@sjcrh/proteinpaint-client 2.208.0 → 2.209.0

package/dist/barchart-SEC6VKQ2.js

@@ -0,0 +1,42 @@
+import {
+  Barchart,
+  barInit,
+  componentInit,
+  getDefaultBarSettings,
+  getPlotConfig,
+  negateTermLabel
+} from "./chunk-C3HEDQPT.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-B6UXFX73.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-3FEP6B5T.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import "./chunk-OBDIJ4QS.js";
+import "./chunk-6FG6JFZP.js";
+import "./chunk-3XBG5HIV.js";
+import "./chunk-SB36AUG7.js";
+import "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-Z2ZITHT4.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  Barchart,
+  barInit,
+  componentInit,
+  getDefaultBarSettings,
+  getPlotConfig,
+  negateTermLabel
+};
+//# sourceMappingURL=barchart-SEC6VKQ2.js.map

package/dist/barchart2-D4FXZCTU.js

@@ -0,0 +1,309 @@
+import {
+  ABBREV_COHORT,
+  FULL_COHORT,
+  getDefaultProfilePlotSettings,
+  getProfilePlotConfig,
+  profilePlot
+} from "./chunk-GYE6FU7P.js";
+import {
+  fillTwLst
+} from "./chunk-C3HEDQPT.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KV4W2ACA.js";
+import "./chunk-B6UXFX73.js";
+import "./chunk-ELJX3QIQ.js";
+import "./chunk-3FEP6B5T.js";
+import "./chunk-EEB5VE2A.js";
+import "./chunk-6RRZRISL.js";
+import "./chunk-2KM4PRQM.js";
+import {
+  dofetch3
+} from "./chunk-OBDIJ4QS.js";
+import "./chunk-6FG6JFZP.js";
+import "./chunk-3XBG5HIV.js";
+import "./chunk-SB36AUG7.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-WINIL2KN.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-7X6NF7NI.js";
+import "./chunk-W5J3LTYS.js";
+import {
+  axisTop
+} from "./chunk-Z2ZITHT4.js";
+import {
+  linear
+} from "./chunk-4OLM3KSB.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// plots/profile/barchart2.ts
+var stepx = 500;
+var barwidth = 400;
+var ProfileBarchart2 = class extends profilePlot {
+  constructor(opts) {
+    super(opts, "profileBarchart2");
+    this.rowCount = 0;
+    this.additionalInputs = [];
+  }
+  static {
+    this.type = "profileBarchart2";
+  }
+  async init(appState) {
+    await super.init(appState);
+    const config = appState.plots.find((p) => p.id === this.id);
+    this.componentNames = config.plotByComponent.map((elem) => ({
+      value: elem.profileComponent.name,
+      label: elem.profileComponent.name
+    }));
+    const profileComponentInput = {
+      label: "Component",
+      type: "dropdown",
+      chartType: "profileBarchart2",
+      options: this.componentNames,
+      settingsKey: "profileComponent",
+      callback: (value) => this.setProfileComponent(value)
+    };
+    this.additionalInputs.push(profileComponentInput);
+  }
+  setProfileComponent(value) {
+    this.settings.profileComponent = value;
+    this.app.dispatch({ type: "plot_edit", id: this.id, config: this.config });
+  }
+  async main() {
+    this.dom.loadingDiv.style("display", "");
+    try {
+      await super.main();
+      this.configProfileComponent = this.config.plotByComponent.find((comp) => comp.profileComponent.name == this.settings.profileComponent) || this.config.plotByComponent[0];
+      this.rowCount = 0;
+      this.scoreTerms = [];
+      for (const group of this.configProfileComponent.groups)
+        for (const row of group.rows) {
+          this.rowCount++;
+          if (row.term1) this.scoreTerms.push(row.term1);
+          if (row.term2) this.scoreTerms.push(row.term2);
+        }
+      await this.setControls(this.additionalInputs);
+      this.profileComponent = this.settings.profileComponent || this.componentNames[0].value;
+      this.plot();
+    } catch (e) {
+      console.error(e);
+      throw `${e} [profileBarchart2 main()]`;
+    } finally {
+      this.dom.loadingDiv.style("display", "none");
+    }
+  }
+  /**
+   * Override setControls() to fetch data from the dedicated barchart2 route.
+   * The base class setControls() builds filter UI and sets this.filter but
+   * skips the data fetch for profileBarchart2 (see profilePlot.ts).
+   * This method calls termdb/profileBarchart2Scores, which derives the facility
+   * term server-side and returns aggregated (median) percentages.
+   */
+  async setControls(additionalInputs = []) {
+    await super.setControls(additionalInputs);
+    this.data = await this.fetchAggregatedScores();
+    if (this.data && "error" in this.data) throw this.data.error;
+  }
+  async fetchAggregatedScores() {
+    return dofetch3("termdb/profileBarchart2Scores", {
+      body: {
+        genome: this.state.vocab.genome,
+        dslabel: this.state.vocab.dslabel,
+        scoreTerms: this.scoreTerms.map((t) => ({
+          score: { term: { id: t.score.term.id }, q: t.score.q },
+          maxScore: typeof t.maxScore === "number" ? t.maxScore : { term: { id: t.maxScore.term.id }, q: t.maxScore.q }
+        })),
+        filterByUserSites: this.settings?.filterByUserSites,
+        filter: this.filter
+      }
+    });
+  }
+  onMouseOut(event) {
+    if (event.target.tagName == "rect" && event.target.getAttribute("fill-opacity") == 0.3) {
+      event.target.setAttribute("fill-opacity", 0);
+    }
+  }
+  onMouseOver(event) {
+    if (event.target.tagName == "rect" && event.target.getAttribute("fill-opacity") == 0) {
+      event.target.setAttribute("fill-opacity", 0.3);
+    }
+  }
+  plot() {
+    const { hasSubjectiveData } = this.createSvg();
+    this.drawTitleAndDefs(hasSubjectiveData);
+    this.drawColumnHeaders(hasSubjectiveData);
+    const yEnd = this.drawComponentRows(hasSubjectiveData);
+    this.drawGuideLines(yEnd, hasSubjectiveData);
+    this.drawLegend(yEnd, hasSubjectiveData);
+  }
+  createSvg() {
+    const hasSubjectiveData = this.configProfileComponent.hasSubjectiveData;
+    const width = this.state.activeCohort == ABBREV_COHORT ? 1e3 : 1300;
+    const height = this.rowCount * 32 + 450;
+    this.dom.svg = this.dom.plotDiv.append("svg").attr("width", width).attr("height", height);
+    return { width, height, hasSubjectiveData };
+  }
+  drawTitleAndDefs(_hasSubjectiveData) {
+    const title = this.state.activeCohort == ABBREV_COHORT ? `Score-based Results for the ${this.profileComponent} Component by Module and Domain Compared with End-User Impression` : `Objective ${this.profileComponent == "Patients and Outcomes" ? "" : "and Subjective "}Score-based Results for the ${this.profileComponent} Component by Module and Domain`;
+    this.dom.svg.append("text").attr("transform", `translate(50, 30)`).attr("font-weight", "bold").text(title);
+    const color = this.configProfileComponent.profileComponent.color;
+    this.dom.svg.append("defs").append("pattern").attr("id", `${this.id}_diagonalHatch`).attr("patternUnits", "userSpaceOnUse").attr("width", 4).attr("height", 4).append("path").attr("d", "M-1,1 l2,-2 M0,4 l4,-4 M3,5 l2,-2").attr("stroke-width", 1).attr("stroke", color);
+  }
+  drawColumnHeaders(hasSubjectiveData) {
+    const svg = this.dom.svg;
+    const config = this.config;
+    for (const [i, c] of config.columnNames.entries()) {
+      if (i == 1 && !hasSubjectiveData) break;
+      const x = (i % 2 == 0 ? 400 : 900) + 10;
+      const y = 70;
+      svg.append("text").attr("transform", `translate(${x}, ${y})`).attr("text-anchor", "start").style("font-weight", "bold").text(c);
+      this.drawAxis(x, y + 30);
+    }
+  }
+  drawAxis(x, y) {
+    const xAxisScale = linear().domain([0, 100]).range([0, barwidth]);
+    this.dom.svg.append("g").attr("transform", `translate(${x}, ${y})`).call(axisTop(xAxisScale));
+  }
+  drawComponentRows(hasSubjectiveData) {
+    const svg = this.dom.svg;
+    const step = 30;
+    let y = 70;
+    for (const group of this.configProfileComponent.groups) {
+      svg.append("text").attr("transform", `translate(${50}, ${y + 40})`).attr("text-anchor", "start").text(`${group.label}`).style("font-weight", "bold");
+      y += step + 20;
+      for (const row of group.rows) {
+        const g = svg.append("g");
+        g.append("rect").attr("transform", `translate(${20}, ${y - 6})`).attr("x", 0).attr("y", 0).attr("width", hasSubjectiveData ? 1500 : 850).attr("height", 30).attr("fill", "#f8d335").attr("fill-opacity", 0);
+        const x = 400;
+        if (row.term1) this.drawRect(x, y, row, "term1", g);
+        if (row.term2) this.drawRect(x + stepx, y, row, "term2", g);
+        y += step;
+      }
+    }
+    return y;
+  }
+  drawRect(x, y, row, field, g) {
+    const hasSubjectiveData = this.configProfileComponent.hasSubjectiveData;
+    const d = row[field];
+    let subjectiveTerm = false;
+    if ((row.name == "Total Module" || row.name == "End-user Impression*") && !row.term2) subjectiveTerm = true;
+    const termColor = d.score.term.color;
+    const value = this.getPercentage(d);
+    const isFirst = field == "term1" || field == "term2" && !row.term1;
+    const pairValue = field == "term1" ? this.getPercentage(row.term2) : this.getPercentage(row.term1);
+    const width = value ? value / 100 * barwidth : 0;
+    if (value) {
+      const isObjective = this.state.activeCohort == FULL_COHORT && this.settings.profileComponent == "Patients and Outcomes" ? true : !subjectiveTerm && (pairValue || !hasSubjectiveData);
+      const rect = g.append("rect").attr("transform", `translate(${x + 10}, ${y})`).attr("pointer-events", "none").attr("x", 0).attr("y", 0).attr("width", width).attr("height", 20);
+      if (isObjective) rect.attr("fill", termColor);
+      else {
+        const termid = this.id + d.score.term.id;
+        g.append("defs").append("pattern").attr("id", termid).attr("patternUnits", "userSpaceOnUse").attr("width", 4).attr("height", 4).append("path").attr("d", "M-1,1 l2,-2 M0,4 l4,-4 M3,5 l2,-2").attr("stroke-width", 1).attr("stroke", termColor);
+        rect.attr("fill", `url(#${termid})`);
+      }
+    }
+    const text = g.append("text").attr("pointer-events", "none").attr("text-anchor", "end").text(`${value || 0}%`);
+    if (width > 0) text.attr("transform", `translate(${x + width + 55}, ${y + 15})`);
+    else if (!pairValue && field == "term1") text.attr("transform", `translate(${x + 35}, ${y + 15})`);
+    if (isFirst)
+      g.append("text").attr("transform", `translate(${field == "term1" ? x : x - stepx}, ${y + 15})`).attr("text-anchor", "end").text(row.name).attr("pointer-events", "none");
+  }
+  drawGuideLines(yEnd, hasSubjectiveData) {
+    this.drawGuide(410, 120, 50, yEnd, "B");
+    this.drawGuide(410, 120, 75, yEnd, "A");
+    if (!hasSubjectiveData) return;
+    this.drawGuide(910, 120, 50, yEnd, "B");
+    this.drawGuide(910, 120, 75, yEnd, "A");
+  }
+  drawGuide(x, y, percent, y2, text) {
+    const svg = this.dom.svg;
+    const x1 = x + percent / 100 * barwidth;
+    svg.append("line").style("stroke", "#aaa").style("stroke-width", 1).style("stroke-dasharray", "5, 5").attr("x1", x1).attr("y1", y).attr("x2", x1).attr("y2", y2);
+    svg.append("text").attr("transform", `translate(${x1 + 0.125 * barwidth}, ${y2 + 20})`).attr("text-anchor", "middle").text(text).style("font-weight", "bold");
+    if (percent == 50)
+      svg.append("text").attr("transform", `translate(${x1 - 0.25 * barwidth}, ${y2 + 20})`).attr("text-anchor", "middle").text("C").style("font-weight", "bold");
+  }
+  drawLegend(yEnd, hasSubjectiveData) {
+    this.legendG = this.dom.svg.append("g").attr("data-testid", "sjpp-profileBarchart2-legend").attr("transform", `translate(400,${yEnd + 90})`);
+    this.filterG = this.dom.svg.append("g").attr("transform", `translate(0,${yEnd + 90})`);
+    if (!this.isComparison) {
+      this.legendG.append("text").attr("text-anchor", "left").style("font-weight", "bold").text("Overall Score").attr("transform", `translate(0, -5)`);
+      this.addLegendItem("A", "More than 75% of possible scorable items", 1);
+      this.addLegendItem("B", "50-75% of possible scorable items", 2);
+      this.addLegendItem("C", "Less than 50% of possible scorable items", 3);
+      if (this.state.activeCohort == ABBREV_COHORT) {
+        this.addEndUserImpressionNote(this.legendG.append("g"));
+      } else this.addPOCNote(this.legendG.append("g"));
+    }
+    this.addFilterLegend();
+    if (!hasSubjectiveData) return;
+    const color = this.configProfileComponent.profileComponent.color;
+    const svg = this.dom.svg;
+    const y = yEnd + 40;
+    let x = 600;
+    const lineG = svg.append("g");
+    this.drawLegendRect(x, y, "and", color, lineG);
+    x += 300;
+    this.drawLegendRect(x, y, "or", color, lineG);
+  }
+  drawLegendRect(x, y, operator, color, lineG) {
+    const rect = lineG.append("g").attr("transform", `translate(${x}, ${y})`).append("rect").attr("x", 0).attr("y", 0).attr("width", 20).attr("height", 20);
+    if (operator == "and") rect.attr("fill", color);
+    else rect.attr("fill", `url(#${this.id}_diagonalHatch)`);
+    const text = this.dom.svg.append("text").attr("transform", `translate(${x + 25}, ${y + 15})`).attr("text-anchor", "start").text("Objective ");
+    text.append("tspan").attr("font-weight", "bold").text(operator);
+    text.append("tspan").text(" Subjective data");
+  }
+};
+async function getPlotConfig(opts, app, _activeCohort) {
+  try {
+    const activeCohort = _activeCohort === void 0 ? app.getState().activeCohort : _activeCohort;
+    const defaults = await getProfilePlotConfig(activeCohort, app, opts);
+    if (!defaults) throw "default config not found in termdbConfig.plotConfigByCohort.profileBarchart2";
+    defaults.settings = { profileBarchart2: getDefaultProfilePlotSettings() };
+    let config = structuredClone(defaults);
+    config = copyMerge(config, opts);
+    config.settings.controls = { isOpen: false };
+    const twlst = [];
+    for (const profileComponent of config.plotByComponent) {
+      profileComponent.hasSubjectiveData = false;
+      for (const group of profileComponent.groups)
+        for (const row of group.rows) {
+          if (row.term1) {
+            row.term1.score.q = row.term1.maxScore.q = { mode: "continuous" };
+            twlst.push(row.term1.score);
+            twlst.push(row.term1.maxScore);
+          }
+          if (row.term2) {
+            row.term2.score.q = row.term2.maxScore.q = { mode: "continuous" };
+            twlst.push(row.term2.score);
+            twlst.push(row.term2.maxScore);
+          }
+          if (row.term1 && row.term2) profileComponent.hasSubjectiveData = true;
+        }
+    }
+    await fillTwLst(twlst, app.vocabApi);
+    return config;
+  } catch (e) {
+    throw `${e} [profileBarchart2 getPlotConfig()]`;
+  }
+}
+var profileBarchart2Init = getCompInit(ProfileBarchart2);
+var componentInit = profileBarchart2Init;
+function getDefaultProfileBarchart2Settings() {
+  return {};
+}
+export {
+  componentInit,
+  getDefaultProfileBarchart2Settings,
+  getPlotConfig,
+  profileBarchart2Init
+};
+//# sourceMappingURL=barchart2-D4FXZCTU.js.map