@sjcrh/proteinpaint-client 2.207.1 → 2.208.0

package/dist/genefusion.ui-IWJMF2BM.js

@@ -1,303 +0,0 @@
-import {
-  makeBtn,
-  makeGenomeDropDown,
-  makeResetBtn,
-  makeTextAreaInput
-} from "./chunk-5EBRF6Z7.js";
-import {
-  Tabs,
-  appear,
-  sayerror
-} from "./chunk-PC4MFDHP.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-HPAW7XDM.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-BZN2O76M.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-52QHIKH2.js";
-import "./chunk-A2ORIMUJ.js";
-import "./chunk-PPSWNLMG.js";
-import "./chunk-RUBZCKIX.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-IWJMF2BM.js.map

package/dist/geneset-APCO4BRX.js

@@ -1,203 +0,0 @@
-import {
-  GeneSetEditUIwithTabs,
-  fillTermWrapper
-} from "./chunk-PC4MFDHP.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-HPAW7XDM.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-BZN2O76M.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3
-} from "./chunk-52QHIKH2.js";
-import "./chunk-A2ORIMUJ.js";
-import "./chunk-PPSWNLMG.js";
-import "./chunk-RUBZCKIX.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-APCO4BRX.js.map