@sjcrh/proteinpaint-client 2.206.0 → 2.207.0

package/dist/geneVariant.integration.spec-ICFHVFIR.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termdb/handlers/test/geneVariant.integration.spec.ts"],
-  "sourcesContent": ["import tape from 'tape'\nimport * as d3s from 'd3-selection'\nimport { SearchHandler } from '../geneVariant.ts'\nimport { dtsnvindel } from '#shared/common.js'\nimport { hg38 } from '../../../test/testdata/genomes'\nimport { sleep } from '../../../test/test.helpers.js'\nimport { vocabInit } from '../../vocabulary'\n\n/*\nTests:\n\tSearch handler layout\n    Single gene input\n    Change mutation type\n    Gene set input\n\tGene set input - custom name\n\tRemembered settings are offered for the picked gene\n\tRemembered settings are applied on Enter\n\tRemembered settings of another mutation type do not lead\n\tRemembered settings are cleared on changing the mutation type\n\tRemembered settings are cleared on changing the input type\n\tRemembered settings are not offered where the q would be dropped\n*/\n\n/*************************\n reusable helper functions\n**************************/\n\nasync function getVocabApi() {\n\tconst vocabApi = vocabInit({ state: { vocab: { genome: 'hg38-test', dslabel: 'TermdbTest' } } })\n\tif (!vocabApi) throw 'vocabApi is missing'\n\tawait vocabApi.getTermdbConfig()\n\treturn vocabApi\n}\n\nconst vocabApi: any = await getVocabApi()\n\nconst handler = new SearchHandler()\n\nfunction getHolder() {\n\tconst holder = d3s.select('body').append('div')\n\treturn holder\n}\n\nasync function initializeSearchHandler(opts) {\n\tconst callback = opts.callback || (() => {})\n\tawait handler.init({\n\t\tholder: opts.holder,\n\t\tapp: { vocabApi: opts.vocabApi || vocabApi },\n\t\tgenomeObj: hg38,\n\t\tkeepsQ: opts.keepsQ,\n\t\tmsg: opts.msg,\n\t\tcallback\n\t})\n}\n\n/**************\n test sections\n***************/\n\ntape('\\n', function (test) {\n\ttest.comment('-***- geneVariant search handler -***-')\n\ttest.end()\n})\n\ntape('Search handler layout', async test => {\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder })\n\tconst mutationTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-mutationTypeRadios\"]')\n\ttest.ok(\n\t\tmutationTypeRadiosDiv.selectAll('input[type=\"radio\"]').size() > 0,\n\t\t'Mutation type radio buttons should be present'\n\t)\n\tconst inputTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-genesetTypeRadios\"]')\n\ttest.equal(\n\t\tinputTypeRadiosDiv.selectAll('input[type=\"radio\"]').size(),\n\t\t2,\n\t\t'Input type radio buttons should be present'\n\t)\n\tconst searchDiv = holder.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\ttest.equal(searchDiv.selectAll('input[type=\"search\"]').size(), 1, 'Gene search input should be present')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Single gene input', async test => {\n\tlet tw\n\tconst callback = _tw => {\n\t\ttw = _tw\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst geneSearchInput: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\t\t.select('input[type=\"search\"]')\n\t\t.node()\n\t// gene name input\n\tgeneSearchInput.value = 'TP53'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(tw.term.type, 'geneVariant', 'term.type should be geneVariant')\n\ttest.equal(tw.q.type, 'predefined-groupset', 'q.type should be predefined-groupset')\n\ttest.equal(tw.q.predefined_groupset_idx, 0, 'q.predefined_groupset_idx should be 0')\n\ttest.equal(tw.term.genes.length, 1, 'term.genes[] should have length of 1')\n\ttest.deepEqual(\n\t\ttw.term.genes[0],\n\t\t{ kind: 'gene', id: 'TP53', gene: 'TP53', name: 'TP53', type: 'geneVariant' },\n\t\t'term.genes[0] should have expected structure'\n\t)\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Change mutation type', async test => {\n\tlet tw\n\tconst callback = _tw => {\n\t\ttw = _tw\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst mutationTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-mutationTypeRadios\"]')\n\tconst mutationTypeRadios = mutationTypeRadiosDiv.selectAll('input[type=\"radio\"]')\n\t// select CNV mutation type\n\tconst thirdRadio: any = mutationTypeRadios.nodes()[2]\n\tthirdRadio.click()\n\t// verify gene set option is hidden for CNV\n\tconst inputTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-genesetTypeRadios\"]')\n\tconst geneSetDiv = inputTypeRadiosDiv.selectAll('div').filter((d: any) => d.value == 'geneset')\n\ttest.equal(geneSetDiv.style('display'), 'none', 'Gene set option should be hidden for CNV')\n\t// enter gene to search\n\tconst geneSearchInput: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\t\t.select('input[type=\"search\"]')\n\t\t.node()\n\tgeneSearchInput.value = 'TP53'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(tw.q.predefined_groupset_idx, 2, 'q.predefined_groupset_idx should be 2 upon selecting third radio button')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Gene set input', async test => {\n\tlet tw\n\tconst callback = _tw => {\n\t\ttw = _tw\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst inputTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-genesetTypeRadios\"]')\n\tconst inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type=\"radio\"]')\n\tconst secondRadio: any = inputTypeRadios.nodes()[1]\n\tsecondRadio.click()\n\tconst geneSearchInput: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\t\t.select('input[type=\"search\"]')\n\t\t.node()\n\tgeneSearchInput.value = 'TP53'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100) // wait for dispatch event\n\tgeneSearchInput.value = 'KRAS'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tconst buttons = holder.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]').selectAll('button').nodes()\n\tconst submitButton: any = buttons.find((btn: any) => btn.textContent.trim() === 'Submit')\n\tawait sleep(100) // wait until submit button is enabled\n\tsubmitButton.click()\n\tawait sleep(100) // wait until tw is populated\n\ttest.equal(tw.term.genes.length, 2, 'term.genes[] should have length of 2')\n\ttest.equal(tw.term.name, 'TP53, KRAS', 'term.name should concatenate gene names')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Gene set input - custom name', async test => {\n\tlet tw\n\tconst callback = _tw => {\n\t\ttw = _tw\n\t}\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({ holder, callback })\n\tconst inputTypeRadiosDiv = holder.select('[data-testid=\"sjpp-genevariant-genesetTypeRadios\"]')\n\tconst inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type=\"radio\"]')\n\tconst secondRadio: any = inputTypeRadios.nodes()[1]\n\tsecondRadio.click()\n\tconst geneSearchInput: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\t\t.select('input[type=\"search\"]')\n\t\t.node()\n\tgeneSearchInput.value = 'TP53'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100) // wait for dispatch event\n\tgeneSearchInput.value = 'KRAS'\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100) // wait for dispatch event\n\tconst nameInput: any = holder.select('[data-testid=\"sja_genesetinput_name\"]').node()\n\tnameInput.value = 'Test gene set'\n\tconst buttons = holder.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]').selectAll('button').nodes()\n\tconst submitButton: any = buttons.find((btn: any) => btn.textContent.trim() === 'Submit')\n\tawait sleep(100) // wait until submit button is enabled\n\tsubmitButton.click()\n\tawait sleep(100) // wait until tw is populated\n\ttest.equal(tw.term.genes.length, 2, 'term.genes[] should have length of 2')\n\ttest.equal(tw.term.name, 'Test gene set', 'term.name should be custom name')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\n/* the settings a mass store remembers for a gene, see remember_gvq() in client/mass/store.ts.\nSupplied through a derived vocabApi, so that the shared one is left alone */\nfunction getVocabApiWithRememberedQ(lst) {\n\treturn Object.assign(Object.create(vocabApi), { getGvQLst: () => structuredClone(lst) })\n}\n\n/* a grouping of the first mutation type of this dataset, SNV/indel (somatic), as it is\nremembered: a customset whose group filter carries the dt term of each tvs */\nfunction getRememberedQ(name) {\n\treturn {\n\t\ttype: 'custom-groupset',\n\t\tcustomset: {\n\t\t\tgroups: [\n\t\t\t\t{\n\t\t\t\t\tname,\n\t\t\t\t\tfilter: {\n\t\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\t\tjoin: '',\n\t\t\t\t\t\tin: true,\n\t\t\t\t\t\tlst: [{ type: 'tvs', tvs: { term: { id: 'snvindel_somatic', dt: dtsnvindel, origin: 'somatic' } } }]\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n}\n\nconst rememberedLst = [\n\t{ label: 'TP53 missense', q: getRememberedQ('TP53 missense') },\n\t{ label: 'TP53 truncating', q: getRememberedQ('TP53 truncating') }\n]\n\nasync function pickGene(holder, gene = 'TP53') {\n\tconst geneSearchInput: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-geneSearchDiv\"]')\n\t\t.select('input[type=\"search\"]')\n\t\t.node()\n\tgeneSearchInput.value = gene\n\tgeneSearchInput.dispatchEvent(new KeyboardEvent('keyup', { key: 'Enter', code: 'Enter', bubbles: true }))\n\tawait sleep(100)\n}\n\ntape('Remembered settings are offered for the picked gene', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst),\n\t\tkeepsQ: true,\n\t\t// as client/plots/summarizeMutationSurvival.ts supplies it\n\t\tmsg: 'Hit ENTER to launch plot.'\n\t})\n\tawait pickGene(holder)\n\n\ttest.equal(tw, undefined, 'should not apply the mutation type while the settings are offered')\n\tconst msgDiv: any = holder\n\t\t.selectAll('div')\n\t\t.nodes()\n\t\t.find((n: any) => n.textContent == 'Hit ENTER to launch plot.')\n\ttest.equal(msgDiv?.style.display, 'none', 'should hide a caller message that no longer describes what happens')\n\tconst remembered = holder.selectAll('[data-testid=\"sjpp-genevariant-rememberedQ\"]')\n\ttest.equal(remembered.size(), 2, 'should offer both remembered settings')\n\ttest.deepEqual(\n\t\tremembered.nodes().map((n: any) => n.textContent),\n\t\t['TP53 missense', 'TP53 truncating'],\n\t\t'should label each by its remembered label'\n\t)\n\tconst options: any[] = holder.selectAll('.sja_menuoption').nodes()\n\ttest.equal(options.length, 3, 'should offer a way to continue with the mutation type instead')\n\ttest.ok(\n\t\toptions.every((n: any) => n.getAttribute('tabindex') == '0'),\n\t\t'should make every option keyboard focusable'\n\t)\n\ttest.equal(document.activeElement, options[0], 'should focus the most recent setting')\n\n\t// arrowing moves within the options and wraps, so focus cannot leave them by accident\n\toptions[0].dispatchEvent(new KeyboardEvent('keydown', { key: 'ArrowDown', bubbles: true }))\n\ttest.equal(document.activeElement, options[1], 'should move focus down')\n\toptions[1].dispatchEvent(new KeyboardEvent('keydown', { key: 'ArrowUp', bubbles: true }))\n\ttest.equal(document.activeElement, options[0], 'should move focus up')\n\toptions[0].dispatchEvent(new KeyboardEvent('keydown', { key: 'ArrowUp', bubbles: true }))\n\ttest.equal(document.activeElement, options[2], 'should wrap to the last option')\n\n\t/* activating on keydown and not keyup: the gene above is picked by pressing Enter in the\n\tsearch box, whose keyup would otherwise land on the option focused here */\n\toptions[2].dispatchEvent(new KeyboardEvent('keydown', { key: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(tw?.q?.type, 'predefined-groupset', 'should continue with the mutation type on Enter')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Remembered settings are applied on Enter', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst),\n\t\tkeepsQ: true\n\t})\n\tawait pickGene(holder)\n\n\tconst first: any = holder.selectAll('[data-testid=\"sjpp-genevariant-rememberedQ\"]').nodes()[0]\n\tfirst.dispatchEvent(new KeyboardEvent('keydown', { key: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(tw.q.type, 'custom-groupset', 'should apply the remembered q')\n\ttest.deepEqual(\n\t\ttw.q.customset.groups.map((g: any) => g.name),\n\t\t['TP53 missense'],\n\t\t'should apply the groups of the setting that was focused'\n\t)\n\ttest.equal(tw.term.name, 'TP53', 'should apply it to the gene that was picked')\n\ttest.equal(\n\t\tholder.select('[data-testid=\"sjpp-genevariant-rememberedQ\"]').empty(),\n\t\ttrue,\n\t\t'should clear the offered settings once one is applied'\n\t)\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Remembered settings of another mutation type do not lead', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst),\n\t\tkeepsQ: true\n\t})\n\t// the settings above group SNV/indel (somatic) variants, so select CNV instead\n\tconst cnvRadio: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-mutationTypeRadios\"]')\n\t\t.selectAll('input[type=\"radio\"]')\n\t\t.nodes()[2]\n\tcnvRadio.click()\n\tawait pickGene(holder)\n\n\tconst options: any[] = holder.selectAll('.sja_menuoption').nodes()\n\ttest.deepEqual(\n\t\toptions.map((n: any) => n.textContent),\n\t\t['Continue with CNV', 'TP53 missense', 'TP53 truncating'],\n\t\t'should lead with the selected mutation type, followed by the settings of other mutation types'\n\t)\n\ttest.equal(document.activeElement, options[0], 'should focus the way to continue with the mutation type')\n\n\toptions[0].dispatchEvent(new KeyboardEvent('keydown', { key: 'Enter', bubbles: true }))\n\tawait sleep(100)\n\ttest.equal(tw?.q?.predefined_groupset_idx, 2, 'should continue with the selected mutation type on Enter')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Remembered settings are cleared on changing the mutation type', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst),\n\t\tkeepsQ: true,\n\t\tmsg: 'Hit ENTER to launch plot.'\n\t})\n\tawait pickGene(holder)\n\ttest.equal(holder.selectAll('.sja_menuoption').size(), 3, 'should offer the settings of the picked gene')\n\n\t// the options were offered against the mutation type selected above, so they no longer apply\n\tconst cnvRadio: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-mutationTypeRadios\"]')\n\t\t.selectAll('input[type=\"radio\"]')\n\t\t.nodes()[2]\n\tcnvRadio.click()\n\tawait sleep(100)\n\n\ttest.equal(holder.selectAll('.sja_menuoption').size(), 0, 'should clear the offered settings')\n\ttest.equal(tw, undefined, 'should not apply anything on its own')\n\tconst msgDiv: any = holder\n\t\t.selectAll('div')\n\t\t.nodes()\n\t\t.find((n: any) => n.textContent == 'Hit ENTER to launch plot.')\n\ttest.equal(msgDiv?.style.display, 'block', 'should put back the caller message that describes picking a gene again')\n\n\t// the gene is picked again, now against the mutation type that was just selected\n\tawait pickGene(holder)\n\tconst options: any[] = holder.selectAll('.sja_menuoption').nodes()\n\ttest.equal(\n\t\toptions[0]?.textContent,\n\t\t'Continue with CNV',\n\t\t'should offer the settings against the mutation type now selected'\n\t)\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Remembered settings are cleared on changing the input type', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst),\n\t\tkeepsQ: true\n\t})\n\tawait pickGene(holder)\n\ttest.equal(holder.selectAll('.sja_menuoption').size(), 3, 'should offer the settings of the picked gene')\n\n\t// the gene input is rebuilt empty, so the settings offered for the gene it held no longer apply\n\tconst geneSetRadio: any = holder\n\t\t.select('[data-testid=\"sjpp-genevariant-genesetTypeRadios\"]')\n\t\t.selectAll('input[type=\"radio\"]')\n\t\t.nodes()[1]\n\tgeneSetRadio.click()\n\tawait sleep(100)\n\n\ttest.equal(holder.selectAll('.sja_menuoption').size(), 0, 'should clear the offered settings')\n\ttest.equal(tw, undefined, 'should not apply anything on its own')\n\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n\ntape('Remembered settings are not offered where the q would be dropped', async test => {\n\tlet tw\n\tconst holder = getHolder()\n\t// a consumer that keeps only the term{}, see keepsQ in client/termdb/TermTypeSearch.ts\n\tawait initializeSearchHandler({\n\t\tholder,\n\t\tcallback: _tw => (tw = _tw),\n\t\tvocabApi: getVocabApiWithRememberedQ(rememberedLst)\n\t})\n\tawait pickGene(holder)\n\n\ttest.equal(\n\t\tholder.select('[data-testid=\"sjpp-genevariant-rememberedQ\"]').empty(),\n\t\ttrue,\n\t\t'should offer no remembered setting'\n\t)\n\ttest.equal(tw.q.type, 'predefined-groupset', 'should apply the mutation type directly')\n\tif (test['_ok']) holder.remove()\n\ttest.end()\n})\n"],
-  "mappings": 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-  "names": ["vocabApi", "tape"]
-}

package/dist/genefusion.ui-ABRCUQFC.js

@@ -1,303 +0,0 @@
-import {
-  makeBtn,
-  makeGenomeDropDown,
-  makeResetBtn,
-  makeTextAreaInput
-} from "./chunk-5EBRF6Z7.js";
-import {
-  Tabs,
-  appear,
-  sayerror
-} from "./chunk-Q5SK3U2T.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-54KC7DAB.js";
-import "./chunk-N7DVQTPC.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-RPDVFM7E.js";
-import "./chunk-M4XXKTH2.js";
-import "./chunk-5ILEFNXJ.js";
-import "./chunk-IZUYLFOX.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 "./chunk-HS5PO5ZQ.js";
-
-// src/genefusion/genefusion.ui.js
-function init_geneFusionUI(holder, genomes) {
-  const wrapper = holder.append("div").style("margin", "20px 20px 20px 40px").style(
-    "font-family",
-    "'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif"
-  ).style("place-items", "center left").style("overflow", "hidden").classed("sjpp-app-ui", true);
-  const obj = {};
-  makeFusionInput(wrapper, obj);
-  const dropdown_div = wrapper.append("div").style("display", "flex").style("align-items", "center").style("margin", "10px");
-  genomeSelection(dropdown_div, genomes, obj);
-  makePositionDropDown(dropdown_div, obj);
-  const controlBtns_div = wrapper.append("div").style("display", "flex").style("align-items", "center").style("margin", "40px 0px 40px 130px");
-  makeSubmit(controlBtns_div, obj, holder, genomes);
-  makeResetBtn(controlBtns_div, obj, ".genefusion_input").style("margin", "0px 10px");
-  makeInfoSection(wrapper);
-  return obj;
-}
-function makeFusionInput(div, obj) {
-  const fusionInput = makeTextAreaInput({
-    div,
-    cols: 70,
-    // Increased to accommodate longer isoform format example
-    placeholder: "Example:\nPAX5,chr9,37002646,-::JAK2,chr9,5081726,+\nOr:\nPAX5,chr9,37002646,-,NM_016734::JAK2,chr9,5081726,+,NM_004972"
-  }).style("border", "1px solid rgb(138, 177, 212)").style("margin", "0px 0px 0px 20px").classed("genefusion_input", true).on("keyup", async () => {
-    obj.data = fusionInput.property("value").trim();
-  });
-}
-async function genomeSelection(div, genomes, obj) {
-  const genome_div = div.append("div").style("margin-left", "40px");
-  const g = makeGenomeDropDown(genome_div, genomes).style("border", "1px solid rgb(138, 177, 212)");
-  obj.genome = g.node();
-}
-async function makePositionDropDown(div, obj) {
-  const dropdown_div = div.append("div");
-  const positionSelect = dropdown_div.append("select").style("border-radius", "5px").style("padding", "5px 10px").style("margin", "1px 10px 1px 10px");
-  positionSelect.append("option").text("Codon position").property("value", "codon");
-  positionSelect.append("option").text("RNA position").property("value", "rna");
-  positionSelect.append("option").text("Genomic position").property("value", "genomic").attr("selected", true);
-  obj.posType = positionSelect.node();
-}
-function makeSubmit(div, obj, holder) {
-  const submit = makeBtn({
-    div,
-    text: "Submit"
-  });
-  const errorMessage_div = div.append("div");
-  submit.style("display", "block").on("click", () => {
-    if (!obj.data || obj.data === void 0) {
-      const sayerrorDiv = errorMessage_div.append("div").style("display", "inline-block").style("max-width", "20vw");
-      sayerror(sayerrorDiv, "Please provide data");
-      setTimeout(() => sayerrorDiv.remove(), 3e3);
-    } else {
-      select_default(".sjpp-app-ui").remove();
-      const runpp_arg = {
-        /** Do not use window.location.origin. See comment: line 180, renderContent(), client/appdrawer/adSandbox.js*/
-        host: sessionStorage.getItem("hostURL"),
-        nobox: true,
-        noheader: true,
-        parseurl: false,
-        genome: obj.genome.options[obj.genome.selectedIndex].text
-      };
-      makeSubmitResult(obj, holder, runpp_arg);
-    }
-  });
-}
-function makeInfoSection(div) {
-  div.append("div").style("margin", "10px").style("opacity", "0.65").html(`Limited to two-gene fusion products.<br>
-		One product per line.<br>
-		<br>
-		<strong>Format 1 (Basic):</strong> Each line has eight fields, four fields for each gene. For each gene join the following fields separated by a comma:
-		<ol><li>Gene symbol</li>
-		<li>Chromosome</li>
-		<li>Position, 1-based coordinate</li>
-		<li>Strand</li>
-		</ol>
-		<strong>Format 2 (With RefSeq isoforms):</strong> Each line has ten fields, five fields for each gene. For each gene join the following fields separated by a comma:
-		<ol><li>Gene symbol</li>
-		<li>Chromosome</li>
-		<li>Position, 1-based coordinate</li>
-		<li>Strand</li>
-		<li>RefSeq isoform (e.g., NM_001754)</li>
-		</ol>
-		Separate the two genes by a double colon (::). <br><br>
-		Examples: <br>
-		<p style="margin-left: 10px">
-		<strong>Format 1:</strong><br>
-		PAX5,chr9,37002646,-::JAK2,chr9,5081726,+<br>
-		ZCCHC7,chr9,37257786,-::PAX5,chr9,37024824,-<br>
-		BCR,chr22,23524427,+::ABL1,chr9,133729449,+<br><br>
-		<strong>Format 2:</strong><br>
-		RUNX1,chr21,36206706,-,NM_001754::MECOM,chr3,169099311,-,NM_004991<br>
-		PAX5,chr9,37002646,-,NM_016734::JAK2,chr9,5081726,+,NM_004972<p>`);
-}
-function validatePosition(position, geneName) {
-  if (!/^\d+$/.test(position)) {
-    throw new Error(`Invalid fusion format: position for ${geneName} must be a positive integer`);
-  }
-  const pos = Number(position);
-  if (pos <= 0) {
-    throw new Error(`Invalid fusion format: position for ${geneName} must be greater than 0 (1-based coordinates)`);
-  }
-}
-function parseFusionLine(line) {
-  const parts = line.trim().split("::");
-  if (parts.length !== 2) {
-    throw new Error('Invalid fusion format: must contain exactly two genes separated by "::"');
-  }
-  const gene1 = parts[0].split(",").map((s) => s.trim());
-  const gene2 = parts[1].split(",").map((s) => s.trim());
-  if (gene1.length !== 4 && gene1.length !== 5 || gene2.length !== 4 && gene2.length !== 5) {
-    throw new Error(
-      `Invalid fusion format: each gene must have 4 or 5 fields. Found gene1: ${gene1.length} fields, gene2: ${gene2.length} fields`
-    );
-  }
-  for (let i = 0; i < 4; i++) {
-    if (!gene1[i] || !gene2[i]) {
-      throw new Error("Invalid fusion format: gene symbol, chromosome, position, and strand are required");
-    }
-  }
-  validatePosition(gene1[2], gene1[0]);
-  validatePosition(gene2[2], gene2[0]);
-  if (!/^[+-]$/.test(gene1[3]) || !/^[+-]$/.test(gene2[3])) {
-    throw new Error('Invalid fusion format: strand must be "+" or "-"');
-  }
-  return [gene1, gene2];
-}
-function createFusionVariant(gene1, gene2) {
-  const variant = {
-    gene1: gene1[0],
-    chr1: gene1[1],
-    pos1: parseInt(gene1[2]) - 1,
-    strand1: gene1[3],
-    gene2: gene2[0],
-    chr2: gene2[1],
-    pos2: parseInt(gene2[2]) - 1,
-    strand2: gene2[3],
-    dt: 2,
-    class: "Fuserna"
-  };
-  const addIsoformIfPresent = (gene, fieldName) => {
-    if (gene.length > 4 && gene[4]?.trim()) {
-      variant[fieldName] = gene[4].trim();
-    }
-  };
-  addIsoformIfPresent(gene1, "isoform1");
-  addIsoformIfPresent(gene2, "isoform2");
-  return variant;
-}
-function makeSubmitResult(obj, div, runpp_arg) {
-  const lines = obj.data.split(/[\r\n]/).filter((line) => line.trim().length > 0);
-  if (lines.length === 1) {
-    try {
-      const [gene1, gene2] = parseFusionLine(lines[0]);
-      return makeFusionTabs(div, runpp_arg, gene1, gene2);
-    } catch (error) {
-      const errorDiv = div.append("div").style("color", "red").style("margin", "20px");
-      sayerror(errorDiv, `Error parsing fusion: ${error.message}`);
-      return;
-    }
-  }
-  const fusionSelect = div.append("div").append("select").style("border-radius", "5px").style("padding", "5px 10px").style("margin", "1px 10px 1px 10px");
-  fusionSelect.append("option").text(`Select Fusion (${lines.length})`);
-  const tabsDiv = div.append("div").style("margin", "20px");
-  const fusionsMap = /* @__PURE__ */ new Map();
-  for (const data of lines) {
-    try {
-      const [gene1, gene2] = parseFusionLine(data);
-      fusionsMap.set(`${gene1[0]}-${gene2[0]}`, [gene1, gene2]);
-    } catch (error) {
-      console.warn(`Skipping invalid fusion line: ${data}. Error: ${error.message}`);
-    }
-  }
-  if (fusionsMap.size === 0) {
-    const errorDiv = div.append("div").style("color", "red").style("margin", "20px");
-    sayerror(errorDiv, "No valid fusion lines found. Please check the format.");
-    return;
-  }
-  for (const fusion of fusionsMap) {
-    fusionSelect.append("option").property("value", fusion[0]).text(fusion[0]);
-  }
-  fusionSelect.on("change", () => {
-    tabsDiv.selectAll("*").remove();
-    const geneArrays = fusionsMap.get(fusionSelect.property("value"));
-    makeFusionTabs(tabsDiv, runpp_arg, geneArrays[0], geneArrays[1]);
-  });
-}
-function makeFusionTabs(div, runpp_arg, gene1, gene2) {
-  const tabs = [
-    // {
-    // ************ Keep for later, will introduce gene fusion view once data format settled *************
-    // 	label: 'Fusion',
-    // 	callback: async div => {
-    // 		if (!tabs[0].rendered) {
-    // 			appear(div)
-    // 			const text = `${gene1[0]}, ${gene1[1]},${gene1[2]},${gene2[0]},${gene2[1]},${gene2[2]}`
-    // 			const runpp_arg = {
-    // 				holder: div
-    // 					.append('div')
-    // 					.style('margin', '20px')
-    // 					.node(),
-    // 				host: window.location.origin,
-    // 				nobox: true,
-    // 				noheader: true,
-    // 				parseurl: false,
-    // 				genome,
-    // 				genefusion: {
-    // 					text,
-    // 					positionType: posType
-    // 					}
-    // 				}
-    // 			console.log(runpp_arg)
-    // 			runproteinpaint(Object.assign(runpp_arg))
-    // 			tabs[0].rendered = true
-    // 		}
-    // 	}
-    // },
-    {
-      label: gene1[0],
-      callback: async (event, tab) => {
-        appear(tab.contentHolder);
-        const variant = createFusionVariant(gene1, gene2);
-        const fusion_arg = {
-          holder: tab.contentHolder.append("div").style("margin", "20px").node(),
-          gene: gene1[0],
-          tracks: [
-            {
-              type: "mds3",
-              name: gene1[0],
-              custom_variants: [variant]
-            }
-          ]
-        };
-        runproteinpaint(Object.assign(runpp_arg, fusion_arg));
-        delete tab.callback;
-      }
-    },
-    {
-      label: gene2[0],
-      callback: async (event, tab) => {
-        appear(tab.contentHolder);
-        const variant = createFusionVariant(gene1, gene2);
-        const fusion_arg = {
-          holder: tab.contentHolder.append("div").style("margin", "20px").node(),
-          gene: gene2[0],
-          tracks: [
-            {
-              type: "mds3",
-              name: gene2[0],
-              custom_variants: [variant]
-            }
-          ]
-        };
-        runproteinpaint(Object.assign(runpp_arg, fusion_arg));
-        delete tab.callback;
-      }
-    }
-  ];
-  new Tabs({ holder: div, tabs }).main();
-}
-export {
-  init_geneFusionUI,
-  parseFusionLine
-};
-//# sourceMappingURL=genefusion.ui-ABRCUQFC.js.map

package/dist/geneset-N42FIVA6.js

@@ -1,203 +0,0 @@
-import {
-  GeneSetEditUIwithTabs,
-  fillTermWrapper
-} from "./chunk-Q5SK3U2T.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-54KC7DAB.js";
-import "./chunk-N7DVQTPC.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3
-} from "./chunk-RPDVFM7E.js";
-import "./chunk-M4XXKTH2.js";
-import "./chunk-5ILEFNXJ.js";
-import "./chunk-IZUYLFOX.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/geneset.js
-var GenesetComp = class _GenesetComp {
-  static type = "geneset";
-  // type: 'geneset'
-  // dom: {
-  // 	[domKey: string]: any // usually a d3-selection
-  // }
-  // opts: {
-  // 	holder: any
-  // 	genes: string[]
-  // 	mode: 'geneVariant' | 'geneExpression'
-  // 	callback: CallbackArg
-  // 	reactsTo?: (action: any) => boolean
-  // 	showWaitMessage?: (waitDiv: any) => void
-  // }
-  constructor(opts) {
-    this.type = _GenesetComp.type;
-    this.dom = {
-      holder: opts.holder.style("position", "relative").style("min-height", "300px").style("margin", "0px 20px").style("max-width", "1000px"),
-      body: opts.holder.append("div"),
-      loadingOverlay: opts.holder.append("div").attr("class", "sjpp-spinner").style("display", "none").style("position", "absolute").style("background-color", "#fff").style("z-index", 10).style("opacity", "0.5")
-      //.style('width', '100%')
-      //.style('height', '100%')
-    };
-  }
-  init() {
-    if (this.opts.reactsTo) this.reactsTo = this.opts.reactsTo;
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    return {
-      vocab: appState.vocab,
-      filter0: appState.termfilter.filter0,
-      config
-    };
-  }
-  async main() {
-    this.dom.body.selectAll("*").remove();
-    this.dom.loadingOverlay.style("display", "");
-    this.noWait().catch(console.warn);
-  }
-  async noWait() {
-    const abortCtrl = new AbortController();
-    try {
-      const [genes, stale] = await this.api.detectStale(() => this.getGenes({ signal: abortCtrl.signal }), {
-        abortCtrl
-      });
-      if (stale) return;
-      if (!genes?.length) this.render();
-      else this.opts.callback(this.api, genes);
-    } catch (e) {
-      if (e == "stale sequenceId" || e.name == "AbortError") return;
-      if (e?.code === "CACHE_BUSY" && this.opts.showWaitMessage) {
-        if (window.confirm(e.message || String(e))) this.main();
-        return;
-      }
-      if (this.opts.showWaitMessage) {
-        this.dom.body.style("margin", "20px").html(e);
-      }
-      throw e;
-    }
-  }
-  async getGenes({ signal }) {
-    const genes = this.opts.genes;
-    const settings = this.state.config.settings;
-    if (this.opts.genes) {
-      if (!Array.isArray(this.opts.genes) || this.opts.genes.length == 0) throw ".genes[] is not non-empty array";
-      return await this.getTwLst(this.opts.genes);
-    }
-    if (this.opts.showEditUI) {
-      return [];
-    }
-    let waitDiv;
-    if (this.opts.showWaitMessage) {
-      waitDiv = this.dom.body.append("div").style("margin", "20px");
-      this.opts.showWaitMessage(waitDiv);
-    }
-    let data;
-    if (this.opts.mode == "geneVariant") {
-      const body = {
-        genome: this.state.vocab.genome,
-        dslabel: this.state.vocab.dslabel
-      };
-      if (settings.maxGenes) body.maxGenes = settings.maxGenes;
-      if (settings.geneFilter) body.geneFilter = settings.geneFilter;
-      if (this.state.filter0) body.filter0 = this.state.filter0;
-      data = await dofetch3("termdb/topMutatedGenes", { body, signal });
-    } else if (this.opts.mode == "geneExpression") {
-      const body = {
-        genome: this.state.vocab.genome,
-        dslabel: this.state.vocab.dslabel,
-        maxGenes: settings.maxGenes
-      };
-      if (this.state.filter0) body.filter0 = this.state.filter0;
-      data = await dofetch3("termdb/topVariablyExpressedGenes", { body, signal });
-    } else {
-      throw "unknown opts.mode [geneset.js]";
-    }
-    if (!data) throw "invalid server response";
-    if (data.error) {
-      if (data.status === 429) throw Object.assign(new Error(data.error), { code: "CACHE_BUSY" });
-      throw data.error;
-    }
-    if (!data.genes) return [];
-    waitDiv.remove();
-    this.dom.loadingOverlay?.style("display", "none");
-    return await this.getTwLst(data.genes);
-  }
-  async getTwLst(genes) {
-    return await Promise.all(
-      // do tempfix of "data.genes.slice(0,3).map" for faster testing
-      genes.map(
-        async (i) => typeof i == "string" ? await fillTermWrapper({ term: { gene: i, type: this.opts.mode } }, this.app.vocabApi) : await fillTermWrapper({ term: { gene: i.gene || i.name, type: this.opts.mode } }, this.app.vocabApi)
-      )
-    );
-  }
-  async render() {
-    if (!this.dom?.holder) return;
-    const settings = this.state.config.settings;
-    this.dom.body.append("p").html(
-      `Define a gene set to launch <span style='text-transform: capitalize'>${this.state.config.toolName.toLowerCase()}</span>.`
-    );
-    new GeneSetEditUIwithTabs(
-      {
-        holder: this.dom.body.append("div"),
-        genome: this.opts.genome,
-        mode: this.opts.mode,
-        vocabApi: this.app.vocabApi,
-        //  await vocabInit({ state: { genome: gdcGenome, dslabel: gdcDslabel } }),
-        maxNumGenes: settings.maxGenes,
-        callback: async (result) => {
-          const twlst = await Promise.all(
-            result.geneList.map(async (i) => {
-              return fillTermWrapper({ term: { gene: i.gene || i.name || i, type: this.opts.mode } }, this.app.vocabApi);
-            })
-          );
-          this.opts.callback(this.api, twlst);
-        }
-      }
-      /*as GeneSetEditArg*/
-    );
-    this.dom.loadingOverlay?.style("display", "none");
-  }
-  destroy() {
-    this.dom.holder.selectAll("*").remove();
-    this.dom.holder.remove();
-    for (const key in this.dom) {
-      delete this.dom[key];
-    }
-  }
-};
-var genesetInit = getCompInit(GenesetComp);
-var componentInit = genesetInit;
-async function getPlotConfig(opts = {}, app) {
-  const config = copyMerge(
-    {
-      chartType: "geneset"
-    },
-    opts
-  );
-  return config;
-}
-export {
-  componentInit,
-  genesetInit,
-  getPlotConfig
-};
-//# sourceMappingURL=geneset-N42FIVA6.js.map