@sjcrh/proteinpaint-client 2.166.0 → 2.167.1

package/dist/customdata.inputui-CBTZFODT.js

@@ -1,278 +0,0 @@
-import {
-  mclasscolor2table
-} from "./chunk-UT6W4ZZL.js";
-import {
-  aa2gmcoord,
-  rna2gmcoord
-} from "./chunk-HJ6L54YS.js";
-import {
-  dofetch3
-} from "./chunk-5TDKRZN5.js";
-import "./chunk-RYRCMHYR.js";
-import {
-  dtcnv,
-  dtfusionrna,
-  dtsnvindel,
-  mclass,
-  mclasscnvgain,
-  mclasscnvloss,
-  mclassfusionrna
-} from "./chunk-ECKWM4HB.js";
-import "./chunk-NXOWHUR4.js";
-import "./chunk-5MWX5HUZ.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-ICNJQHQZ.js";
-import "./chunk-FYTZCTJC.js";
-import "./chunk-7NTZWOJV.js";
-import "./chunk-OMO754MK.js";
-import "./chunk-RA5EXEHB.js";
-import "./chunk-PMZS3SHH.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-HFNDKYVF.js";
-
-// mds3/customdata.inputui.js
-function customdata_inputui_default(block) {
-  if (!block.usegm) {
-    return;
-  }
-  const div = block.tip.d.append("div").style("margin", "20px");
-  div.append("p").text(`Add mutation and/or fusion to show over ${block.usegm.name} ${block.usegm.isoform}`);
-  const textarea2 = div.append("textarea").attr("cols", "50").attr("rows", "5").property("placeholder", "Enter data");
-  textarea2.node().focus();
-  const nameinput = div.append("div").append("input").attr("type", "text").style("width", "130px").property("placeholder", "Dataset name");
-  const row = div.append("div").style("margin-top", "5px");
-  const select = row.append("select");
-  select.append("option").text("Codon position");
-  select.append("option").text("RNA position");
-  select.append("option").text("Genomic position");
-  row.append("button").style("margin-left", "5px").text("Submit").on("click", async () => {
-    const v = textarea2.property("value");
-    if (v == "") return;
-    says.style("display", "none");
-    const selecti = select.node().selectedIndex, mlst = [], bad = [];
-    for (const line0 of v.trim().split("\n")) {
-      const line = line0.trim();
-      if (!line) continue;
-      const l = line.split(line.includes("	") ? "	" : line.includes(",") ? "," : " ");
-      try {
-        if (l.length == 3 || l.length == 4) {
-          if (Number.isFinite(Number(l[2]))) {
-            parseCnv(l, mlst, selecti, block);
-          } else {
-            parseMutation(l, mlst, selecti, block);
-          }
-          continue;
-        }
-        if (l.length == 6 || l.length == 7) {
-          await parseFusion(l, mlst, selecti, block);
-          continue;
-        }
-        throw `Line="${l}" does not match the mutation, fusion, or cnv format. Please review.`;
-      } catch (e) {
-        bad.push(line + ": " + (e.message || e));
-      }
-    }
-    if (mlst.find((m) => m.sample) && mlst.find((m) => !m.sample)) {
-      bad.push("sample name is provided for some but not all variants");
-    }
-    if (bad.length) {
-      says.style("display", "block").text("Rejected: " + bad.join("\n"));
-    }
-    if (mlst.length == 0) return;
-    const tk = block.block_addtk_template({
-      type: "mds3",
-      name: nameinput.property("value") || "Custom data",
-      iscustom: true,
-      custom_variants: mlst
-    });
-    block.tk_load(tk);
-  });
-  row.append("button").text("Clear").style("margin-left", "5px").on("click", () => {
-    textarea2.property("value", "");
-    nameinput.property("value", "");
-  });
-  const says = div.append("div").style("display", "none", "margin-top", "20px");
-  printHelp(div);
-}
-function parseMutation(l, mlst, selecti, block) {
-  const _class = l[2].trim();
-  if (!mclass[_class]) throw `Invalid mutation class=${_class}`;
-  const m = {
-    class: _class,
-    dt: dtsnvindel,
-    isoform: block.usegm.isoform,
-    mname: l[0].trim()
-  };
-  if (!m.mname) throw "missing mutation name";
-  const o = parsePositionFromGm(selecti, l[1].trim(), block.usegm);
-  m.chr = o[0];
-  m.pos = o[1];
-  if (l[3]) m.sample = l[3];
-  mlst.push(m);
-}
-async function parseFusion(l, mlst, selecti, block) {
-  const m = {
-    class: mclassfusionrna,
-    dt: dtfusionrna
-    // compute and assign gene1/2, chr1/2, pos1/2
-  };
-  if (l[6]) m.sample = l[6];
-  const [gene1, isoform1, pos1, gene2, isoform2, pos2] = l;
-  if (!gene1) throw "gene1 is missing";
-  if (!gene2) throw "gene2 is missing";
-  if (!isoform1) throw "isoform1 is missing";
-  if (!isoform2) throw "isoform2 is missing";
-  if (!pos1) throw "pos1 is missing";
-  if (!pos2) throw "pos2 is missing";
-  {
-    const d = await dofetch3("genelookup", { body: { deep: 1, genome: block.genome.name, input: gene1 } });
-    if (d.error) throw "invalid gene1";
-    const gm = d.gmlst.find((i) => i.isoform == isoform1);
-    if (!gm) throw "invalid isoform1";
-    m.gene1 = gene1;
-    m.chr1 = gm.chr;
-    const o = parsePositionFromGm(selecti, pos1, gm);
-    m.pos1 = o[1];
-    m.strand1 = gm.strand;
-  }
-  {
-    const d = await dofetch3("genelookup", { body: { deep: 1, genome: block.genome.name, input: gene2 } });
-    if (d.error) throw "invalid gene2";
-    const gm = d.gmlst.find((i) => i.isoform == isoform2);
-    if (!gm) throw "invalid isoform2";
-    m.gene2 = gene2;
-    m.chr2 = gm.chr;
-    const o = parsePositionFromGm(selecti, pos2, gm);
-    m.pos2 = o[1];
-    m.strand2 = gm.strand;
-  }
-  mlst.push(m);
-}
-function parseCnv(l, mlst, selecti, block) {
-  const value = Number(l[2].trim());
-  if (!Number.isFinite(value)) throw "CNV value is not number";
-  const m = {
-    chr: block.usegm.chr,
-    dt: dtcnv,
-    value,
-    class: value > 0 ? mclasscnvgain : mclasscnvloss
-  };
-  if (l[3]) m.sample = l[3];
-  const a = parsePositionFromGm(selecti, l[0].trim(), block.usegm), b = parsePositionFromGm(selecti, l[1].trim(), block.usegm);
-  m.start = Math.min(a[1], b[1]);
-  m.stop = Math.max(a[1], b[1]);
-  mlst.push(m);
-}
-function parsePositionFromGm(selecti, str, gm) {
-  const value = parseInputPosition(str, gm.chr);
-  if (!Number.isInteger(value)) throw "position is not integer";
-  if (selecti == 0) {
-    const p = aa2gmcoord(value, gm);
-    if (p == null) throw "cannot convert codon to genomic position";
-    return [gm.chr, p];
-  }
-  if (selecti == 1) {
-    const p = rna2gmcoord(value, gm);
-    if (p == null) throw "cannot convert RNA position to genomic position";
-    return [gm.chr, p];
-  }
-  if (selecti == 2) {
-    return [gm.chr, value - 1];
-  }
-  throw "unknown selection";
-}
-function parseInputPosition(str, chr) {
-  let value;
-  if (str.includes(":")) {
-    const tmp = str.split(":");
-    if (tmp[0] != chr) throw `Included chromosome=${tmp[0]} does not match current chromosome position=${chr}`;
-    value = Number(tmp[1]);
-  } else {
-    value = Number(str);
-  }
-  return value;
-}
-function printHelp(div) {
-  {
-    const [label, infodiv] = makeHelpDiv(div);
-    label.text("Mutation format: mutation name, position, class, sample");
-    infodiv.html(
-      `One mutation per line. Fields are joined by tab, comma or space. Please do not use both comma and space as separator.
-		<ol>
-			<li>Mutation name, can be any string</li>
-			<li>Mutation position</li>
-			<li>Mutation class code</li>
-			<li>Optional sample name</li>
-		</ol>
-		Position types:
-		<ul><li>Codon position: integer, 1-based (do not use for noncoding gene)</li>
-		<li>RNA position: integer, 1-based, beginning from transcription start site</li>
-		<li>Genomic position: integer, 1-based coordinate</li></ul>`
-    );
-    mclasscolor2table(infodiv.append("table").style("margin-top", "3px"), true);
-  }
-  {
-    const [label, infodiv] = makeHelpDiv(div);
-    label.text("SV/fusion format: gene1, isoform1, position1, gene2, isoform2, position2, sample");
-    infodiv.html(
-      `Limited to two-gene fusion products. One product per line.
-			Fields are joined by tab, comma or space. Please do not use both comma and space as separator.
-		<ol><li>N-term gene symbol</li>
-		<li>N-term gene isoform</li>
-		<li>N-term gene break-end position</li>
-		<li>C-term gene symbol</li>
-		<li>C-term gene isoform</li>
-		<li>C-term gene break-end position</li>
-		<li>Optional sample name</li>
-		</ol>
-		Break-end position types:
-		<ul><li>Codon position: integer, 1-based</li>
-		<li>RNA position: integer, 1-based, beginning from transcription start site</li>
-		<li>Genomic position: 1-based coordinate</li></ul>
-		Either one of the isoforms must be already displayed.`
-    );
-  }
-  {
-    const [label, infodiv] = makeHelpDiv(div);
-    label.text("CNV format: segment start, segment stop, CNV value, sample");
-    infodiv.html(
-      `One CNV segment per line. Fields are joined by tab, comma or space. Please do not use both comma and space as separator.
-		<ol>
-			<li>Segment start position</li>
-			<li>Segment stop position</li>
-			<li>Copy number change value, positive value for gain, negative value for loss. Do not use 0</li>
-			<li>Optional sample name</li>
-		</ol>
-		Position types:
-		<ul><li>Codon position: integer, 1-based (do not use for noncoding gene)</li>
-		<li>RNA position: integer, 1-based, beginning from transcription start site</li>
-		<li>Genomic position: integer, 1-based coordinate</li></ul>`
-    );
-  }
-}
-function makeHelpDiv(div) {
-  const p = div.append("p");
-  const label = p.append("span").style("opacity", 0.6);
-  p.append("span").attr("class", "sja_clbtext").style("margin-left", "10px").text("Show details").on("click", (event) => {
-    const show = infodiv.style("display") == "none";
-    infodiv.style("display", show ? "" : "none");
-    event.target.innerHTML = show ? "Hide details" : "Show details";
-  });
-  const infodiv = div.append("div").style("display", "none").style("margin-left", "20px").style("padding-left", "10px").style("border-left", "solid 1px black").style("color", "#858585");
-  return [label, infodiv];
-}
-export {
-  customdata_inputui_default as default,
-  parseCnv,
-  parseFusion,
-  parseInputPosition,
-  parseMutation,
-  parsePositionFromGm
-};
-//# sourceMappingURL=customdata.inputui-CBTZFODT.js.map

package/dist/dataDownload-ZTGRVI4Q.js

@@ -1,320 +0,0 @@
-import {
-  fillTermWrapper,
-  sayerror,
-  termsettingInit
-} from "./chunk-UT6W4ZZL.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-5TDKRZN5.js";
-import "./chunk-RYRCMHYR.js";
-import "./chunk-ECKWM4HB.js";
-import "./chunk-NXOWHUR4.js";
-import "./chunk-5MWX5HUZ.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-ICNJQHQZ.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-FYTZCTJC.js";
-import "./chunk-7NTZWOJV.js";
-import "./chunk-OMO754MK.js";
-import "./chunk-RA5EXEHB.js";
-import "./chunk-PMZS3SHH.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/dataDownload.js
-var DataDownload = class {
-  constructor(opts) {
-    this.type = "dataDownload";
-    this.genomeObj = opts.app.opts.genome;
-    this.pillBy$id = {};
-  }
-  async init(appState) {
-    setInteractivity(this);
-    setRenderers(this);
-    this.dom = {
-      header: this.opts.header,
-      // header is optional
-      errordiv: this.opts.holder.append("div"),
-      titleDiv: this.opts.holder.append("div").style("margin", "10px"),
-      // the whole holder has white-space=nowrap (likely from sjpp-output-sandbox-content)
-      terms: this.opts.holder.append("div").style("white-space", "normal"),
-      submitDiv: this.opts.holder.append("div").style("margin", "10px")
-    };
-    this.dom.submitBtn = this.dom.submitDiv.append("button").html("Download").on("click", this.download);
-    this.dom.submitNote = this.dom.submitDiv.append("span").style("margin-left", "5px").style("font-style", "italic");
-  }
-  getState(appState, sub) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    this.termdbConfig = appState.termdbConfig;
-    return {
-      vocab: appState.vocab,
-      activeCohort: appState.activeCohort,
-      termfilter: appState.termfilter,
-      config,
-      hasVerifiedToken: this.app.vocabApi.hasVerifiedToken(),
-      tokenVerificationPayload: this.app.vocabApi.tokenVerificationPayload
-    };
-  }
-  /* do not set reactsTo
-  so it reacts to all actions matching with the plot id (controlled by store method)
-  including filter/cohort change
-  */
-  async main() {
-    try {
-      this.config = structuredClone(this.state.config);
-      this.mayUpdateSandboxHeader();
-      if (this.mayRequireToken()) return;
-      const reqOpts = await this.getDataRequestOpts();
-      this.data = await this.app.vocabApi.getAnnotatedSampleData(reqOpts);
-      this.processData();
-      const n = this.activeSamples.length;
-      this.dom.submitBtn.property("disabled", n < 1);
-      this.dom.submitNote.html(n ? `${n} samples` : "no sample data");
-      this.render();
-    } catch (e) {
-      sayerror(this.dom.errordiv, "Error: " + (e.error || e));
-      if (e.stack) console.log(e.stack);
-    }
-  }
-  mayUpdateSandboxHeader() {
-    if (!this.dom.header) return;
-    this.dom.header.html("<span>Data download</span>");
-  }
-  mayRequireToken() {
-    if (this.state.hasVerifiedToken) {
-      this.dom.titleDiv.style("color", "").html("Selected terms");
-      this.dom.terms.style("display", "");
-      this.dom.submitDiv.style("display", "");
-      return false;
-    } else {
-      const e = this.state.tokenVerificationPayload;
-      const missingAccess = e?.error == "Missing access" && this.termdbConfig.dataDownloadCatch?.missingAccess;
-      const message = missingAccess?.message?.replace("MISSING-ACCESS-LINK", missingAccess?.links[e?.linkKey]);
-      const helpLink = this.termdbConfig.dataDownloadCatch?.helpLink;
-      this.dom.titleDiv.style("color", "#e44").html(
-        message || (this.state.tokenVerificationMessage || "Requires sign-in") + (helpLink ? ` <a href='${helpLink}' target=_blank>Tutorial</a>` : "")
-      );
-      this.dom.terms.style("display", "none");
-      this.dom.submitDiv.style("display", "none");
-      return true;
-    }
-  }
-  // creates an opts object for the vocabApi.getNestedChartsData()
-  async getDataRequestOpts() {
-    const terms = this.config.terms;
-    return { terms, filter: this.state.termfilter.filter };
-  }
-  processData() {
-    const { lst, bySampleId } = this.data;
-    this.activeSamples = [];
-    for (const d of lst) {
-      for (const tw of this.config.terms) {
-        if (tw.term && tw.$id in d) {
-          this.activeSamples.push(d);
-          break;
-        }
-      }
-    }
-  }
-  async getNewPill(holder, d) {
-    const pill = await termsettingInit({
-      placeholder: "+Add variable",
-      holder,
-      menuOptions: "all",
-      vocabApi: this.app.vocabApi,
-      activeCohort: this.state.activeCohort,
-      debug: this.app.opts.debug,
-      usecase: { target: "dataDownload" },
-      numericEditMenuVersion: ["continuous", "discrete"],
-      noTermPromptOptions: this.getNoTermPromptOptions(),
-      genomeObj: this.genomeObj,
-      abbrCutoff: 50,
-      defaultQ4fillTW: {
-        condition: { mode: "cuminc" },
-        numeric: { mode: "continuous" }
-      },
-      callback: (tw) => {
-        const termsCopy = this.config.terms.slice(0);
-        const i = this.config.terms.findIndex((tw2) => tw2.$id === d.tw.$id);
-        if (!tw?.term) {
-          termsCopy.splice(i, 1);
-        } else if (i === -1) {
-          tw.$id = d.tw.$id;
-          if (!tw.q?.mode && (tw.term.type == "integer" || tw.term.type == "float")) {
-            tw.q.mode = "continuous";
-          }
-          termsCopy.push(tw);
-        } else {
-          tw.$id = d.tw.$id;
-          termsCopy[i] = tw;
-        }
-        this.app.dispatch({
-          type: "plot_edit",
-          id: this.id,
-          chartType: "dataDownload",
-          config: {
-            terms: termsCopy
-          }
-        });
-      }
-    });
-    this.pillBy$id[d.tw.$id] = pill;
-    return pill;
-  }
-  getNoTermPromptOptions() {
-    const lst = [];
-    if (this.termdbConfig.allowedTermTypes.includes("snplst")) {
-      lst.push({
-        termtype: "snplst",
-        text: "A list of variants",
-        q: {
-          doNotRestrictAncestry: 1,
-          geneticModel: 3,
-          // by genotype
-          AFcutoff: 0
-          // do not drop any
-        }
-      });
-    }
-    if (this.termdbConfig.allowedTermTypes.includes("snplocus")) {
-      lst.push({
-        termtype: "snplocus",
-        text: "Variants from a locus",
-        q: {
-          doNotRestrictAncestry: 1,
-          geneticModel: 3,
-          // by genotype
-          AFcutoff: 0
-          // do not drop any
-        }
-      });
-    }
-    if (lst.length) lst.unshift({ isDictionary: true, text: "Dictionary variable" });
-    return lst;
-  }
-};
-var dataDownloadInit = getCompInit(DataDownload);
-var componentInit = dataDownloadInit;
-var idSuffix = `_ts_${(+/* @__PURE__ */ new Date()).toString().slice(-8)}_${Math.random().toString().slice(-6)}`;
-var $id = 0;
-function getTw$id() {
-  return `${$id++}${idSuffix}`;
-}
-function setRenderers(self) {
-  self.render = function() {
-    const data = self.config.terms.map((tw) => {
-      return { tw, pill: self.pillBy$id[tw.$id] };
-    });
-    data.push({ tw: { $id: getTw$id() } });
-    const terms = self.dom.terms.selectAll(":scope>.sja-data-download-term").data(data, (d) => d.tw?.$id);
-    terms.exit().remove();
-    terms.each(self.renderTerm);
-    terms.enter().append("div").attr("class", "sja-data-download-term").each(self.addTerm);
-  };
-  self.addTerm = async function(d) {
-    const div = select_default(this).style("display", d.tw?.term ? "inline-block" : "block").style("width", "fit-content").style("margin", "10px").style("padding", "5px");
-    d.pill = await self.getNewPill(div, d);
-    await d.pill.main({
-      term: d.tw?.term,
-      q: d.tw?.q,
-      filter: self.state.termfilter.filter,
-      activeCohort: self.state.activeCohort,
-      numericEditMenuVersion: ["continuous", "discrete"]
-    });
-  };
-  self.renderTerm = async function(d) {
-    if (!d.pill) throw `no pill on update renderTerm()`;
-    select_default(this).style("display", d.tw.term ? "inline-block" : "block");
-    await d.pill.main({
-      term: d.tw?.term,
-      q: d.tw.q,
-      filter: self.state.termfilter.filter,
-      activeCohort: self.state.activeCohort
-    });
-  };
-}
-function setInteractivity(self) {
-  self.download = async () => {
-    const header = ["sample"];
-    for (const tw of self.config.terms) {
-      if (tw.term.type == "condition") {
-        header.push(`${tw.term.name}_event (0=censored, 1=grade ${tw.q.breaks[0]}-5, 2=non-${tw.term.name} death)`);
-        header.push(`${tw.term.name}_time (years from diagnosis to event)`);
-      } else if (tw.term.snps) {
-        for (const s of tw.term.snps) {
-          header.push(s.snpid);
-        }
-      } else {
-        header.push(tw.term.name);
-      }
-    }
-    const rows = [header];
-    for (const s of self.activeSamples) {
-      const row = [s.sampleName || self.data.refs.bySampleId[s.sample]?.label];
-      for (const tw of self.config.terms) {
-        if (!s[tw.$id]) row.push("");
-        else {
-          if (tw.term.type == "condition") {
-            row.push(s[tw.$id].key, s[tw.$id].value);
-          } else if (tw.term.snps) {
-            for (const snp of tw.term.snps) {
-              row.push(s[tw.$id]?.[snp.snpid] || ".");
-            }
-          } else {
-            const v = tw.term.values?.[s[tw.$id].key] || s[tw.$id];
-            row.push(v.label || v.key);
-          }
-        }
-      }
-      rows.push(row);
-    }
-    const matrix = rows.map((row) => row.join("	")).join("\n");
-    const a = document.createElement("a");
-    document.body.appendChild(a);
-    a.addEventListener(
-      "click",
-      function() {
-        a.download = "cohortData.txt";
-        a.href = URL.createObjectURL(new Blob([matrix], { type: "text/tab-separated-values" }));
-        document.body.removeChild(a);
-      },
-      false
-    );
-    a.click();
-    self.app.vocabApi.trackDsAction({
-      action: "download",
-      details: {
-        terms: self.config.terms.map((tw) => !("id" in tw.term) ? tw.term.name : tw.term.id),
-        filter: self.state.termfilter.filter
-      }
-    });
-  };
-}
-var _ID_ = 1;
-async function getPlotConfig(opts, app) {
-  const id = "id" in opts ? opts.id : `_DATADOWNLOAD_${_ID_++}`;
-  const config = { id, terms: [] };
-  copyMerge(config, opts);
-  for (const tw of config.terms) {
-    await fillTermWrapper(tw, app.vocabApi);
-  }
-  return config;
-}
-export {
-  componentInit,
-  dataDownloadInit,
-  getPlotConfig
-};
-//# sourceMappingURL=dataDownload-ZTGRVI4Q.js.map