = this.opts.holder.append("div").attr("data-testid", "sjpp-imagePlot-holder");
-    this.dom = {
-      holder,
-      controlsHolder: holder.append("div").attr("data-testid", "sjpp-imagePlot-controlsDiv").style("display", "inline-block"),
-      imageHolder: holder.append("div").attr("data-testid", "sjpp-imagePlot-imagesDiv").style("display", "inline-block")
-    };
-    const sampleId = config.sample?.sampleId || config.sample?.sID;
-    let images;
-    if (config?.imgDir) {
-      const img = await dofetch3(
-        `img?file=${config.imgDir.folder}${config.imgDir.folder.endsWith("/") ? "" : "/"}${sampleId}/${config.imgDir.fileName}`
-      );
-      if (!img || img?.error) throw new Error(img?.error || "Error fetching image");
-      images = [img];
-    } else {
-      const result = await this.app.vocabApi.getSampleImages(sampleId);
-      if (result.error) throw new Error(result.error);
-      images = result.images;
-    }
-    for (const img of images) {
-      this.dom.imageHolder.append("img").style("padding", "10px").attr("src", img.src).attr("width", config.settings.imagePlot.width).attr("height", config.settings.imagePlot.height);
-    }
-  }
-  async setControls() {
-    this.components = {
-      controls: await controlsInit({
-        app: this.app,
-        id: this.id,
-        holder: this.dom.controlsHolder,
-        inputs: [
-          {
-            label: "Image width",
-            type: "number",
-            chartType: this.type,
-            settingsKey: "width"
-          },
-          {
-            label: "Image height",
-            type: "number",
-            chartType: this.type,
-            settingsKey: "height"
-          }
-        ]
-      })
-    };
-  }
-  async main() {
-  }
-};
-async function getPlotConfig(opts) {
-  const settings = getDefaultImagePlotSettings();
-  if (opts.settings) copyMerge(settings, opts.settings);
-  const config = {
-    settings: {
-      controls: {
-        isOpen: false
-      },
-      imagePlot: settings
-    }
-  };
-  return copyMerge(config, opts);
-}
-function getDefaultImagePlotSettings() {
-  return {
-    width: 500,
-    height: 500
-  };
-}
-var imagePlotInit = getCompInit(ImagePlot);
-var componentInit = imagePlotInit;
-async function renderImagePlot(state, holder, sample) {
-  const opts = {
-    holder,
-    state: {
-      vocab: state.vocab,
-      plots: [
-        {
-          chartType: "imagePlot",
-          sample
-        }
-      ]
-    }
-  };
-  const plot = await import("./plot.app-MLBP6WFP.js");
-  await plot.appInit(opts);
-}
-export {
-  componentInit,
-  getDefaultImagePlotSettings,
-  getPlotConfig,
-  imagePlotInit,
-  renderImagePlot
-};
-//# sourceMappingURL=imagePlot-BBEXA754.js.map

package/dist/importPlot-7QGANZGK.js

@@ -1,8 +0,0 @@
-import {
-  importPlot
-} from "./chunk-Z5U6HOE4.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  importPlot
-};
-//# sourceMappingURL=importPlot-7QGANZGK.js.map

package/dist/isoformExpression-4SLLCVFD.js

@@ -1,40 +0,0 @@
-import {
-  SearchHandler,
-  filterIsoforms
-} from "./chunk-EZ4LZ6ZT.js";
-import "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.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";
-export {
-  SearchHandler,
-  filterIsoforms
-};
-//# sourceMappingURL=isoformExpression-4SLLCVFD.js.map

package/dist/isoformExpression.unit.spec-GEL4JJ64.js

@@ -1,208 +0,0 @@
-import {
-  SearchHandler,
-  filterIsoforms
-} from "./chunk-EZ4LZ6ZT.js";
-import {
-  require_tape
-} from "./chunk-TUMA63WX.js";
-import "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import {
-  ISOFORM_EXPRESSION
-} from "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// termdb/handlers/test/isoformExpression.unit.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-function mockGm(isoform) {
-  return { isoform, chr: "chr1", start: 0, stop: 100, exon: [[0, 100]] };
-}
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- termdb/handlers/isoformExpression -***-");
-  test.end();
-});
-(0, import_tape.default)("selectIsoform() should call callback with configured unit from termdbConfig", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {
-          isoformExpression: { unit: "TPM" }
-        }
-      }
-    }
-  };
-  handler.selectIsoform("ENST00000269305", "TP53");
-  test.equal(selected?.isoform, "ENST00000269305", "Should pass selected isoform");
-  test.equal(selected?.gene, "TP53", "Should pass gene");
-  test.equal(selected?.name, "ENST00000269305 TPM", "Should include configured unit in term name");
-  test.equal(selected?.type, ISOFORM_EXPRESSION, "Should set type to isoformExpression");
-  test.end();
-});
-(0, import_tape.default)("selectIsoform() should use default unit when not configured", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {}
-      }
-    }
-  };
-  handler.selectIsoform("ENST00000269305", "TP53");
-  test.equal(selected?.isoform, "ENST00000269305", "Should pass selected isoform");
-  test.equal(selected?.name, "ENST00000269305 TPM", "Should use default unit TPM");
-  test.equal(selected?.type, ISOFORM_EXPRESSION, "Should set type to isoformExpression");
-  test.end();
-});
-(0, import_tape.default)("selectCollection() should create a custom termCollection from multiple isoforms", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {
-          isoformExpression: { unit: "TPM" }
-        }
-      }
-    }
-  };
-  handler.selectCollection([mockGm("ENST00000256078"), mockGm("ENST00000311936")], "KRAS");
-  test.equal(selected?.type, "termCollection", "Should set type to termCollection");
-  test.equal(selected?.isCustom, true, "Should set isCustom flag");
-  test.equal(selected?.memberType, "numeric", "Should set memberType to numeric");
-  test.equal(selected?.name, "KRAS Isoforms (TPM)", "Should include gene and unit in name");
-  test.equal(selected?.isleaf, true, "Should set isleaf");
-  test.deepEqual(selected?.propsByTermId, {}, "Should have empty propsByTermId");
-  test.equal(selected?.termlst?.length, 2, "Should have 2 member terms");
-  const mt = selected.termlst[0];
-  test.equal(mt.id, "ENST00000256078", "Member term id should be the isoform ID");
-  test.equal(mt.name, "ENST00000256078", "Member term name should be the isoform ID");
-  test.equal(mt.type, "isoformExpression", "Member term type should be isoformExpression");
-  test.equal(mt.isoform, "ENST00000256078", "Member term should carry isoform field");
-  test.end();
-});
-(0, import_tape.default)("selectCollection() should use default unit when not configured", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {}
-      }
-    }
-  };
-  handler.selectCollection([mockGm("ENST00000256078"), mockGm("ENST00000311936")], "KRAS");
-  test.equal(selected?.name, "KRAS Isoforms (TPM)", "Should use default unit TPM");
-  test.end();
-});
-(0, import_tape.default)("showIsoforms multi-select: single isoform calls selectIsoform, multiple calls selectCollection", (test) => {
-  const handler = new SearchHandler();
-  const calls = [];
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {
-          isoformExpression: { unit: "TPM" }
-        }
-      }
-    }
-  };
-  handler.selectIsoform = (isoform, gene) => {
-    calls.push({ method: "selectIsoform", args: { isoform, gene } });
-  };
-  handler.selectCollection = (gms, gene) => {
-    calls.push({ method: "selectCollection", args: { gms, gene } });
-  };
-  const onMultiSelect1 = (selected) => {
-    if (selected.length === 1) handler.selectIsoform(selected[0].isoform, "TP53");
-    else handler.selectCollection(selected, "TP53");
-  };
-  onMultiSelect1([mockGm("ENST00000269305")]);
-  test.equal(calls.length, 1, "Should have one call");
-  test.equal(calls[0].method, "selectIsoform", "Single isoform should call selectIsoform");
-  const onMultiSelect2 = (selected) => {
-    if (selected.length === 1) handler.selectIsoform(selected[0].isoform, "KRAS");
-    else handler.selectCollection(selected, "KRAS");
-  };
-  onMultiSelect2([mockGm("ENST00000256078"), mockGm("ENST00000311936")]);
-  test.equal(calls.length, 2, "Should have two calls total");
-  test.equal(calls[1].method, "selectCollection", "Multiple isoforms should call selectCollection");
-  test.equal(calls[1].args.gms.length, 2, "Should pass both gene models");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should return only ENST isoforms present in availableItems", (test) => {
-  const gmlst = [mockGm("ENST00000269305"), mockGm("ENST00000413465"), mockGm("NM_000546"), mockGm("ENST00000359597")];
-  const availableItems = ["ENST00000269305", "ENST00000359597"];
-  const result = filterIsoforms(gmlst, availableItems);
-  test.equal(result.length, 2, "Should return 2 matching isoforms");
-  test.equal(result[0].isoform, "ENST00000269305", "First match correct");
-  test.equal(result[1].isoform, "ENST00000359597", "Second match correct");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should exclude non-ENST isoforms even if in availableItems", (test) => {
-  const gmlst = [mockGm("NM_000546"), mockGm("NR_176326"), mockGm("ENST00000269305")];
-  const availableItems = ["NM_000546", "ENST00000269305"];
-  const result = filterIsoforms(gmlst, availableItems);
-  test.equal(result.length, 1, "Should only return ENST isoform");
-  test.equal(result[0].isoform, "ENST00000269305", "Should be the ENST match");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should return all ENST isoforms when availableItems is empty", (test) => {
-  const gmlst = [mockGm("ENST00000269305"), mockGm("ENST00000413465"), mockGm("NM_000546")];
-  const result = filterIsoforms(gmlst, []);
-  test.equal(result.length, 2, "Should return all ENST isoforms when no filter");
-  test.equal(result[0].isoform, "ENST00000269305", "First ENST correct");
-  test.equal(result[1].isoform, "ENST00000413465", "Second ENST correct");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should return empty array when no ENST isoforms match", (test) => {
-  const gmlst = [mockGm("ENST00000269305"), mockGm("ENST00000413465")];
-  const availableItems = ["ENST00000999999"];
-  const result = filterIsoforms(gmlst, availableItems);
-  test.equal(result.length, 0, "Should return empty when no matches");
-  test.end();
-});
-//# sourceMappingURL=isoformExpression.unit.spec-GEL4JJ64.js.map

package/dist/isoformExpression.unit.spec-GEL4JJ64.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termdb/handlers/test/isoformExpression.unit.spec.ts"],
-  "sourcesContent": ["import tape from 'tape'\nimport { SearchHandler, filterIsoforms } from '../isoformExpression.ts'\nimport type { GeneModel } from '#dom/types/isoformSelect'\nimport { ISOFORM_EXPRESSION } from '#shared/terms.js'\n\n/** Helper to create a minimal GeneModel for testing */\nfunction mockGm(isoform: string): GeneModel {\n\treturn { isoform, chr: 'chr1', start: 0, stop: 100, exon: [[0, 100]] }\n}\n\n/**************\n test sections\n***************/\n\ntape('\\n', function (test) {\n\ttest.comment('-***- termdb/handlers/isoformExpression -***-')\n\ttest.end()\n})\n\ntape('selectIsoform() should call callback with configured unit from termdbConfig', test => {\n\tconst handler = new SearchHandler()\n\tlet selected: any\n\n\thandler.callback = t => {\n\t\tselected = t\n\t}\n\thandler.app = {\n\t\tvocabApi: {\n\t\t\ttermdbConfig: {\n\t\t\t\tqueries: {\n\t\t\t\t\tisoformExpression: { unit: 'TPM' }\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} as any\n\n\thandler.selectIsoform('ENST00000269305', 'TP53')\n\ttest.equal(selected?.isoform, 'ENST00000269305', 'Should pass selected isoform')\n\ttest.equal(selected?.gene, 'TP53', 'Should pass gene')\n\ttest.equal(selected?.name, 'ENST00000269305 TPM', 'Should include configured unit in term name')\n\ttest.equal(selected?.type, ISOFORM_EXPRESSION, 'Should set type to isoformExpression')\n\n\ttest.end()\n})\n\ntape('selectIsoform() should use default unit when not configured', test => {\n\tconst handler = new SearchHandler()\n\tlet selected: any\n\n\thandler.callback = t => {\n\t\tselected = t\n\t}\n\thandler.app = {\n\t\tvocabApi: {\n\t\t\ttermdbConfig: {\n\t\t\t\tqueries: {}\n\t\t\t}\n\t\t}\n\t} as any\n\n\thandler.selectIsoform('ENST00000269305', 'TP53')\n\ttest.equal(selected?.isoform, 'ENST00000269305', 'Should pass selected isoform')\n\ttest.equal(selected?.name, 'ENST00000269305 TPM', 'Should use default unit TPM')\n\ttest.equal(selected?.type, ISOFORM_EXPRESSION, 'Should set type to isoformExpression')\n\n\ttest.end()\n})\n\ntape('selectCollection() should create a custom termCollection from multiple isoforms', test => {\n\tconst handler = new SearchHandler()\n\tlet selected: any\n\n\thandler.callback = t => {\n\t\tselected = t\n\t}\n\thandler.app = {\n\t\tvocabApi: {\n\t\t\ttermdbConfig: {\n\t\t\t\tqueries: {\n\t\t\t\t\tisoformExpression: { unit: 'TPM' }\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} as any\n\n\thandler.selectCollection([mockGm('ENST00000256078'), mockGm('ENST00000311936')], 'KRAS')\n\ttest.equal(selected?.type, 'termCollection', 'Should set type to termCollection')\n\ttest.equal(selected?.isCustom, true, 'Should set isCustom flag')\n\ttest.equal(selected?.memberType, 'numeric', 'Should set memberType to numeric')\n\ttest.equal(selected?.name, 'KRAS Isoforms (TPM)', 'Should include gene and unit in name')\n\ttest.equal(selected?.isleaf, true, 'Should set isleaf')\n\ttest.deepEqual(selected?.propsByTermId, {}, 'Should have empty propsByTermId')\n\n\t// termlst shape\n\ttest.equal(selected?.termlst?.length, 2, 'Should have 2 member terms')\n\tconst mt = selected.termlst[0]\n\ttest.equal(mt.id, 'ENST00000256078', 'Member term id should be the isoform ID')\n\ttest.equal(mt.name, 'ENST00000256078', 'Member term name should be the isoform ID')\n\ttest.equal(mt.type, 'isoformExpression', 'Member term type should be isoformExpression')\n\ttest.equal(mt.isoform, 'ENST00000256078', 'Member term should carry isoform field')\n\n\ttest.end()\n})\n\ntape('selectCollection() should use default unit when not configured', test => {\n\tconst handler = new SearchHandler()\n\tlet selected: any\n\n\thandler.callback = t => {\n\t\tselected = t\n\t}\n\thandler.app = {\n\t\tvocabApi: {\n\t\t\ttermdbConfig: {\n\t\t\t\tqueries: {}\n\t\t\t}\n\t\t}\n\t} as any\n\n\thandler.selectCollection([mockGm('ENST00000256078'), mockGm('ENST00000311936')], 'KRAS')\n\ttest.equal(selected?.name, 'KRAS Isoforms (TPM)', 'Should use default unit TPM')\n\n\ttest.end()\n})\n\ntape('showIsoforms multi-select: single isoform calls selectIsoform, multiple calls selectCollection', test => {\n\tconst handler = new SearchHandler()\n\tconst calls: { method: string; args: any }[] = []\n\n\thandler.app = {\n\t\tvocabApi: {\n\t\t\ttermdbConfig: {\n\t\t\t\tqueries: {\n\t\t\t\t\tisoformExpression: { unit: 'TPM' }\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t} as any\n\n\t// Spy on both methods\n\thandler.selectIsoform = (isoform: string, gene: string) => {\n\t\tcalls.push({ method: 'selectIsoform', args: { isoform, gene } })\n\t}\n\thandler.selectCollection = (gms: GeneModel[], gene: string) => {\n\t\tcalls.push({ method: 'selectCollection', args: { gms, gene } })\n\t}\n\n\t// Simulate multi-select callback with 1 isoform\n\tconst onMultiSelect1 = (selected: GeneModel[]) => {\n\t\tif (selected.length === 1) handler.selectIsoform(selected[0].isoform, 'TP53')\n\t\telse handler.selectCollection(selected, 'TP53')\n\t}\n\tonMultiSelect1([mockGm('ENST00000269305')])\n\ttest.equal(calls.length, 1, 'Should have one call')\n\ttest.equal(calls[0].method, 'selectIsoform', 'Single isoform should call selectIsoform')\n\n\t// Simulate multi-select callback with 2 isoforms\n\tconst onMultiSelect2 = (selected: GeneModel[]) => {\n\t\tif (selected.length === 1) handler.selectIsoform(selected[0].isoform, 'KRAS')\n\t\telse handler.selectCollection(selected, 'KRAS')\n\t}\n\tonMultiSelect2([mockGm('ENST00000256078'), mockGm('ENST00000311936')])\n\ttest.equal(calls.length, 2, 'Should have two calls total')\n\ttest.equal(calls[1].method, 'selectCollection', 'Multiple isoforms should call selectCollection')\n\ttest.equal(calls[1].args.gms.length, 2, 'Should pass both gene models')\n\n\ttest.end()\n})\n\ntape('filterIsoforms() should return only ENST isoforms present in availableItems', test => {\n\tconst gmlst = [mockGm('ENST00000269305'), mockGm('ENST00000413465'), mockGm('NM_000546'), mockGm('ENST00000359597')]\n\tconst availableItems = ['ENST00000269305', 'ENST00000359597']\n\n\tconst result = filterIsoforms(gmlst, availableItems)\n\ttest.equal(result.length, 2, 'Should return 2 matching isoforms')\n\ttest.equal(result[0].isoform, 'ENST00000269305', 'First match correct')\n\ttest.equal(result[1].isoform, 'ENST00000359597', 'Second match correct')\n\n\ttest.end()\n})\n\ntape('filterIsoforms() should exclude non-ENST isoforms even if in availableItems', test => {\n\tconst gmlst = [mockGm('NM_000546'), mockGm('NR_176326'), mockGm('ENST00000269305')]\n\tconst availableItems = ['NM_000546', 'ENST00000269305']\n\n\tconst result = filterIsoforms(gmlst, availableItems)\n\ttest.equal(result.length, 1, 'Should only return ENST isoform')\n\ttest.equal(result[0].isoform, 'ENST00000269305', 'Should be the ENST match')\n\n\ttest.end()\n})\n\ntape('filterIsoforms() should return all ENST isoforms when availableItems is empty', test => {\n\tconst gmlst = [mockGm('ENST00000269305'), mockGm('ENST00000413465'), mockGm('NM_000546')]\n\n\tconst result = filterIsoforms(gmlst, [])\n\ttest.equal(result.length, 2, 'Should return all ENST isoforms when no filter')\n\ttest.equal(result[0].isoform, 'ENST00000269305', 'First ENST correct')\n\ttest.equal(result[1].isoform, 'ENST00000413465', 'Second ENST correct')\n\n\ttest.end()\n})\n\ntape('filterIsoforms() should return empty array when no ENST isoforms match', test => {\n\tconst gmlst = [mockGm('ENST00000269305'), mockGm('ENST00000413465')]\n\tconst availableItems = ['ENST00000999999']\n\n\tconst result = filterIsoforms(gmlst, availableItems)\n\ttest.equal(result.length, 0, 'Should return empty when no matches')\n\n\ttest.end()\n})\n"],
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package/dist/launch.adhoc-LWLBQJS5.js

@@ -1,42 +0,0 @@
-import {
-  launch
-} from "./chunk-ZTHM2TKP.js";
-import "./chunk-GAPI4MML.js";
-import "./chunk-USFSHSCJ.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-4KY4XKJV.js";
-import "./chunk-5VOPABBA.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-Z5U6HOE4.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5ABGFJSP.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-XPY6AWXO.js";
-import "./chunk-NELOT3NJ.js";
-import "./chunk-M6EF3WVV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-LFCYMSVA.js";
-import "./chunk-I6WR4CG7.js";
-import "./chunk-2X6W4E3W.js";
-import "./chunk-NYRZNRG5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-3XVVN66M.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-NSTL4MY2.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";
-export {
-  launch
-};
-//# sourceMappingURL=launch.adhoc-LWLBQJS5.js.map