@sjcrh/proteinpaint-client 2.210.1 → 2.211.0

package/dist/hierCluster.integration.spec-TNJD2QT6.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 '#types'\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-PEEJ3BRC.js

@@ -1,49 +0,0 @@
-import {
-  addSelectedRowsOptions,
-  addSelectedSamplesOptions,
-  getAllChildrenClusterIds,
-  getClusterFromLeftDendrogram,
-  getClusterFromTopDendrogram,
-  setClusteringBtn,
-  showTable4selectedRows,
-  showTable4selectedSamples,
-  triggerZoomBranch
-} from "./chunk-KCX54MGS.js";
-import "./chunk-CSAS3PVJ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-T4RYLTR3.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-Y3SDMRDX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VTHZGUSZ.js";
-import "./chunk-3TV5WWUN.js";
-import "./chunk-4Y5W26UF.js";
-import "./chunk-UYKJOBRO.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  addSelectedRowsOptions,
-  addSelectedSamplesOptions,
-  getAllChildrenClusterIds,
-  getClusterFromLeftDendrogram,
-  getClusterFromTopDendrogram,
-  setClusteringBtn,
-  showTable4selectedRows,
-  showTable4selectedSamples,
-  triggerZoomBranch
-};
-//# sourceMappingURL=hierCluster.interactivity-PEEJ3BRC.js.map

package/dist/hierCluster.renderers-7ESGKIGM.js

@@ -1,19 +0,0 @@
-import {
-  maySetSandboxHeader,
-  plotDendrogramHclust,
-  renderImage
-} from "./chunk-SDYFM3UL.js";
-import "./chunk-4Y5W26UF.js";
-import "./chunk-UYKJOBRO.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  maySetSandboxHeader,
-  plotDendrogramHclust,
-  renderImage
-};
-//# sourceMappingURL=hierCluster.renderers-7ESGKIGM.js.map

package/dist/imagePlot-LWL6JMKM.js

@@ -1,156 +0,0 @@
-import {
-  PlotBase,
-  controlsInit
-} from "./chunk-CSAS3PVJ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-T4RYLTR3.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-Y3SDMRDX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3
-} from "./chunk-VTHZGUSZ.js";
-import "./chunk-3TV5WWUN.js";
-import "./chunk-4Y5W26UF.js";
-import "./chunk-UYKJOBRO.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/imagePlot.ts
-var ImagePlot = class _ImagePlot extends PlotBase {
-  static {
-    this.type = "imagePlot";
-  }
-  constructor(opts, api) {
-    super(opts, 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.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-5YUAVZA4.js");
-  await plot.appInit(opts);
-}
-export {
-  componentInit,
-  getDefaultImagePlotSettings,
-  getPlotConfig,
-  imagePlotInit,
-  renderImagePlot
-};
-//# sourceMappingURL=imagePlot-LWL6JMKM.js.map

package/dist/importPlot-CLBY6QZN.js

@@ -1,8 +0,0 @@
-import {
-  importPlot
-} from "./chunk-T4RYLTR3.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  importPlot
-};
-//# sourceMappingURL=importPlot-CLBY6QZN.js.map

package/dist/isoformExpression-36P3BBN7.js

@@ -1,35 +0,0 @@
-import {
-  SearchHandler,
-  filterIsoforms
-} from "./chunk-ODHQPTHU.js";
-import "./chunk-CSAS3PVJ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-T4RYLTR3.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-Y3SDMRDX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VTHZGUSZ.js";
-import "./chunk-3TV5WWUN.js";
-import "./chunk-4Y5W26UF.js";
-import "./chunk-UYKJOBRO.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  SearchHandler,
-  filterIsoforms
-};
-//# sourceMappingURL=isoformExpression-36P3BBN7.js.map

package/dist/isoformExpression.unit.spec-SF2SPTRC.js

@@ -1,237 +0,0 @@
-import {
-  SearchHandler,
-  filterIsoforms
-} from "./chunk-ODHQPTHU.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-CSAS3PVJ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-T4RYLTR3.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-Y3SDMRDX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VTHZGUSZ.js";
-import "./chunk-3TV5WWUN.js";
-import "./chunk-4Y5W26UF.js";
-import {
-  ISOFORM_EXPRESSION
-} from "./chunk-UYKJOBRO.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.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.ok(selected?.propsByTermId.ENST00000256078.color, "Should assign the first isoform a color");
-  test.ok(selected?.propsByTermId.ENST00000311936.color, "Should assign the second isoform a color");
-  test.notEqual(
-    selected?.propsByTermId.ENST00000256078.color,
-    selected?.propsByTermId.ENST00000311936.color,
-    "Should assign distinct member colors"
-  );
-  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)("selectCollection() renders fraction choices when requested", (test) => {
-  const handler = new SearchHandler();
-  const holder = select_default("body").append("div");
-  let selected;
-  handler.callback = (term) => {
-    selected = term;
-  };
-  handler.app = {
-    vocabApi: { termdbConfig: { queries: { isoformExpression: { unit: "TPM" } } } }
-  };
-  handler.termCollectionSelectionMode = "fraction";
-  handler.dom = { errDiv: holder.append("div"), isoformDiv: holder.append("div") };
-  handler.selectCollection([mockGm("ENST00000256078"), mockGm("ENST00000311936")], "KRAS");
-  test.ok(holder.text().includes("Denominator"), "renders denominator choices");
-  holder.select('[data-testid="sjpp-term-collection-fraction-select"]').node().click();
-  test.equal(selected?.type, "TermCollectionTWFraction", "returns a fraction wrapper");
-  test.deepEqual(
-    selected?.q.denominators,
-    ["ENST00000256078", "ENST00000311936"],
-    "defaults every isoform as a denominator"
-  );
-  test.deepEqual(selected?.q.numerators, ["ENST00000256078"], "defaults only the first isoform as numerator");
-  test.equal(selected?.term.termlst.length, 2, "retains every isoform on the collection term");
-  holder.remove();
-  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-SF2SPTRC.js.map

package/dist/junction-B7DSIG4E.js

@@ -1,36 +0,0 @@
-import {
-  SearchHandler,
-  getJunctionCustomTerms
-} from "./chunk-PUSSP76H.js";
-import "./chunk-Q3PAXUCU.js";
-import "./chunk-CSAS3PVJ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-T4RYLTR3.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-Y3SDMRDX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VTHZGUSZ.js";
-import "./chunk-3TV5WWUN.js";
-import "./chunk-4Y5W26UF.js";
-import "./chunk-UYKJOBRO.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  SearchHandler,
-  getJunctionCustomTerms
-};
-//# sourceMappingURL=junction-B7DSIG4E.js.map

package/dist/junction.customTerm-7VZS4JDE.js

@@ -1,16 +0,0 @@
-import {
-  junctionCustomTermSource,
-  makeJunctionCustomTerm
-} from "./chunk-Q3PAXUCU.js";
-import "./chunk-UYKJOBRO.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  junctionCustomTermSource,
-  makeJunctionCustomTerm
-};
-//# sourceMappingURL=junction.customTerm-7VZS4JDE.js.map