@sjcrh/proteinpaint-client 2.183.0 → 2.183.2-0

package/dist/genefusion.ui-VKAINMY7.js

@@ -1,249 +0,0 @@
-import {
-  makeBtn,
-  makeGenomeDropDown,
-  makeResetBtn,
-  makeTextAreaInput
-} from "./chunk-CUSG5PZE.js";
-import {
-  Tabs,
-  appear,
-  sayerror
-} from "./chunk-OXJ2TWDO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-V6DLLX4N.js";
-import "./chunk-7RN3L2BX.js";
-import "./chunk-A6TQGNDQ.js";
-import "./chunk-HYZG6OPC.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-SEQLC4AD.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-KQMEJUWI.js";
-import "./chunk-UJU3Q7QJ.js";
-import "./chunk-WGL6FIUE.js";
-import "./chunk-6ITDJ5UR.js";
-import "./chunk-XYFDBYOY.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.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: 50,
-    placeholder: "Example: PAX5,chr9,37002646,-::JAK2,chr9,5081726,+"
-  }).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>
-		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>
-		Separate the two genes by a double colon (::). <br><br>
-		Example: <br>
-		<p style="margin-left: 10px">
-		PAX5,chr9,37002646,-::JAK2,chr9,5081726,+<br>
-		ZCCHC7,chr9,37257786,-::PAX5,chr9,37024824,-<br>
-		BCR,chr22,23524427,+::ABL1,chr9,133729449,+<p>`);
-}
-function makeSubmitResult(obj, div, runpp_arg) {
-  if (obj.data.split(/[\r\n]/).length == 1) {
-    const line = obj.data.trim().split("::");
-    const gene1 = line[0].split(",");
-    const gene2 = line[1].split(",");
-    return makeFusionTabs(div, runpp_arg, gene1, gene2);
-  }
-  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 (${obj.data.split(/[\r\n]/).length})`);
-  const tabsDiv = div.append("div").style("margin", "20px");
-  const fusionsMap = /* @__PURE__ */ new Map();
-  for (const data of obj.data.split(/[\r\n]/)) {
-    const line = data.trim().split("::");
-    const gene1 = line[0].split(",");
-    const gene2 = line[1].split(",");
-    fusionsMap.set(`${gene1[0]}-${gene2[0]}`, [gene1, gene2]);
-  }
-  for (const fusion of fusionsMap) {
-    fusionSelect.append("option").property("value", fusion[0]).text(fusion[0]);
-  }
-  fusionSelect.on("change", () => {
-    tabsDiv.selectAll("*").remove();
-    const geneArrays = fusionsMap.get(fusionSelect.property("value"));
-    makeFusionTabs(tabsDiv, runpp_arg, geneArrays[0], geneArrays[1]);
-  });
-}
-function makeFusionTabs(div, runpp_arg, gene1, gene2) {
-  const tabs = [
-    // {
-    // ************ Keep for later, will introduce gene fusion view once data format settled *************
-    // 	label: 'Fusion',
-    // 	callback: async div => {
-    // 		if (!tabs[0].rendered) {
-    // 			appear(div)
-    // 			const text = `${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 fusion_arg = {
-          holder: tab.contentHolder.append("div").style("margin", "20px").node(),
-          gene: gene1[0],
-          tracks: [
-            {
-              type: "mds3",
-              name: gene1[0],
-              custom_variants: [
-                {
-                  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"
-                }
-              ]
-            }
-          ]
-        };
-        runproteinpaint(Object.assign(runpp_arg, fusion_arg));
-        delete tab.callback;
-      }
-    },
-    {
-      label: gene2[0],
-      callback: async (event, tab) => {
-        appear(tab.contentHolder);
-        const fusion_arg = {
-          holder: tab.contentHolder.append("div").style("margin", "20px").node(),
-          gene: gene2[0],
-          tracks: [
-            {
-              type: "mds3",
-              name: gene2[0],
-              custom_variants: [
-                {
-                  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"
-                }
-              ]
-            }
-          ]
-        };
-        runproteinpaint(Object.assign(runpp_arg, fusion_arg));
-        delete tab.callback;
-      }
-    }
-  ];
-  new Tabs({ holder: div, tabs }).main();
-}
-export {
-  init_geneFusionUI
-};
-//# sourceMappingURL=genefusion.ui-VKAINMY7.js.map

package/dist/genefusion.ui-VKAINMY7.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../src/genefusion/genefusion.ui.js"],
-  "sourcesContent": ["import * as uiutils from '#dom/uiUtils'\nimport { select as d3select, selectAll as d3selectAll } from 'd3-selection'\nimport { sayerror } from '../client'\nimport { Tabs } from '../../dom/toggleButtons'\nimport { appear } from '#dom/animation'\n\n/*\n------ EXPORTED ------ \ninit_geneFusionUI()\n\tholder \n\tgenomes\n\n------ Internal ------ \nmakeFusionInput\ngenomeSelection\nmakePositionDropDown\nmakeSubmit\nmakeInfoSection\nmakeSubmitResult\nmakeFusionTabs\n\n*/\n\nexport function init_geneFusionUI(holder, genomes) {\n\tconst wrapper = holder\n\t\t.append('div')\n\t\t.style('margin', '20px 20px 20px 40px')\n\t\t.style(\n\t\t\t'font-family',\n\t\t\t\"'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif\"\n\t\t)\n\t\t.style('place-items', 'center left')\n\t\t.style('overflow', 'hidden')\n\t\t.classed('sjpp-app-ui', true)\n\n\tconst obj = {}\n\n\tmakeFusionInput(wrapper, obj)\n\n\tconst dropdown_div = wrapper\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'center')\n\t\t.style('margin', '10px')\n\tgenomeSelection(dropdown_div, genomes, obj)\n\tmakePositionDropDown(dropdown_div, obj)\n\n\tconst controlBtns_div = wrapper\n\t\t.append('div')\n\t\t.style('display', 'flex')\n\t\t.style('align-items', 'center')\n\t\t.style('margin', '40px 0px 40px 130px')\n\tmakeSubmit(controlBtns_div, obj, holder, genomes)\n\tuiutils.makeResetBtn(controlBtns_div, obj, '.genefusion_input').style('margin', '0px 10px')\n\n\tmakeInfoSection(wrapper)\n\n\treturn obj\n}\n\nfunction makeFusionInput(div, obj) {\n\tconst fusionInput = uiutils\n\t\t.makeTextAreaInput({\n\t\t\tdiv,\n\t\t\tcols: 50,\n\t\t\tplaceholder: 'Example: PAX5,chr9,37002646,-::JAK2,chr9,5081726,+'\n\t\t})\n\t\t.style('border', '1px solid rgb(138, 177, 212)')\n\t\t.style('margin', '0px 0px 0px 20px')\n\t\t.classed('genefusion_input', true)\n\t\t.on('keyup', async () => {\n\t\t\tobj.data = fusionInput.property('value').trim()\n\t\t})\n}\n\nasync function genomeSelection(div, genomes, obj) {\n\tconst genome_div = div.append('div').style('margin-left', '40px')\n\tconst g = uiutils.makeGenomeDropDown(genome_div, genomes).style('border', '1px solid rgb(138, 177, 212)')\n\tobj.genome = g.node()\n}\n\nasync function makePositionDropDown(div, obj) {\n\tconst dropdown_div = div.append('div')\n\n\tconst positionSelect = dropdown_div\n\t\t.append('select')\n\t\t.style('border-radius', '5px')\n\t\t.style('padding', '5px 10px')\n\t\t.style('margin', '1px 10px 1px 10px')\n\tpositionSelect.append('option').text('Codon position').property('value', 'codon')\n\tpositionSelect.append('option').text('RNA position').property('value', 'rna')\n\tpositionSelect.append('option').text('Genomic position').property('value', 'genomic').attr('selected', true)\n\tobj.posType = positionSelect.node()\n}\n\nfunction makeSubmit(div, obj, holder) {\n\tconst submit = uiutils.makeBtn({\n\t\tdiv,\n\t\ttext: 'Submit'\n\t})\n\tconst errorMessage_div = div.append('div')\n\tsubmit.style('display', 'block').on('click', () => {\n\t\tif (!obj.data || obj.data == undefined) {\n\t\t\tconst sayerrorDiv = errorMessage_div.append('div').style('display', 'inline-block').style('max-width', '20vw')\n\t\t\tsayerror(sayerrorDiv, 'Please provide data')\n\t\t\tsetTimeout(() => sayerrorDiv.remove(), 3000)\n\t\t} else {\n\t\t\td3select('.sjpp-app-ui').remove()\n\t\t\tconst runpp_arg = {\n\t\t\t\t/** Do not use window.location.origin. See comment: line 180, renderContent(), client/appdrawer/adSandbox.js*/\n\t\t\t\thost: sessionStorage.getItem('hostURL'),\n\t\t\t\tnobox: true,\n\t\t\t\tnoheader: true,\n\t\t\t\tparseurl: false,\n\t\t\t\tgenome: obj.genome.options[obj.genome.selectedIndex].text\n\t\t\t}\n\t\t\tmakeSubmitResult(obj, holder, runpp_arg)\n\t\t}\n\t})\n}\n\nfunction makeInfoSection(div) {\n\tdiv.append('div').style('margin', '10px').style('opacity', '0.65').html(`Limited to two-gene fusion products.<br>\n\t\tOne product per line.<br>\n\t\tEach line has eight fields. four fields for each gene. For each gene join the following fields separated by a comma:\n\t\t<ol><li>Gene symbol</li>\n\t\t<li>Chromosome</li>\n\t\t<li>Position, 1-based coordinate</li>\n\t\t<li>Strand</li>\n\t\t</ol>\n\t\tSeparate the two genes by a double colon (::). <br><br>\n\t\tExample: <br>\n\t\t<p style=\"margin-left: 10px\">\n\t\tPAX5,chr9,37002646,-::JAK2,chr9,5081726,+<br>\n\t\tZCCHC7,chr9,37257786,-::PAX5,chr9,37024824,-<br>\n\t\tBCR,chr22,23524427,+::ABL1,chr9,133729449,+<p>`)\n}\n\nfunction makeSubmitResult(obj, div, runpp_arg) {\n\tif (obj.data.split(/[\\r\\n]/).length == 1) {\n\t\t//Only one line entered, no dropdown\n\t\tconst line = obj.data.trim().split('::')\n\t\tconst gene1 = line[0].split(',')\n\t\tconst gene2 = line[1].split(',')\n\t\treturn makeFusionTabs(div, runpp_arg, gene1, gene2)\n\t}\n\t//Make dropdown to select fusions\n\t//On select, toggle tabs for each gene appears underneath with the track for each gene\n\tconst fusionSelect = div\n\t\t.append('div')\n\t\t.append('select')\n\t\t.style('border-radius', '5px')\n\t\t.style('padding', '5px 10px')\n\t\t.style('margin', '1px 10px 1px 10px')\n\n\tfusionSelect.append('option').text(`Select Fusion (${obj.data.split(/[\\r\\n]/).length})`)\n\n\tconst tabsDiv = div.append('div').style('margin', '20px')\n\n\tconst fusionsMap = new Map()\n\n\tfor (const data of obj.data.split(/[\\r\\n]/)) {\n\t\tconst line = data.trim().split('::')\n\t\tconst gene1 = line[0].split(',')\n\t\tconst gene2 = line[1].split(',')\n\t\tfusionsMap.set(`${gene1[0]}-${gene2[0]}`, [gene1, gene2])\n\t}\n\n\tfor (const fusion of fusionsMap) {\n\t\tfusionSelect.append('option').property('value', fusion[0]).text(fusion[0])\n\t}\n\tfusionSelect.on('change', () => {\n\t\ttabsDiv.selectAll('*').remove()\n\t\tconst geneArrays = fusionsMap.get(fusionSelect.property('value'))\n\t\tmakeFusionTabs(tabsDiv, runpp_arg, geneArrays[0], geneArrays[1])\n\t})\n}\n\nfunction makeFusionTabs(div, runpp_arg, gene1, gene2) {\n\tconst tabs = [\n\t\t// {\n\t\t// ************ Keep for later, will introduce gene fusion view once data format settled *************\n\t\t// \tlabel: 'Fusion',\n\t\t// \tcallback: async div => {\n\t\t// \t\tif (!tabs[0].rendered) {\n\t\t// \t\t\tappear(div)\n\t\t// \t\t\tconst text = `${gene1[0]}, ${gene1[1]},${gene1[2]},${gene2[0]},${gene2[1]},${gene2[2]}`\n\t\t// \t\t\tconst runpp_arg = {\n\t\t// \t\t\t\tholder: div\n\t\t// \t\t\t\t\t.append('div')\n\t\t// \t\t\t\t\t.style('margin', '20px')\n\t\t// \t\t\t\t\t.node(),\n\t\t// \t\t\t\thost: window.location.origin,\n\t\t// \t\t\t\tnobox: true,\n\t\t// \t\t\t\tnoheader: true,\n\t\t// \t\t\t\tparseurl: false,\n\t\t// \t\t\t\tgenome,\n\t\t// \t\t\t\tgenefusion: {\n\t\t// \t\t\t\t\ttext,\n\t\t// \t\t\t\t\tpositionType: posType\n\t\t// \t\t\t\t\t}\n\t\t// \t\t\t\t}\n\t\t// \t\t\tconsole.log(runpp_arg)\n\t\t// \t\t\trunproteinpaint(Object.assign(runpp_arg))\n\t\t// \t\t\ttabs[0].rendered = true\n\t\t// \t\t}\n\t\t// \t}\n\t\t// },\n\t\t{\n\t\t\tlabel: gene1[0],\n\t\t\tcallback: async (event, tab) => {\n\t\t\t\tappear(tab.contentHolder)\n\t\t\t\tconst fusion_arg = {\n\t\t\t\t\tholder: tab.contentHolder.append('div').style('margin', '20px').node(),\n\t\t\t\t\tgene: gene1[0],\n\t\t\t\t\ttracks: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'mds3',\n\t\t\t\t\t\t\tname: gene1[0],\n\t\t\t\t\t\t\tcustom_variants: [\n\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\tgene1: gene1[0],\n\t\t\t\t\t\t\t\t\tchr1: gene1[1],\n\t\t\t\t\t\t\t\t\tpos1: parseInt(gene1[2]) - 1,\n\t\t\t\t\t\t\t\t\tstrand1: gene1[3],\n\t\t\t\t\t\t\t\t\tgene2: gene2[0],\n\t\t\t\t\t\t\t\t\tchr2: gene2[1],\n\t\t\t\t\t\t\t\t\tpos2: parseInt(gene2[2]) - 1,\n\t\t\t\t\t\t\t\t\tstrand2: gene2[3],\n\t\t\t\t\t\t\t\t\tdt: 2,\n\t\t\t\t\t\t\t\t\tclass: 'Fuserna'\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t]\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t\trunproteinpaint(Object.assign(runpp_arg, fusion_arg))\n\t\t\t\tdelete tab.callback\n\t\t\t}\n\t\t},\n\t\t{\n\t\t\tlabel: gene2[0],\n\t\t\tcallback: async (event, tab) => {\n\t\t\t\tappear(tab.contentHolder)\n\t\t\t\tconst fusion_arg = {\n\t\t\t\t\tholder: tab.contentHolder.append('div').style('margin', '20px').node(),\n\t\t\t\t\tgene: gene2[0],\n\t\t\t\t\ttracks: [\n\t\t\t\t\t\t{\n\t\t\t\t\t\t\ttype: 'mds3',\n\t\t\t\t\t\t\tname: gene2[0],\n\t\t\t\t\t\t\tcustom_variants: [\n\t\t\t\t\t\t\t\t{\n\t\t\t\t\t\t\t\t\tgene1: gene1[0],\n\t\t\t\t\t\t\t\t\tchr1: gene1[1],\n\t\t\t\t\t\t\t\t\tpos1: parseInt(gene1[2]) - 1,\n\t\t\t\t\t\t\t\t\tstrand1: gene1[3],\n\t\t\t\t\t\t\t\t\tgene2: gene2[0],\n\t\t\t\t\t\t\t\t\tchr2: gene2[1],\n\t\t\t\t\t\t\t\t\tpos2: parseInt(gene2[2]) - 1,\n\t\t\t\t\t\t\t\t\tstrand2: gene2[3],\n\t\t\t\t\t\t\t\t\tdt: 2,\n\t\t\t\t\t\t\t\t\tclass: 'Fuserna'\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t]\n\t\t\t\t\t\t}\n\t\t\t\t\t]\n\t\t\t\t}\n\t\t\t\trunproteinpaint(Object.assign(runpp_arg, fusion_arg))\n\t\t\t\tdelete tab.callback\n\t\t\t}\n\t\t}\n\t]\n\n\tnew Tabs({ holder: div, tabs }).main()\n}\n"],
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-}

package/dist/geneset-673KAZVX.js

@@ -1,194 +0,0 @@
-import {
-  GeneSetEditUI,
-  fillTermWrapper
-} from "./chunk-OXJ2TWDO.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-V6DLLX4N.js";
-import {
-  dofetch3
-} from "./chunk-7RN3L2BX.js";
-import "./chunk-A6TQGNDQ.js";
-import "./chunk-HYZG6OPC.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-5EF5U7MX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-UCLS2SVB.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-MVTCBVSX.js";
-import "./chunk-SEQLC4AD.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-KQMEJUWI.js";
-import "./chunk-UJU3Q7QJ.js";
-import "./chunk-WGL6FIUE.js";
-import "./chunk-6ITDJ5UR.js";
-import "./chunk-XYFDBYOY.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.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"),
-      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;
-      else {
-        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);
-    }
-    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) 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;
-    this.dom.body.append("p").text(`No default genes. Please change the cohort or define a gene set to launch ${this.state.config.toolName}.`);
-    new GeneSetEditUI(
-      {
-        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 } }),
-        callback: async (result) => {
-          const twlst = await Promise.all(
-            result.geneList.map(async (i) => {
-              return fillTermWrapper({ term: { gene: i.gene || i.name || i, type: "geneVariant" } }, 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-673KAZVX.js.map

package/dist/geneset-673KAZVX.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../plots/geneset.js"],
-  "sourcesContent": ["import { getCompInit, copyMerge, sleep } from '../rx'\nimport { GeneSetEditUI /*, GeneSetEditArg, CallbackArg*/ } from '../dom/GeneSetEdit/GeneSetEditUI.ts'\nimport { fillTermWrapper } from '#termsetting'\nimport { dofetch3 } from '#common/dofetch'\n\n// This is a reactive geneset component, meant for use within plotApp.\n// The usage in client/gdc/oncomatrix.js and geneExpClustering.js is as follows:\n//\n// 1. plotApp is initialized with geneset as the first plot/component\n// 2. if there are opts.genes, geneset would simply call its opts.callback right away (not even render the edit UI)\n// 3. if not, then geneset would render the edit UI, and also use its opts.callback to supply the wrapped genes\n// 4. in opts.[matrix | hierCluster].callbacks.firstRender,\n//    the matrix/hierCluster will dispatch plot_delete to remove the geneset as the plot,\n//    and also plot_create to render the target plot (like matrix, hierCluster)\n//\n// The reactivity is required to toggle loading overlay visibility\n// and to create a new plot within the same plot app, once a valid geneset is\n// obtained from the server.\n//\n// opts{}\n// .genome     see GeneSetArg.ClientGenome\n// .holder     the DOM element where the geneset edit UI will be rendered\n// .genes[]    an array of strings gene symbols, see Note #2 above\n// .mode       'geneVariant' | 'geneExpression', see dom/GeneSetEdit for details\n// .callback   see GeneSetEditArg.callback in dom/GeneSetEdit\n// .reactsTo   the state changes that this component would react to, see example in matrix opts\n// .showWaitMessage(waitDiv)  optional function to display a custom message while genes are being loaded\n\nclass GenesetComp {\n\tstatic type = 'geneset'\n\t// type: 'geneset'\n\t// dom: {\n\t// \t[domKey: string]: any // usually a d3-selection\n\t// }\n\t// opts: {\n\t// \tholder: any\n\t// \tgenes: string[]\n\t// \tmode: 'geneVariant' | 'geneExpression'\n\t// \tcallback: CallbackArg\n\t// \treactsTo?: (action: any) => boolean\n\t// \tshowWaitMessage?: (waitDiv: any) => void\n\t// }\n\n\tconstructor(opts) {\n\t\tthis.type = GenesetComp.type\n\n\t\tthis.dom = {\n\t\t\tholder: opts.holder.style('position', 'relative').style('min-height', '300px'),\n\t\t\tbody: opts.holder.append('div'),\n\t\t\tloadingOverlay: opts.holder\n\t\t\t\t.append('div')\n\t\t\t\t.attr('class', 'sjpp-spinner')\n\t\t\t\t.style('display', 'none')\n\t\t\t\t.style('position', 'absolute')\n\t\t\t\t.style('background-color', '#fff')\n\t\t\t\t.style('z-index', 10)\n\t\t\t\t.style('opacity', '0.5')\n\t\t\t//.style('width', '100%')\n\t\t\t//.style('height', '100%')\n\t\t}\n\t}\n\n\tinit() {\n\t\tif (this.opts.reactsTo) this.reactsTo = this.opts.reactsTo\n\t}\n\n\tgetState(appState) {\n\t\tconst config = appState.plots.find(p => p.id === this.id)\n\t\treturn {\n\t\t\tvocab: appState.vocab,\n\t\t\tfilter0: appState.termfilter.filter0,\n\t\t\tconfig\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.dom.body.selectAll('*').remove()\n\t\tthis.dom.loadingOverlay.style('display', '')\n\t\t// do not await, since this main may be called as part of the initial dispatch\n\t\t// in the app init(), and that app instance should return without having to wait\n\t\t// for this component to finish the initial genes request and fully render\n\t\t// NOTE: This is an important accomodation of rapid-fire cohort changes in the gdc portal\n\t\tthis.noWait().catch(console.warn)\n\t}\n\n\tasync noWait() {\n\t\tconst abortCtrl = new AbortController()\n\t\ttry {\n\t\t\tconst [genes, stale] = await this.api.detectStale(() => this.getGenes({ signal: abortCtrl.signal }), {\n\t\t\t\tabortCtrl\n\t\t\t})\n\t\t\tif (stale) return\n\t\t\tif (!genes?.length) this.render()\n\t\t\telse this.opts.callback(this.api, genes)\n\t\t} catch (e) {\n\t\t\t// may ignore this error\n\t\t\tif (e == 'stale sequenceId' || e.name == 'AbortError') return\n\t\t\telse {\n\t\t\t\tif (this.opts.showWaitMessage) {\n\t\t\t\t\tthis.dom.body.style('margin', '20px').html(e)\n\t\t\t\t}\n\t\t\t\tthrow e\n\t\t\t}\n\t\t}\n\t}\n\n\tasync getGenes({ signal }) {\n\t\tconst genes = this.opts.genes\n\t\tconst settings = this.state.config.settings\n\t\tif (this.opts.genes) {\n\t\t\t// genes are predefined\n\t\t\tif (!Array.isArray(this.opts.genes) || this.opts.genes.length == 0) throw '.genes[] is not non-empty array'\n\t\t\treturn await this.getTwLst(this.opts.genes)\n\t\t}\n\n\t\tlet waitDiv\n\t\tif (this.opts.showWaitMessage) {\n\t\t\twaitDiv = this.dom.body.append('div').style('margin', '20px')\n\t\t\tthis.opts.showWaitMessage(waitDiv)\n\t\t}\n\n\t\t// genes are not predefined. query to get top genes using the current cohort\n\t\tlet data\n\t\tif (this.opts.mode == 'geneVariant') {\n\t\t\tconst body = {\n\t\t\t\tgenome: this.state.vocab.genome,\n\t\t\t\tdslabel: this.state.vocab.dslabel\n\t\t\t}\n\t\t\tif (settings.maxGenes) body.maxGenes = settings.maxGenes\n\t\t\tif (settings.geneFilter) body.geneFilter = settings.geneFilter\n\t\t\tif (this.state.filter0) body.filter0 = this.state.filter0\n\t\t\t// XXX this is optional query!! if ds is missing then should show input ui instead\n\t\t\t// TODO why cannot use vocab method?\n\t\t\t// TODO purpose of 2nd and 3rd arguments?\n\t\t\tdata = await dofetch3('termdb/topMutatedGenes', { body, signal })\n\t\t} else if (this.opts.mode == 'geneExpression') {\n\t\t\tconst body = {\n\t\t\t\tgenome: this.state.vocab.genome,\n\t\t\t\tdslabel: this.state.vocab.dslabel,\n\t\t\t\tmaxGenes: settings.maxGenes\n\t\t\t}\n\t\t\tif (this.state.filter0) body.filter0 = this.state.filter0\n\t\t\t// XXX this is optional query!! if ds is missing then should show input ui instead\n\t\t\tdata = await dofetch3('termdb/topVariablyExpressedGenes', { body, signal })\n\t\t} else {\n\t\t\tthrow 'unknown opts.mode [geneset.js]'\n\t\t}\n\n\t\tif (!data) throw 'invalid server response'\n\t\tif (data.error) throw data.error\n\n\t\tif (!data.genes) return [] // do not throw and halt. downstream will detect no genes and handle it by showing edit ui\n\t\twaitDiv.remove()\n\t\tthis.dom.loadingOverlay?.style('display', 'none')\n\t\treturn await this.getTwLst(data.genes)\n\t}\n\n\tasync getTwLst(genes) {\n\t\treturn await Promise.all(\n\t\t\t// do tempfix of \"data.genes.slice(0,3).map\" for faster testing\n\t\t\tgenes.map(async i =>\n\t\t\t\ttypeof i == 'string'\n\t\t\t\t\t? await fillTermWrapper({ term: { gene: i, type: this.opts.mode } }, this.app.vocabApi)\n\t\t\t\t\t: await fillTermWrapper({ term: { gene: i.gene || i.name, type: this.opts.mode } }, this.app.vocabApi)\n\t\t\t)\n\t\t)\n\t}\n\n\tasync render() {\n\t\tif (!this.dom?.holder) return\n\t\tthis.dom.body\n\t\t\t.append('p')\n\t\t\t.text(`No default genes. Please change the cohort or define a gene set to launch ${this.state.config.toolName}.`)\n\t\tnew GeneSetEditUI(\n\t\t\t{\n\t\t\t\tholder: this.dom.body.append('div'),\n\t\t\t\tgenome: this.opts.genome,\n\t\t\t\tmode: this.opts.mode,\n\t\t\t\tvocabApi: this.app.vocabApi, //  await vocabInit({ state: { genome: gdcGenome, dslabel: gdcDslabel } }),\n\t\t\t\tcallback: async result => {\n\t\t\t\t\tconst twlst = await Promise.all(\n\t\t\t\t\t\tresult.geneList.map(async i => {\n\t\t\t\t\t\t\treturn fillTermWrapper({ term: { gene: i.gene || i.name || i, type: 'geneVariant' } }, this.app.vocabApi)\n\t\t\t\t\t\t})\n\t\t\t\t\t)\n\n\t\t\t\t\tthis.opts.callback(this.api, twlst)\n\t\t\t\t}\n\t\t\t} /*as GeneSetEditArg*/\n\t\t)\n\t\tthis.dom.loadingOverlay?.style('display', 'none')\n\t}\n\n\tdestroy() {\n\t\t// the dom.holder itself is not a d3-selection,\n\t\t// so need to specify a destroy function here\n\t\t// since the default rx.componentApi.destroy()\n\t\t// does not work when dom.holder is not a d3-selection\n\t\tthis.dom.holder.selectAll('*').remove()\n\t\tthis.dom.holder.remove()\n\t\tfor (const key in this.dom) {\n\t\t\tdelete this.dom[key]\n\t\t}\n\t}\n}\n\nexport const genesetInit = getCompInit(GenesetComp)\n// this alias will allow abstracted dynamic imports\nexport const componentInit = genesetInit\n\nexport async function getPlotConfig(opts = {}, app) {\n\tconst config = copyMerge(\n\t\t{\n\t\t\tchartType: 'geneset'\n\t\t},\n\t\topts\n\t)\n\n\treturn config\n}\n"],
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-}