@sjcrh/proteinpaint-client 2.183.0 → 2.183.1

package/dist/customdata.inputui-PBA5LZRT.js

@@ -0,0 +1,287 @@
+import {
+  mclasscolor2table
+} from "./chunk-2LCTMDCS.js";
+import {
+  aa2gmcoord,
+  rna2gmcoord
+} from "./chunk-HJ6L54YS.js";
+import "./chunk-E5JQ3PN6.js";
+import {
+  dofetch3
+} from "./chunk-RCYTUKAJ.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-UCLS2SVB.js";
+import "./chunk-MVTCBVSX.js";
+import "./chunk-F6V4AYWP.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-JOT4WDJE.js";
+import "./chunk-OTCYJP7G.js";
+import "./chunk-GXINX3WK.js";
+import "./chunk-SOED2SLH.js";
+import {
+  dtcnv,
+  dtfusionrna,
+  dtsnvindel,
+  mclass,
+  mclasscnvgain,
+  mclasscnvloss,
+  mclassfusionrna
+} from "./chunk-XRVBHNCW.js";
+import "./chunk-BEWDIM6H.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";
+
+// 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;
+    m.isoform1 = isoform1;
+  }
+  {
+    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;
+    m.isoform2 = isoform2;
+  }
+  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-PBA5LZRT.js.map

package/dist/dataDownload-CRGQTCOW.js

@@ -0,0 +1,328 @@
+import {
+  fillTermWrapper,
+  sayerror,
+  termsettingInit
+} from "./chunk-2LCTMDCS.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-E5JQ3PN6.js";
+import "./chunk-RCYTUKAJ.js";
+import "./chunk-A6TQGNDQ.js";
+import "./chunk-HYZG6OPC.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-5EF5U7MX.js";
+import "./chunk-IQIXGTQV.js";
+import "./chunk-UCLS2SVB.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-MVTCBVSX.js";
+import "./chunk-F6V4AYWP.js";
+import "./chunk-5OHXYXLD.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-JOT4WDJE.js";
+import "./chunk-OTCYJP7G.js";
+import "./chunk-GXINX3WK.js";
+import "./chunk-SOED2SLH.js";
+import "./chunk-XRVBHNCW.js";
+import "./chunk-BEWDIM6H.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";
+
+// plots/dataDownload.js
+var DataDownload = class _DataDownload {
+  static type = "dataDownload";
+  constructor(opts) {
+    this.type = _DataDownload.type;
+    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-CRGQTCOW.js.map