@sjcrh/proteinpaint-client 2.196.0 → 2.198.0

package/dist/dataDownload-VBSJBKMP.js

@@ -0,0 +1,330 @@
+import {
+  fillTermWrapper,
+  sayerror,
+  termsettingInit
+} from "./chunk-5VOPABBA.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-Z5U6HOE4.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-5ABGFJSP.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-XPY6AWXO.js";
+import "./chunk-NELOT3NJ.js";
+import "./chunk-M6EF3WVV.js";
+import "./chunk-7IYJZZQI.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-LFCYMSVA.js";
+import "./chunk-I6WR4CG7.js";
+import "./chunk-2X6W4E3W.js";
+import "./chunk-NYRZNRG5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-3XVVN66M.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-NSTL4MY2.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";
+
+// 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-VBSJBKMP.js.map

package/dist/dataDownload.integration.spec-LUFSETOP.js

@@ -0,0 +1,193 @@
+import {
+  detectGte
+} from "./chunk-ECIBJXFT.js";
+import {
+  getRunPp
+} from "./chunk-M2G5R4WB.js";
+import {
+  require_tape
+} from "./chunk-TUMA63WX.js";
+import "./chunk-VJ6UFVGC.js";
+import "./chunk-QNHT74XC.js";
+import "./chunk-CTQ3IUCA.js";
+import "./chunk-PFRWS4CR.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-4IH7DORZ.js";
+import "./chunk-MKAF2BHB.js";
+import "./chunk-WKNI3HRQ.js";
+import "./chunk-7OHRR2IE.js";
+import "./chunk-2GYWFQML.js";
+import "./chunk-5VOPABBA.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-Z5U6HOE4.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-5ABGFJSP.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-XPY6AWXO.js";
+import "./chunk-NELOT3NJ.js";
+import "./chunk-M6EF3WVV.js";
+import "./chunk-7IYJZZQI.js";
+import "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-LFCYMSVA.js";
+import "./chunk-I6WR4CG7.js";
+import "./chunk-2X6W4E3W.js";
+import "./chunk-NYRZNRG5.js";
+import "./chunk-JNITUVXP.js";
+import "./chunk-3XVVN66M.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-NSTL4MY2.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// plots/test/dataDownload.integration.spec.js
+var import_tape = __toESM(require_tape(), 1);
+var runpp = getRunPp("mass", {
+  state: {
+    nav: {
+      header_mode: "hide_search",
+      activeTab: 1
+    },
+    vocab: {
+      dslabel: "TermdbTest",
+      genome: "hg38-test"
+    }
+  },
+  debug: 1
+});
+(0, import_tape.default)("\n", (test) => {
+  test.comment("-***- plots/dataDownload -***-");
+  test.end();
+});
+(0, import_tape.default)("Data download with no selected terms", (test) => {
+  test.timeoutAfter(1e3);
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "dataDownload"
+        }
+      ]
+    },
+    dataDownload: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  function runTests(dataDownload) {
+    dataDownload.on("postRender.test", null);
+    const ddDom = dataDownload.Inner.dom;
+    test.equal(ddDom.terms.node().querySelectorAll(".term_name_btn").length, 0, `Should render no term pills`);
+    test.equal(
+      ddDom.terms.node().querySelectorAll(".sja_filter_tag_btn.add_term_btn").length,
+      1,
+      `Should render 1 'Add variable' button`
+    );
+    test.equal(
+      ddDom.submitNote.node().innerText,
+      `no sample data`,
+      `Should render "no sample data" next to Download button`
+    );
+    test.ok(ddDom.submitBtn.node().disabled, `Should show Download button as disabled`);
+    if (test._ok) dataDownload.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("Data download with terms selected", (test) => {
+  test.timeoutAfter(2e3);
+  const terms = [
+    { $id: 0, id: "sex" },
+    { $id: 1, id: "agedx" },
+    { $id: 2, id: "genetic_race" },
+    { $id: 3, id: "aaclassic_5" },
+    { $id: 4, id: "Arrhythmias" }
+  ];
+  runpp({
+    state: {
+      plots: [
+        {
+          chartType: "dataDownload",
+          terms
+        }
+      ]
+    },
+    dataDownload: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(dataDownload) {
+    dataDownload.on("postRender.test", null);
+    const ddDom = dataDownload.Inner.dom;
+    await detectGte({
+      elem: ddDom.terms.node(),
+      selector: ".term_name_btn",
+      count: 5
+    });
+    test.equal(
+      ddDom.terms.node().querySelectorAll(".term_name_btn").length,
+      terms.length,
+      `Should render ${terms.length} term pills`
+    );
+    test.equal(
+      ddDom.submitNote.node().innerText,
+      `${dataDownload.Inner.activeSamples.length} samples`,
+      `Should render "${dataDownload.Inner.activeSamples.length} samples" next to Download button`
+    );
+    if (test._ok) dataDownload.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("protected dataset", (test) => {
+  test.timeoutAfter(3e3);
+  const runpp2 = getRunPp("mass", {
+    state: {
+      nav: {
+        header_mode: "hide_search",
+        activeTab: 1
+      },
+      vocab: {
+        dslabel: "ProtectedTest",
+        genome: "hg38-test"
+      }
+    },
+    debug: 1
+  });
+  runpp2({
+    state: {
+      plots: [
+        {
+          chartType: "dataDownload"
+        }
+      ]
+    },
+    dataDownload: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(dataDownload) {
+    dataDownload.on("postRender.test", null);
+    test.true(
+      dataDownload.Inner.dom.titleDiv.text().includes("Requires sign-in"),
+      "should not open by default for protected dataset"
+    );
+    if (test._ok) dataDownload.Inner.app.destroy();
+    test.end();
+  }
+});
+//# sourceMappingURL=dataDownload.integration.spec-LUFSETOP.js.map