@sjcrh/proteinpaint-client 2.190.2 → 2.191.2

package/dist/geneVariant.integration.spec-OESHXKBV.js

@@ -1,198 +0,0 @@
-import {
-  hg38
-} from "./chunk-7VB2BKXW.js";
-import {
-  sleep
-} from "./chunk-E4IHE23N.js";
-import {
-  require_tape
-} from "./chunk-QWOE5YTB.js";
-import {
-  SearchHandler,
-  vocabInit
-} from "./chunk-UK3PTE3P.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IFA3COXY.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5X6J6UAT.js";
-import "./chunk-3L32ZXRS.js";
-import "./chunk-GRNZWYOJ.js";
-import "./chunk-X27TRPIZ.js";
-import "./chunk-STQU7XZV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-5V43Y2RC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-B4VRYXOQ.js";
-import "./chunk-XOCO3LVN.js";
-import "./chunk-EBKERML3.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// termdb/handlers/test/geneVariant.integration.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-async function getVocabApi() {
-  const vocabApi2 = vocabInit({ state: { vocab: { genome: "hg38-test", dslabel: "TermdbTest" } } });
-  if (!vocabApi2) throw "vocabApi is missing";
-  await vocabApi2.getTermdbConfig();
-  return vocabApi2;
-}
-var vocabApi = await getVocabApi();
-var handler = new SearchHandler();
-function getHolder() {
-  const holder = select_default("body").append("div");
-  return holder;
-}
-async function initializeSearchHandler(opts) {
-  const callback = opts.callback || (() => {
-  });
-  await handler.init({
-    holder: opts.holder,
-    app: { vocabApi },
-    genomeObj: hg38,
-    callback
-  });
-}
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- geneVariant search handler -***-");
-  test.end();
-});
-(0, import_tape.default)("Search handler layout", async (test) => {
-  const holder = getHolder();
-  await initializeSearchHandler({ holder });
-  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
-  test.ok(
-    mutationTypeRadiosDiv.selectAll('input[type="radio"]').size() > 0,
-    "Mutation type radio buttons should be present"
-  );
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  test.equal(
-    inputTypeRadiosDiv.selectAll('input[type="radio"]').size(),
-    2,
-    "Input type radio buttons should be present"
-  );
-  const searchDiv = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]');
-  test.equal(searchDiv.selectAll('input[type="search"]').size(), 1, "Gene search input should be present");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Single gene input", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(tw.term.type, "geneVariant", "term.type should be geneVariant");
-  test.equal(tw.q.type, "predefined-groupset", "q.type should be predefined-groupset");
-  test.equal(tw.q.predefined_groupset_idx, 0, "q.predefined_groupset_idx should be 0");
-  test.equal(tw.term.genes.length, 1, "term.genes[] should have length of 1");
-  test.deepEqual(
-    tw.term.genes[0],
-    { kind: "gene", id: "TP53", gene: "TP53", name: "TP53", type: "geneVariant" },
-    "term.genes[0] should have expected structure"
-  );
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Change mutation type", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
-  const mutationTypeRadios = mutationTypeRadiosDiv.selectAll('input[type="radio"]');
-  const thirdRadio = mutationTypeRadios.nodes()[2];
-  thirdRadio.click();
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  const geneSetDiv = inputTypeRadiosDiv.selectAll("div").filter((d) => d.value == "geneset");
-  test.equal(geneSetDiv.style("display"), "none", "Gene set option should be hidden for CNV");
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(tw.q.predefined_groupset_idx, 2, "q.predefined_groupset_idx should be 2 upon selecting third radio button");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Gene set input", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
-  const secondRadio = inputTypeRadios.nodes()[1];
-  secondRadio.click();
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  geneSearchInput.value = "KRAS";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
-  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
-  await sleep(100);
-  submitButton.click();
-  await sleep(100);
-  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
-  test.equal(tw.term.name, "TP53, KRAS", "term.name should concatenate gene names");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Gene set input - custom name", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
-  const secondRadio = inputTypeRadios.nodes()[1];
-  secondRadio.click();
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  geneSearchInput.value = "KRAS";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  const nameInput = holder.select('[data-testid="sja_genesetinput_name"]').node();
-  nameInput.value = "Test gene set";
-  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
-  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
-  await sleep(100);
-  submitButton.click();
-  await sleep(100);
-  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
-  test.equal(tw.term.name, "Test gene set", "term.name should be custom name");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-//# sourceMappingURL=geneVariant.integration.spec-OESHXKBV.js.map

package/dist/genefusion.ui-TOSPIGTE.js

@@ -1,309 +0,0 @@
-import {
-  makeBtn,
-  makeGenomeDropDown,
-  makeResetBtn,
-  makeTextAreaInput
-} from "./chunk-5EBRF6Z7.js";
-import {
-  appear,
-  sayerror
-} from "./chunk-UK3PTE3P.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IFA3COXY.js";
-import "./chunk-HYOEWQ5P.js";
-import {
-  Tabs
-} from "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-5X6J6UAT.js";
-import "./chunk-3L32ZXRS.js";
-import "./chunk-GRNZWYOJ.js";
-import "./chunk-X27TRPIZ.js";
-import "./chunk-STQU7XZV.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-5V43Y2RC.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-B4VRYXOQ.js";
-import "./chunk-XOCO3LVN.js";
-import "./chunk-EBKERML3.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.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: 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-TOSPIGTE.js.map