@sjcrh/proteinpaint-client 2.222.0 → 2.224.0

package/dist/chunk-CIF2HSFF.js

@@ -0,0 +1,848 @@
+import {
+  PlotBase,
+  getBrainImagingSampleSet,
+  sayerror
+} from "./chunk-U45YALDI.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import {
+  DEFAULT_SAMPLE_TYPE,
+  ROOT_SAMPLE_TYPE,
+  getDateStrFromNumber,
+  isNumericTerm
+} from "./chunk-JHLF2ZC2.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-HBNB5TRH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+
+// plots/sampleView.ts
+var root_ID = "root";
+var samplesLimit = 15;
+var SampleView = class _SampleView extends PlotBase {
+  static {
+    this.type = "sampleView";
+  }
+  constructor(opts, api) {
+    super(opts, api);
+    this.type = _SampleView.type;
+    this.setDom(opts);
+    setInteractivity(this);
+    setRenderers(this);
+  }
+  setDom(opts) {
+    opts.holder.style("position", "relative");
+    const div = opts.holder.append("div");
+    const controlsDiv = div.append("div").style("display", "inline-block");
+    const headerDiv = div.append("div").style("display", "inline-block").style("padding", "20px");
+    const contentDiv = div.append("div").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("justify-content", "flex-start").style("width", "100vw");
+    const plotsDiv = contentDiv;
+    const sampleDiv = headerDiv.insert("div").style("display", "inline-block");
+    const showPlotsDiv = headerDiv.append("div").style("display", "inline-block").style("vertical-align", "top");
+    const loadingDiv = opts.holder.append("div").attr("class", "sjpp-loading-overlay").style("display", "none");
+    loadingDiv.append("div").attr("class", "sjpp-spinner");
+    this.dom = {
+      header: opts.header,
+      holder: opts.holder,
+      controlsDiv,
+      sampleDiv,
+      showPlotsDiv,
+      loadingDiv,
+      plotsDiv
+    };
+  }
+  async init(appState) {
+    this.termsByCohort = {};
+    await this.setSampleSelect(appState);
+    const state = this.getState(appState);
+    await this.setControls(state);
+  }
+  async setSampleSelect(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    const sampleDiv = this.dom.sampleDiv;
+    if (this.dom.header) this.dom.header.html(`Sample View`);
+    if (config.samples && config.samples.length > 1) {
+      const select = sampleDiv.insert("select").style("margin", "0px 5px").property("multiple", true).attr("id", "select");
+      select.selectAll("option").data(config.samples).enter().append("option").attr("value", (d) => d.sampleId).property("selected", (d, _i) => _i < samplesLimit).text((d) => d.sampleName);
+      this.dom.noteDiv = sampleDiv.insert("div").style("display", "none").style("vertical-align", "top").style("font-size", "0.8em").style("color", "#aaa").html(
+        `*Note that only ${samplesLimit} samples can be selected.<br/>&nbsp;Navigate through the list to view all the samples.`
+      );
+      if (config.samples.length > samplesLimit) this.dom.noteDiv.style("display", "inline-block");
+      select.on("change", () => {
+        const options = select.node().options;
+        const samples = [];
+        let count = 0;
+        for (const option of options) {
+          if (option.selected) {
+            if (count < samplesLimit) {
+              const sampleId = Number(option.value);
+              const sampleName = config.samples.find((s) => s.sampleId == sampleId).sampleName;
+              const sample = { sampleId, sampleName };
+              samples.push(sample);
+              count++;
+            } else option.selected = false;
+          }
+        }
+        this.app.dispatch({ type: "plot_edit", id: this.id, config: { samples } });
+      });
+    } else {
+      this.samplesData = await this.vocabApi.getSamplesByName({
+        filter: appState.termfilter?.filter
+      });
+      if (Object.keys(this.samplesData).length == 0) throw "No accessible samples found";
+      const callback = (sampleName2) => {
+        if (this.samplesData[sampleName2]) {
+          const samples = getSamplesRelated(this.samplesData, sampleName2, null, void 0);
+          this.app.dispatch({ type: "plot_edit", id: this.id, config: { samples } });
+          this.dom.downloadbt.property("disabled", false);
+        } else {
+          this.dom.tableDiv.style("display", "none");
+          for (const div of this.discoPlots) div.cellDiv.style("display", "none");
+          for (const div of Object.values(this.singleSamplePlots)) {
+            div.forEach((p) => p.cellDiv.style("display", "none"));
+          }
+          for (const div of this.brainPlots) div.cellDiv.style("display", "none");
+          this.swimmerDiv?.style("display", "none");
+          if (sampleName2 != "") {
+            this.dom.downloadbt.property("disabled", true);
+            const errorDiv = sampleDiv.append("div");
+            sayerror(errorDiv, `Invalid sample ID: ${sampleName2}. Please check the sample ID.`);
+            setTimeout(() => {
+              errorDiv.remove();
+            }, 6e3);
+          }
+        }
+      };
+      const hasSampleAncestry = appState.termdbConfig.hasSampleAncestry;
+      const sampleName = searchSampleInput(this.dom.sampleDiv, this.samplesData, hasSampleAncestry, callback, void 0);
+      this.sample = config.sample || { sampleId: this.samplesData[sampleName].id, sampleName };
+      if (config.sample?.sampleName) sampleDiv.select("input").property("value", config.sample.sampleName);
+      this.dom.downloadbt = sampleDiv.insert("button").style("margin-left", "10px").style("vertical-align", "top").text("Download").on("click", () => {
+        this.downloadData();
+      });
+      this.dom.messageDiv = sampleDiv.insert("div").style("display", "inline-block").style("display", "none").style("vertical-align", "top").html("&nbsp;&nbsp;Downloading data ...");
+    }
+  }
+  getState(appState) {
+    const config = appState.plots?.find((p) => p.id === this.id);
+    let samples = config.samples || getSamplesRelated(this.samplesData, this.sample.sampleName, null, void 0);
+    if (config.samples?.length > 15) samples = config.samples.filter((s, i) => i < 15);
+    const q = appState.termdbConfig.queries;
+    const state = {
+      config,
+      termfilter: appState.termfilter,
+      // TODO: use state.config drectly, instead of having to extract
+      // selected config.key-values into the component state
+      activeCohort: config.activeCohort,
+      terms: config.terms,
+      expandedTermIds: config.expandedTermIds,
+      samples,
+      singleSampleGenomeQuantification: q?.singleSampleGenomeQuantification,
+      singleSampleMutation: q?.singleSampleMutation,
+      NIdata: q?.NIdata,
+      hasVerifiedToken: this.app.vocabApi.hasVerifiedToken(),
+      tokenVerificationPayload: this.app.vocabApi.tokenVerificationPayload,
+      termdbConfig: appState.termdbConfig,
+      vocab: appState.vocab
+    };
+    if (appState.termdbConfig.selectCohort) {
+      state.toSelectCohort = true;
+      const choice = appState.termdbConfig.selectCohort.values[state.activeCohort];
+      if (choice) {
+        state.cohortValuelst = choice.keys;
+      }
+    }
+    return state;
+  }
+  async main() {
+    if (this.mayRequireToken()) return;
+    this.dom.loadingDiv.style("display", "");
+    try {
+      this.config = structuredClone(this.state.config);
+      this.settings = this.state.config.settings.sampleView;
+      this.dom.plotsDiv.selectAll("*").remove();
+      this.termsById = this.getTermsById(this.state);
+      this.sampleDataByTermId = {};
+      const root = this.termsById[root_ID];
+      root.terms = await this.requestTermRecursive(root);
+      this.orderedVisibleTerms = this.getOrderedVisibleTerms(root);
+      if (this.dom.downloadbt)
+        this.dom.downloadbt.style("display", this.settings.showDictionary ? "inline-block" : "none");
+      if (this.settings.showDictionary) this.renderSampleDictionary();
+      this.dom.tableDiv.style("display", this.settings.showDictionary ? "block" : "none");
+      await this.renderPlots(this.state, this.state.samples);
+      this.showVisiblePlots();
+    } finally {
+      this.dom.loadingDiv.style("display", "none");
+    }
+  }
+  async setControls(state) {
+    const q = state.termdbConfig.queries;
+    const hasPlots = q?.singleSampleMutation || q?.singleSampleGenomeQuantification || q?.NIdata || q?.images || q?.swimmer;
+    if (hasPlots) {
+      this.dom.showPlotsDiv.append("input").attr("id", "showDictionary").attr("type", "checkbox").property("checked", true).on("change", (e) => {
+        this.app.dispatch({
+          type: "plot_edit",
+          id: this.id,
+          config: { settings: { sampleView: { showDictionary: e.target.checked } } }
+        });
+      });
+      this.dom.showPlotsDiv.append("label").text("Show Dictionary").attr("for", "showDictionary");
+    }
+    if (q?.singleSampleMutation) {
+      this.dom.showPlotsDiv.append("input").attr("type", "checkbox").property("checked", true).attr("id", "showDisco").on("change", (e) => {
+        this.app.dispatch({
+          type: "plot_edit",
+          id: this.id,
+          config: { settings: { sampleView: { showDisco: e.target.checked } } }
+        });
+      });
+      this.dom.showPlotsDiv.append("label").text("Show Disco").attr("for", "showDisco");
+    }
+    if (q?.singleSampleGenomeQuantification) {
+      for (const ssgqKey in q.singleSampleGenomeQuantification) {
+        const label = ssgqKey.replace(/([a-z](?=[A-Z]))/g, "$1 ");
+        this.dom.showPlotsDiv.append("input").attr("type", "checkbox").property("checked", true).attr("id", ssgqKey).on("change", (e) => {
+          this.app.dispatch({
+            type: "plot_edit",
+            id: this.id,
+            config: { settings: { sampleView: { [ssgqKey]: e.target.checked } } }
+          });
+        });
+        this.dom.showPlotsDiv.append("label").text("Show " + label).attr("for", ssgqKey);
+      }
+    }
+    if (q?.images) {
+      this.dom.showPlotsDiv.append("input").attr("type", "checkbox").property("checked", true).attr("id", "showImages").on("change", (e) => {
+        this.app.dispatch({
+          type: "plot_edit",
+          id: this.id,
+          config: { settings: { sampleView: { showImages: e.target.checked } } }
+        });
+      });
+      this.dom.showPlotsDiv.append("label").text("Show Images").attr("for", "showImages");
+    }
+    if (q?.NIdata) {
+      this.dom.showPlotsDiv.append("input").attr("type", "checkbox").property("checked", true).attr("id", "showBrainImaging").on("change", (e) => {
+        this.app.dispatch({
+          type: "plot_edit",
+          id: this.id,
+          config: { settings: { sampleView: { showBrainImaging: e.target.checked } } }
+        });
+      });
+      this.dom.showPlotsDiv.append("label").text("Show brain imaging").attr("for", "showBrainImaging");
+    }
+    if (q?.swimmer) {
+      this.dom.showPlotsDiv.append("input").attr("type", "checkbox").property("checked", true).attr("id", "showSwimmer").on("change", (e) => {
+        this.app.dispatch({
+          type: "plot_edit",
+          id: this.id,
+          config: { settings: { sampleView: { showSwimmer: e.target.checked } } }
+        });
+      });
+      this.dom.showPlotsDiv.append("label").text("Show swimmer plot").attr("for", "showSwimmer");
+    }
+  }
+  getTermsById(state) {
+    if (!(state.activeCohort in this.termsByCohort)) {
+      this.termsByCohort[state.activeCohort] = {
+        [root_ID]: {
+          id: root_ID,
+          __tree_isroot: true
+          // must not delete this flag
+        }
+      };
+    }
+    return this.termsByCohort[state.activeCohort];
+  }
+  async requestTermRecursive(term, _ancestry = [root_ID]) {
+    const data = await this.vocabApi.getTermChildren(
+      term,
+      this.state.toSelectCohort ? this.state.cohortValuelst : null,
+      this.state.termfilter.filter
+    );
+    if (data.error) throw data.error;
+    if (!data.lst || data.lst.length == 0) {
+      return [];
+    }
+    const terms = [];
+    const parent_id = _ancestry.slice(-1)[0];
+    for (const t of data.lst) {
+      t.parent_id = parent_id;
+      const ancestry = [..._ancestry];
+      const copy = structuredClone(t);
+      copy.ancestry = ancestry;
+      terms.push(copy);
+      if (!copy.isleaf && this.config.expandedTermIds.includes(copy.id)) {
+        copy.terms = await this.requestTermRecursive(copy, [...ancestry, t.id]);
+        if (this.state.samples) await this.fillSampleData(copy.terms);
+      } else {
+        const t0 = this.termsById[copy.id];
+        if (this.state.samples) await this.fillSampleData([copy]);
+        if (t0 && t0.terms) {
+          copy.terms = t0.terms;
+        }
+      }
+      this.termsById[copy.id] = copy;
+    }
+    return terms;
+  }
+  getOrderedVisibleTerms(_root) {
+    const visibleTerms = Object.values(this.termsById).filter(this.isVisibleTermId.bind(this));
+    const orderedVisibleTerms = [];
+    this.sortVisibleTerms(this.termsById[root_ID], visibleTerms, orderedVisibleTerms);
+    return orderedVisibleTerms;
+  }
+  isVisibleTermId(term) {
+    if (term.parent_id == root_ID) return true;
+    if (!term.ancestry) return false;
+    for (const pid of term.ancestry) {
+      if (pid === root_ID) continue;
+      if (!this.config.expandedTermIds.includes(pid)) return false;
+    }
+    return true;
+  }
+  sortVisibleTerms(currParent, remainingTerms, currOrder = []) {
+    const unorderedTerms = [];
+    const orderedTerms = [];
+    for (const term of remainingTerms) {
+      if (term.parent_id == currParent.id) {
+        orderedTerms.push(term);
+      } else unorderedTerms.push(term);
+    }
+    remainingTerms.splice(0, remainingTerms.length, ...unorderedTerms);
+    if (remainingTerms.length) {
+      for (const term of orderedTerms) {
+        currOrder.push(term);
+        if (!term.isleaf && remainingTerms.length) {
+          this.sortVisibleTerms(term, remainingTerms, currOrder);
+        }
+      }
+    } else {
+      currOrder.push(...orderedTerms);
+    }
+  }
+  async fillSampleData(terms) {
+    const term_ids = [];
+    for (const term of terms) term_ids.push(term.id);
+    for (const sample of this.state.samples) {
+      const data = await this.vocabApi.getSingleSampleData({
+        sampleId: sample.sampleId,
+        term_ids,
+        filter: this.state.termfilter.filter
+      });
+      if ("error" in data) throw data.error;
+      if (!this.sampleDataByTermId[sample.sampleId]) this.sampleDataByTermId[sample.sampleId] = {};
+      for (const id in data) this.sampleDataByTermId[sample.sampleId][id] = data[id];
+    }
+  }
+  async downloadData() {
+    this.dom.messageDiv.style("display", "block");
+    this.dom.downloadbt.style("display", "none");
+    const filename = `samples.tsv`;
+    const sampleData = {};
+    let lines = "Sample";
+    for (const sample of this.state.samples) {
+      sampleData[sample.sampleId] = await this.vocabApi.getSingleSampleData({
+        sampleId: sample.sampleId,
+        /** term_ids is required for getSingleSampleData but not
+         * available in this instance. Pass empty array.*/
+        term_ids: [],
+        filter: this.state.termfilter.filter || []
+      });
+      lines += `	${sample.sampleName}`;
+    }
+    lines += "\n";
+    const sampleId = this.state.samples[0].sampleId;
+    for (const termId in sampleData[sampleId]) {
+      const term = sampleData[sampleId][termId].term;
+      lines += `${term.name}`;
+      for (const sampleId2 in sampleData) {
+        const data = sampleData[sampleId2];
+        let value = getTermValue(term, data);
+        if (value == null) value = "Missing";
+        lines += `	${value}`;
+      }
+      lines += "\n";
+    }
+    const dataStr = "data:text/tsv;charset=utf-8," + encodeURIComponent(lines);
+    const link = document.createElement("a");
+    link.setAttribute("href", dataStr);
+    link.setAttribute("download", filename);
+    document.body.appendChild(link);
+    link.click();
+    link.remove();
+    this.dom.messageDiv.style("display", "none");
+    this.dom.downloadbt.style("display", "inline-block");
+  }
+  mayRequireToken() {
+    if (this.state.hasVerifiedToken) {
+      this.dom.holder.style("display", "block");
+      return false;
+    } else {
+      const e = this.state.tokenVerificationPayload;
+      const missingAccess = e?.error == "Missing access" && this.state.termdbConfig.dataDownloadCatch?.missingAccess;
+      const message = missingAccess?.message?.replace("MISSING-ACCESS-LINK", missingAccess?.links[e?.linkKey]);
+      const helpLink = this.state.termdbConfig.dataDownloadCatch?.helpLink;
+      this.dom.holder.style("color", "#e44").style("padding", "10px").html(
+        message || (this.state.tokenVerificationMessage || "Requires sign-in") + (helpLink ? ` <a href='${helpLink}' target=_blank>Tutorial</a>` : "")
+      );
+      return true;
+    }
+  }
+  showVisiblePlots() {
+    this.visiblePlots = false;
+    this.showPlotsFromCategory(this.discoPlots, "showDisco");
+    for (const ssgqKey in this.state.singleSampleGenomeQuantification)
+      this.showPlotsFromCategory(this.singleSamplePlots[ssgqKey], ssgqKey);
+    this.showPlotsFromCategory(this.brainPlots, "showBrain");
+    this.showPlotsFromCategory(this.imagePlots, "showImages");
+    if (this.swimmerDiv) {
+      this.swimmerDiv.style("display", this.settings.showSwimmer ? "block" : "none");
+      if (this.settings.showSwimmer) this.visiblePlots = true;
+    }
+    if (this.state.samples.length == 1 && this.visiblePlots)
+      this.dom.tableDiv.style("max-width", "48vw").style("max-height", "40vw").attr("class", "sjpp_show_scrollbar");
+    else this.dom.tableDiv.style("max-width", "").style("max-height", "").attr("class", "");
+  }
+  showPlotsFromCategory(plots, key) {
+    for (const div of plots) {
+      const visibleSample = this.state.samples.find((s) => s.sampleName == div.sample.sampleName);
+      const visiblePlot = this.settings[key] && visibleSample;
+      if (visiblePlot) this.visiblePlots = true;
+      div.cellDiv.style("display", visiblePlot ? "table-cell" : "none");
+    }
+  }
+  async renderPlots(state, samples) {
+    const plotsDiv = this.dom.plotsDiv;
+    this.discoPlots = [];
+    this.singleSamplePlots = {};
+    this.brainPlots = [];
+    this.imagePlots = [];
+    delete this.swimmerDiv;
+    this.swimmerRenderer?.destroy();
+    delete this.swimmerRenderer;
+    if (state.termdbConfig?.queries?.singleSampleMutation) {
+      const div = plotsDiv.append("div");
+      if (state.samples.length == 1) div.style("display", "inline-block").style("width", "50vw");
+      let someFound = false;
+      for (const sample of samples) {
+        const cellDiv = div.append("div").style("display", "inline-block");
+        this.discoPlots.push({ sample, cellDiv });
+        const header = cellDiv.insert("div");
+        const discoPlotImport = await import("./plot.disco-YY3ITSSS.js");
+        const found = await discoPlotImport.default(
+          state.termdbConfig,
+          state.vocab.dslabel,
+          { sample_id: sample.sampleName },
+          cellDiv,
+          this.app.opts.genome,
+          {},
+          //overrides
+          false
+          //showError
+        );
+        if (found) {
+          if (state.samples.length > 1)
+            header.style("font-weight", "bold").style("padding-left", "20px").text(sample.sampleName);
+          someFound = true;
+        }
+      }
+      this.dom.showPlotsDiv.select("input[id=showDisco").style("display", someFound ? "inline-block" : "none");
+      this.dom.showPlotsDiv.select("label[for=showDisco").style("display", someFound ? "inline-block" : "none");
+    }
+    if (state.termdbConfig.queries?.singleSampleGenomeQuantification) {
+      for (const k in state.termdbConfig.queries.singleSampleGenomeQuantification) {
+        let someFound = false;
+        this.singleSamplePlots[k] = [];
+        const div = plotsDiv.append("div");
+        if (state.samples.length == 1) div.style("display", "inline-block").style("width", "50vw");
+        for (const sample of samples) {
+          const label = (k.match(/[A-Z][a-z]+|[0-9]+/g) || []).join(" ");
+          const plotDiv = div.insert("div").style("display", "table-cell").style("padding", "20px");
+          this.singleSamplePlots[k].push({ sample, cellDiv: plotDiv });
+          if (state.samples.length > 1)
+            plotDiv.insert("div").style("font-weight", "bold").text(`${sample.sampleName} ${label}`);
+          const ssgqImport = await import("./plot.ssgq-3UGJTTCN.js");
+          const found = await ssgqImport.plotSingleSampleGenomeQuantification(
+            state.termdbConfig,
+            state.vocab.dslabel,
+            k,
+            { sample_id: sample.sampleName },
+            plotDiv.insert("div"),
+            this.app.opts.genome,
+            null,
+            //geneName
+            false
+            //showError
+          );
+          if (found) someFound = true;
+        }
+        this.dom.showPlotsDiv.select(`input[id=${k}`).style("display", someFound ? "inline-block" : "none");
+        this.dom.showPlotsDiv.select(`label[for=${k}`).style("display", someFound ? "inline-block" : "none");
+      }
+    }
+    if (state.termdbConfig.queries?.NIdata) {
+      const k = Object.keys(state.termdbConfig.queries.NIdata.references)[0];
+      let available = /* @__PURE__ */ new Set();
+      try {
+        available = k ? await getBrainImagingSampleSet(state.vocab.genome, state.vocab.dslabel, k) : /* @__PURE__ */ new Set();
+      } catch (e) {
+        console.error("brainImagingSamples request failed:", e);
+      }
+      const samplesWithImaging = samples.filter((s) => available.has(s.sampleName));
+      if (samplesWithImaging.length) {
+        const div = plotsDiv.append("div");
+        if (state.samples.length == 1) div.style("display", "inline-block").style("width", "50vw");
+        for (const sample of samplesWithImaging) {
+          const plotDiv = div.insert("div").style("display", "inline-block");
+          this.brainPlots.push({ sample, cellDiv: plotDiv });
+          if (state.samples.length > 1)
+            plotDiv.insert("div").style("font-weight", "bold").style("padding-left", "20px").text(sample.sampleName);
+          const brainImagingImport = await import("./plot.brainImaging-Y36M3BBW.js");
+          brainImagingImport.default(
+            state.termdbConfig,
+            state.vocab.dslabel,
+            k,
+            { sample_id: sample.sampleName },
+            plotDiv,
+            this.app.opts.genome
+          );
+        }
+      }
+    }
+    if (state.termdbConfig?.queries?.images) {
+      const div = plotsDiv.append("div");
+      if (state.samples.length == 1) div.style("display", "inline-block").style("width", "50vw");
+      for (const sample of samples) {
+        const cellDiv = div.append("div").style("display", "inline-block");
+        this.imagePlots.push({ sample, cellDiv });
+        if (state.samples.length > 1)
+          cellDiv.insert("div").style("font-weight", "bold").style("padding-left", "20px").text(sample.sampleName);
+        const imagePlotImport = await import("./imagePlot-BJAQGEBF.js");
+        imagePlotImport.renderImagePlot(state, cellDiv, sample);
+      }
+    }
+    if (state.termdbConfig?.queries?.swimmer) await this.renderSwimmer(state, samples);
+  }
+  /** the swimmer lane of the shown samples' patient (found from any sample of the patient), drawn once
+  below the other plots. the checkbox is hidden when there is no lane */
+  async renderSwimmer(state, samples) {
+    if (!samples.length) return;
+    const { fetchSwimmerLanes, SwimmerRenderer, getDefaultSwimmerSettings } = await import("./swimmer-HO32NUCE.js");
+    let lanes = [];
+    let timeReference;
+    try {
+      const result = await fetchSwimmerLanes({
+        genome: state.vocab.genome,
+        dslabel: state.vocab.dslabel,
+        samples: samples.map((s) => s.sampleName),
+        // set when opened from a swimmer plot, to show the same time reference; unset: the ds default
+        timeReference: state.config.swimmerTimeReference
+      });
+      lanes = result.lanes;
+      timeReference = result.timeReference;
+    } catch (e) {
+      console.error("swimmer request failed:", e);
+    }
+    this.dom.showPlotsDiv.select("input[id=showSwimmer]").style("display", lanes.length ? "inline-block" : "none");
+    this.dom.showPlotsDiv.select("label[for=showSwimmer]").style("display", lanes.length ? "inline-block" : "none");
+    if (!lanes.length) return;
+    const div = this.dom.plotsDiv.append("div").attr("data-testid", "sjpp-sampleview-swimmer").style("width", "100%");
+    this.swimmerDiv = div;
+    div.append("div").style("font-weight", "bold").style("padding", "10px 20px 0 20px").text("Swimmer plot");
+    const renderer = new SwimmerRenderer(this.app, {
+      plotDiv: div.append("div").style("padding", "10px"),
+      noteDiv: div.append("div").style("padding", "0 20px").style("font-size", ".9em").style("opacity", 0.7),
+      tip: new Menu({ padding: "5px" })
+    });
+    this.swimmerRenderer = renderer;
+    renderer.update({
+      swimmer: state.termdbConfig.queries.swimmer,
+      settings: getDefaultSwimmerSettings(),
+      lanes,
+      timeReference
+    });
+  }
+  destroy() {
+    this.swimmerRenderer?.destroy();
+  }
+};
+function getTermValue(term, data) {
+  let value = data[term.id]?.value;
+  if (value == null || value == void 0 || value == "undefined") return null;
+  if (term.type == "date") return getDateStrFromNumber(value);
+  if (isNumericTerm(term)) {
+    value = term.values?.[value]?.label || term.values?.[value]?.key || value;
+    if (isNaN(value)) return value;
+    return value % 1 == 0 ? value.toString() : value.toFixed(2).toString();
+  }
+  if (term.type == "categorical") return term.values[value]?.label || term.values[value]?.key;
+  if (term.type == "condition") {
+    const values = value.toString().split(" ");
+    const [years, statusKey] = values;
+    const status = term.values[statusKey].label || term.values[statusKey].key;
+    return `Max grade: ${status}, Time to event: ${Number(years).toFixed(1)} years`;
+  }
+  if (term.type == "survival") {
+    const values = value.split(" ");
+    const [years, statusKey] = values;
+    const status = term.values?.[statusKey]?.label || term.values?.[statusKey]?.key || statusKey;
+    return `${status} after ${Number(years).toFixed(1)} years`;
+  }
+  return null;
+}
+var sampleViewInit = getCompInit(SampleView);
+var componentInit = sampleViewInit;
+function setRenderers(self) {
+  self.renderSampleDictionary = function() {
+    this.dom.tableDiv = this.dom.plotsDiv.append("div").style("display", "inline-block").style("padding", "20px");
+    const table = this.dom.tableDiv.append("table").style("border-collapse", "collapse");
+    const thead = table.append("thead");
+    const theadrow = thead.append("tr");
+    const tbody = table.append("tbody");
+    const visibleSamples = [];
+    for (const sample of self.state.samples) visibleSamples.push(self.sampleDataByTermId[sample.sampleId]);
+    self.renderTHead(["", ...self.state.samples.map((s) => s.sampleName)], theadrow);
+    const tBodyData = self.orderedVisibleTerms.map((term, _trIndex) => [
+      { term },
+      // first column, no sample data
+      // create data to bind for each sample column
+      ...visibleSamples.map((sample) => ({ term, sample }))
+    ]);
+    self.renderTBody(tBodyData, tbody);
+  };
+  self.renderTHead = function(data, theadrow) {
+    const trs = theadrow.selectAll("th").data(data);
+    trs.exit().remove();
+    trs.text(self.getThHtml);
+    trs.enter().append("th").style("padding", "5px 10px").style("text-align", "end").text(self.getThHtml);
+  };
+  self.getThHtml = (d) => d;
+  self.renderTBody = function(data, tbody) {
+    const trs = tbody.selectAll("tr").data(data);
+    trs.exit().remove();
+    trs.each(self.renderTr);
+    trs.enter().append("tr").each(self.renderTr);
+  };
+  self.renderTr = function(trData, _trIndex) {
+    const tds = select_default(this).selectAll("td").data(trData, (d) => d);
+    tds.exit().remove();
+    tds.each(self.renderTd);
+    tds.enter().append("td").style("border-bottom", "solid 1px rgb(245,245,245)").style("text-align", (d, _i) => _i === 0 ? "left" : "center").style("padding", "2px 10px").each(self.renderTd);
+  };
+  self.renderTd = function(d, _i) {
+    if (!d.sample) {
+      self.renderTerm(select_default(this));
+      return;
+    }
+    const term = d.term;
+    const isNumeric = isNumericTerm(term);
+    const value = getTermValue(d.term, d.sample);
+    const td = select_default(this).datum(d).style("text-align", "end").style("padding", "5px 10px").text(d.sample[d.term.id]?.label || value);
+    if (isNumeric)
+      td.append("button").style("margin-left", "5px").text("Plot").on("click", () => {
+        const tw = { id: term.id, q: { mode: "continuous" } };
+        self.app.dispatch({ type: "plot_create", config: { chartType: "violin", term: tw, value } });
+      });
+  };
+  self.renderTerm = function(td) {
+    const d = td.datum();
+    if (!td.select("span").size()) {
+      const span2 = td.append("span");
+      span2.append("button").style("border-width", 0).style("border-radius", "5px").style("width", "28px").style("height", "28px").style("cursor", "pointer");
+      span2.append("span").style("margin-left", `3px`).style("cursor", "pointer");
+      td.on("click", self.toggleTerm);
+    }
+    const leftIndent = (d.term.ancestry.length - 1) * 24;
+    const span = td.select(":scope>span").style("margin-left", `${leftIndent}px`);
+    span.select("button").style("display", d.term.isleaf ? "none" : "").html(self.config.expandedTermIds.includes(d.term.id) ? "-" : "+");
+    span.select("span").text(d.term.name);
+    return;
+  };
+}
+function setInteractivity(self) {
+  self.toggleTerm = function() {
+    const d = select_default(this).datum();
+    if (d.term.isleaf) return;
+    const expandedTermIds = self.config.expandedTermIds.slice();
+    const i = expandedTermIds.indexOf(d.term.id);
+    if (i == -1) expandedTermIds.push(d.term.id);
+    else expandedTermIds.splice(i, 1);
+    self.app.dispatch({
+      type: "plot_edit",
+      id: self.id,
+      config: { expandedTermIds }
+    });
+  };
+}
+async function getPlotConfig(opts, app) {
+  const q = app.getState()?.termdbConfig?.queries;
+  const settings = {
+    sampleView: {
+      showDictionary: true,
+      showDisco: true,
+      showBrain: true,
+      showImages: true,
+      showSwimmer: true
+    }
+  };
+  if (q)
+    for (const ssgqKey in q.singleSampleGenomeQuantification) settings.sampleView[ssgqKey] = true;
+  const config = { activeCohort: 0, sample: null, expandedTermIds: [root_ID], settings, hidePlotFilter: true };
+  return copyMerge(config, opts);
+}
+function searchSampleInput(holder, samplesData, hasSampleAncestry, callback, keyUpCallback) {
+  const limit = 100;
+  const allSamples = [];
+  for (const sample in samplesData) {
+    const sample_type = samplesData[sample].sample_type;
+    if (sample_type == ROOT_SAMPLE_TYPE || sample_type == null || !hasSampleAncestry && sample_type == DEFAULT_SAMPLE_TYPE)
+      allSamples.push(sample);
+  }
+  const isBigDataset = allSamples.length > 1e4;
+  if (allSamples.length == 0)
+    return;
+  const { childrenByParent, rootFor } = buildHierarchy(samplesData);
+  const sampleName = allSamples[0];
+  const input = holder.append("input").attr("list", "sampleDatalist").property("autocomplete", "off").attr("placeholder", sampleName).style("width", "250px");
+  holder.style("opacity", "0.8");
+  const datalist = holder.append("datalist").attr("id", "sampleDatalist");
+  addOptions(allSamples);
+  input.on("keyup", () => {
+    datalist.selectAll("*").remove();
+    const str = input.node().value.toLowerCase();
+    if (keyUpCallback) keyUpCallback(str);
+    const options = [];
+    for (const sample of allSamples) {
+      if (sample.toLowerCase().startsWith(str)) options.push(sample);
+      if (options.length == limit && allSamples.length > 1e4) break;
+    }
+    for (const sample of allSamples) {
+      if (sample.toLowerCase().includes(str) && !options.includes(sample)) options.push(sample);
+      if (options.length == limit && allSamples.length > 1e4) break;
+    }
+    if (options.length > 1 || options.length == 1 && input.node().value != options[0]) addOptions(options);
+  });
+  input.on("change", () => {
+    const sampleName2 = input.node().value;
+    callback(sampleName2);
+  });
+  function addOptions(options) {
+    datalist.selectAll("option").data(options.filter((s, i) => i < limit)).enter().append("option").attr("value", (d) => d).attr(
+      "label",
+      (d, i) => getLabel(d, childrenByParent, rootFor) + (i + 1 == limit ? isBigDataset ? ` Showing first ${i + 1} hits` : ` Showing ${i + 1} of ${options.length} hits` : i + 1 === options.length && i > 0 ? `  (Found ${options.length} hits)` : "")
+    );
+  }
+  function getLabel(sampleName2, childrenByParent2, rootFor2) {
+    const rootName = rootFor2.get(sampleName2) || sampleName2;
+    if (!childrenByParent2.has(rootName)) return sampleName2;
+    const rootChildren = childrenByParent2.get(rootName) || [];
+    if (rootChildren.length === 0) return sampleName2;
+    const parts = [];
+    for (const child of rootChildren) {
+      const chain = [child];
+      let cur = child;
+      let kids = childrenByParent2.get(cur) || [];
+      while (kids.length > 0) {
+        chain.push(kids[0]);
+        cur = kids[0];
+        kids = childrenByParent2.get(cur) || [];
+      }
+      parts.push(chain.length > 1 ? chain.join(" > ") : child);
+    }
+    return parts.join(", ");
+  }
+  return sampleName;
+}
+function buildHierarchy(samplesData) {
+  const childrenByParent = /* @__PURE__ */ new Map();
+  const rootFor = /* @__PURE__ */ new Map();
+  for (const s of Object.values(samplesData)) {
+    const childName = s.name;
+    const parentName = s.ancestor_name;
+    if (parentName) {
+      if (!childrenByParent.has(parentName)) {
+        childrenByParent.set(parentName, []);
+      }
+      childrenByParent.get(parentName).push(childName);
+    }
+    let root = childName;
+    let curr = s;
+    while (curr?.ancestor_name) {
+      root = curr.ancestor_name;
+      curr = samplesData[root];
+    }
+    rootFor.set(childName, root);
+  }
+  for (const list of childrenByParent.values()) {
+    list.sort((a, b) => {
+      const na = Number(a);
+      const nb = Number(b);
+      return !isNaN(na) && !isNaN(nb) ? na - nb : a.localeCompare(b);
+    });
+  }
+  return { childrenByParent, rootFor };
+}
+function getSamplesRelated(samplesData, sampleName, childrenByParent = null, rootFor) {
+  if (!samplesData[sampleName]) return [];
+  let rootName;
+  if (rootFor && childrenByParent) {
+    rootName = rootFor.get(sampleName);
+  } else {
+    rootName = sampleName;
+    let current = samplesData[sampleName];
+    while (current?.ancestor_name) {
+      rootName = current.ancestor_name;
+      current = samplesData[rootName];
+    }
+  }
+  const root = samplesData[rootName];
+  if (!root) return [];
+  let kidsMap = childrenByParent;
+  if (!kidsMap) {
+    kidsMap = /* @__PURE__ */ new Map();
+    for (const s of Object.values(samplesData)) {
+      if (s.ancestor_name) {
+        if (!kidsMap.has(s.ancestor_name)) kidsMap.set(s.ancestor_name, []);
+        kidsMap.get(s.ancestor_name).push(s);
+      }
+    }
+    for (const list of kidsMap.values()) {
+      list.sort((a, b) => {
+        const na = Number(a.name);
+        const nb = Number(b.name);
+        if (!isNaN(na) && !isNaN(nb)) return na - nb;
+        return a.name.localeCompare(b.name);
+      });
+    }
+  }
+  const samples = [];
+  const hasChildren = (kidsMap.get(rootName) || []).length > 0;
+  if (root.sample_type !== ROOT_SAMPLE_TYPE || !hasChildren) {
+    samples.push({ sampleId: root.id, sampleName: root.name });
+  }
+  function traverse(parentName) {
+    const kids = kidsMap.get(parentName) || [];
+    for (const kid of kids) {
+      samples.push({ sampleId: kid.id, sampleName: kid.name });
+      traverse(kid.name);
+    }
+  }
+  traverse(rootName);
+  return samples;
+}
+
+export {
+  getTermValue,
+  sampleViewInit,
+  componentInit,
+  getPlotConfig,
+  searchSampleInput,
+  getSamplesRelated
+};
+//# sourceMappingURL=chunk-CIF2HSFF.js.map