@sjcrh/proteinpaint-client 2.219.1 → 2.221.0

package/dist/chunk-H3YF55ZI.js

@@ -1,848 +0,0 @@
-import {
-  PlotBase,
-  getBrainImagingSampleSet,
-  sayerror
-} from "./chunk-BKW35Z4U.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  DEFAULT_SAMPLE_TYPE,
-  ROOT_SAMPLE_TYPE,
-  getDateStrFromNumber,
-  isNumericTerm
-} from "./chunk-GN2A5NL5.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-X7KCDWGX.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} ${label}`);
-          const ssgqImport = await import("./plot.ssgq-GYRVHTC7.js");
-          const found = await ssgqImport.plotSingleSampleGenomeQuantification(
-            state.termdbConfig,
-            state.vocab.dslabel,
-            k,
-            { sample_id: sample.sampleName },
-            plotDiv.insert("div"),
-            this.app.opts.genome,
-            null,
-            //geneName
-            false
-            //showError
-          );
-          if (found) someFound = true;
-        }
-        this.dom.showPlotsDiv.select(`input[id=${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-H3ABPPD3.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-ZJEZPBX7.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-2EJZH5PP.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-H3YF55ZI.js.map