@sjcrh/proteinpaint-client 2.166.0 → 2.167.0

package/dist/polar-K5Z5FYKV.js

@@ -1,179 +0,0 @@
-import {
-  getDefaultProfilePlotSettings,
-  getProfilePlotConfig,
-  profilePlot
-} from "./chunk-U5QRRS7K.js";
-import "./chunk-FOXJTDTH.js";
-import "./chunk-I2GCD26Y.js";
-import "./chunk-CZTC4MTE.js";
-import "./chunk-GZ2B634M.js";
-import "./chunk-4XDKCFFT.js";
-import {
-  fillTwLst,
-  renderTable
-} from "./chunk-UT6W4ZZL.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-5TDKRZN5.js";
-import "./chunk-RYRCMHYR.js";
-import "./chunk-ECKWM4HB.js";
-import "./chunk-NXOWHUR4.js";
-import "./chunk-5MWX5HUZ.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-ICNJQHQZ.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-FYTZCTJC.js";
-import "./chunk-7NTZWOJV.js";
-import "./chunk-OMO754MK.js";
-import "./chunk-RA5EXEHB.js";
-import {
-  arc_default
-} from "./chunk-PMZS3SHH.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/profile/polar.ts
-var ProfilePolar = class extends profilePlot {
-  constructor(opts) {
-    super(opts, "profilePolar");
-    this.radius = 250;
-    this.arcGenerator = arc_default().innerRadius(0);
-  }
-  async init(appState) {
-    await super.init(appState);
-    const config = appState.plots.find((p) => p.id === this.id);
-    this.scoreTerms = config.terms;
-    this.angle = Math.PI * 2 / config.terms.length;
-  }
-  async main() {
-    await super.main();
-    await this.setControls();
-    this.plot();
-  }
-  onMouseOut(event) {
-    const target = event.target;
-    if (target.tagName === "path") {
-      target.setAttribute("stroke", "white");
-      if (target.getAttribute("stroke-opacity") === "0") {
-        target.setAttribute("stroke-opacity", "1");
-      }
-    }
-    this.tip.hide();
-  }
-  onMouseOver(event) {
-    const target = event.target;
-    if (target.tagName === "path") {
-      target.setAttribute("stroke-opacity", "0");
-      const d = target.__data__;
-      const menu = this.tip.clear();
-      const percentage = this.getPercentage(d);
-      menu.d.text(`${d.module} ${percentage}%`);
-      menu.show(event.clientX, event.clientY, true, true);
-    } else {
-      this.onMouseOut(event);
-    }
-  }
-  plot() {
-    const config = this.config;
-    const width = this.isComparison ? 800 : 1e3, height = 600;
-    this.dom.svg = this.dom.plotDiv.append("div").style("display", "inline-block").append("svg").attr("width", width).attr("height", height);
-    this.dom.tableDiv = this.dom.plotDiv.append("div").attr("data-testid", "sjpp-profilePolar-data-table").style("display", "inline-block").style("vertical-align", "top").style("margin", "45px 20px");
-    this.dom.svg.append("text").attr("transform", `translate(130, ${40})`).attr("font-weight", "bold").text(config.title);
-    const rows = [];
-    const columns = [{ label: "Color" }, { label: "Module" }, { label: "Score", align: "center" }];
-    const radius = this.radius;
-    const x = 280;
-    const y = 330;
-    const polarG = this.dom.svg.append("g").attr("transform", `translate(${x},${y})`);
-    this.polarG = polarG;
-    this.legendG = this.dom.svg.append("g").attr("data-testid", "sjpp-profilePolar-legend").attr("transform", `translate(${x + 280}, ${y - 200})`);
-    this.filterG = this.dom.svg.append("g").attr("transform", `translate(${x + 280},${y})`);
-    for (let i2 = 0; i2 <= 10; i2++) addCircle(i2 * 10);
-    const angle = this.angle;
-    let i = 0;
-    for (const d of config.terms) {
-      const name = d.module;
-      d.i = i;
-      const color = d.score.term.color;
-      const percentage = this.getPercentage(d);
-      rows.push([{ color, disabled: true }, { value: name }, { value: percentage }]);
-      polarG.append("g").append("path").datum(d).attr("fill", color).attr("stroke", "white").attr(
-        "d",
-        this.arcGenerator({
-          outerRadius: percentage / 100 * radius,
-          startAngle: i * angle,
-          endAngle: (i + 1) * angle
-        })
-      ).on("click", (event) => this.onMouseOver(event));
-      i++;
-    }
-    this.dom.tableDiv.selectAll("*").remove();
-    if (!this.isComparison)
-      renderTable({
-        rows,
-        columns,
-        div: this.dom.tableDiv,
-        showLines: true,
-        resize: true,
-        maxHeight: "50vh"
-      });
-    addCircle(50, "C");
-    addCircle(75, "B");
-    addCircle(100, "A");
-    for (let i2 = 0; i2 <= 10; i2++) {
-      const percent = i2 * 10;
-      polarG.append("text").attr("transform", `translate(-10, ${-percent / 100 * radius + 5})`).attr("text-anchor", "end").style("font-size", "0.8rem").text(`${percent}%`).attr("pointer-events", "none");
-    }
-    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);
-    }
-    this.addFilterLegend();
-    function addCircle(percent, text) {
-      const circle = polarG.append("circle").attr("r", percent / 100 * radius).style("fill", "none").style("opacity", "0.5");
-      if (percent != 50) circle.style("stroke", "#aaa");
-      if (text) {
-        if (percent != 100) circle.style("stroke-dasharray", "5, 5").style("stroke-width", "2").style("stroke", "black");
-        polarG.append("text").attr("transform", `translate(15, ${-(percent / 100 - 0.125) * radius + 10})`).attr("text-anchor", "middle").text(text).style("font-weight", "bold").style("font-size", "24px").attr("pointer-events", "none");
-      }
-    }
-  }
-};
-async function getPlotConfig(opts, app, _activeCohort) {
-  try {
-    const activeCohort = _activeCohort === void 0 ? app.getState().activeCohort : _activeCohort;
-    const defaults = await getProfilePlotConfig(activeCohort, app, opts);
-    if (!defaults) throw "default config not found in termdbConfig.plotConfigByCohort.profilePolar";
-    const settings = getDefaultProfilePlotSettings();
-    defaults.settings = { profilePolar: settings };
-    const config = copyMerge(structuredClone(defaults), opts);
-    config.settings.controls = { isOpen: false };
-    const twlst = [];
-    for (const data of config.terms) {
-      data.score.q = { mode: "continuous" };
-      data.maxScore.q = { mode: "continuous" };
-      twlst.push(data.score, data.maxScore);
-    }
-    await fillTwLst(twlst, app.vocabApi);
-    return config;
-  } catch (e) {
-    throw new Error(`${e} [profilePolar getPlotConfig()]`);
-  }
-}
-var profilePolarInit = getCompInit(ProfilePolar);
-var componentInit = profilePolarInit;
-export {
-  componentInit,
-  getPlotConfig,
-  profilePolarInit
-};
-//# sourceMappingURL=polar-K5Z5FYKV.js.map

package/dist/profile.spec-A6EADWEC.js

@@ -1,71 +0,0 @@
-import {
-  getRunPp
-} from "./chunk-XATIKUGU.js";
-import "./chunk-OQSP66C6.js";
-import {
-  require_tape
-} from "./chunk-EFPC6YYT.js";
-import "./chunk-JXHU2FIA.js";
-import "./chunk-CT3LPTWW.js";
-import "./chunk-AZ276Z7T.js";
-import "./chunk-KGSCQRQ5.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-47X254B7.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-RQUXELHE.js";
-import "./chunk-M7QVMSRW.js";
-import "./chunk-RS3G3HE7.js";
-import "./chunk-UT6W4ZZL.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-5TDKRZN5.js";
-import "./chunk-RYRCMHYR.js";
-import "./chunk-ECKWM4HB.js";
-import "./chunk-NXOWHUR4.js";
-import "./chunk-5MWX5HUZ.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-ICNJQHQZ.js";
-import "./chunk-FYTZCTJC.js";
-import "./chunk-7NTZWOJV.js";
-import "./chunk-OMO754MK.js";
-import "./chunk-RA5EXEHB.js";
-import "./chunk-PMZS3SHH.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-NDWTN4U5.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// plots/test/profile.spec.js
-var import_tape = __toESM(require_tape(), 1);
-var runpp = getRunPp("mass", {
-  state: {
-    vocab: {
-      dslabel: "profile",
-      genome: "hg38"
-    }
-  },
-  debug: 1
-});
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- plots/profile -***-");
-  test.end();
-});
-(0, import_tape.default)("Test polar", function(test) {
-  async function runTests(plot) {
-    if (test._ok) self.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)("Test barchart", function(test) {
-  async function runTests(plot) {
-    const self2 = plot.Inner;
-    if (test._ok) self2.app.destroy();
-    test.end();
-  }
-});
-//# sourceMappingURL=profile.spec-A6EADWEC.js.map

package/dist/profileBarchart-EFLPJK2P.js

@@ -1,260 +0,0 @@
-import {
-  ABBREV_COHORT,
-  FULL_COHORT,
-  getDefaultProfilePlotSettings,
-  getProfilePlotConfig,
-  profilePlot
-} from "./chunk-U5QRRS7K.js";
-import "./chunk-FOXJTDTH.js";
-import "./chunk-I2GCD26Y.js";
-import "./chunk-CZTC4MTE.js";
-import "./chunk-GZ2B634M.js";
-import "./chunk-4XDKCFFT.js";
-import {
-  fillTwLst
-} from "./chunk-UT6W4ZZL.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-5TDKRZN5.js";
-import "./chunk-RYRCMHYR.js";
-import "./chunk-ECKWM4HB.js";
-import "./chunk-NXOWHUR4.js";
-import "./chunk-5MWX5HUZ.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-ICNJQHQZ.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-FYTZCTJC.js";
-import "./chunk-7NTZWOJV.js";
-import "./chunk-OMO754MK.js";
-import "./chunk-RA5EXEHB.js";
-import "./chunk-PMZS3SHH.js";
-import {
-  axisTop
-} from "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import {
-  linear
-} from "./chunk-W2IWHXLL.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-UJUXE42U.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-NDWTN4U5.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/profile/profileBarchart.ts
-var stepx = 500;
-var barwidth = 400;
-var profileBarchart = class extends profilePlot {
-  constructor(opts) {
-    super(opts, "profileBarchart");
-    this.rowCount = 0;
-    this.additionalInputs = [];
-  }
-  async init(appState) {
-    await super.init(appState);
-    const config = appState.plots.find((p) => p.id === this.id);
-    this.componentNames = config.plotByComponent.map((elem) => {
-      return { value: elem.profileComponent.name, label: elem.profileComponent.name };
-    });
-    const profileComponentInput = {
-      label: "Component",
-      type: "dropdown",
-      chartType: "profileBarchart",
-      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() {
-    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} [profileBarchart main()]`;
-    }
-  }
-  onMouseOut(event) {
-    if (event.target.tagName == "rect" && event.target.getAttribute("fill-opacity") == 0.3) {
-      const rect = event.target;
-      rect.setAttribute("fill-opacity", 0);
-    }
-  }
-  onMouseOver(event) {
-    if (event.target.tagName == "rect" && event.target.getAttribute("fill-opacity") == 0) {
-      const rect = event.target;
-      rect.setAttribute("fill-opacity", 0.3);
-    }
-  }
-  plot() {
-    const config = this.config;
-    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);
-    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 ${this.profileComponent} Component by Module and Domain`;
-    this.dom.svg.append("text").attr("transform", `translate(50, 30)`).attr("font-weight", "bold").text(title);
-    const svg = this.dom.svg;
-    const color = this.configProfileComponent.profileComponent.color;
-    this.dom.svg.append("defs").append("pattern").attr("id", `${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);
-    let x;
-    let y;
-    const step = 30;
-    for (const [i, c] of config.columnNames.entries()) {
-      if (i == 1 && !hasSubjectiveData) break;
-      x = i % 2 == 0 ? 400 : 900;
-      x += 10;
-      y = 70;
-      svg.append("text").attr("transform", `translate(${x}, ${y})`).attr("text-anchor", "start").style("font-weight", "bold").text(c);
-      drawAxes(x, y + 30);
-      x += stepx;
-    }
-    y = 70;
-    for (const group of this.configProfileComponent.groups) {
-      svg.append("text").attr("transform", `translate(${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}, ${y - 6})`).attr("x", 0).attr("y", 0).attr("width", hasSubjectiveData ? 1500 : 850).attr("height", 30).attr("fill", "#f8d335").attr("fill-opacity", 0);
-        x = 400;
-        if (row.term1) this.drawRect(x, y, row, "term1", g);
-        if (row.term2) this.drawRect(x + stepx, y, row, "term2", g);
-        y += step;
-      }
-    }
-    drawLine(410, 120, 50, y, "B");
-    drawLine(410, 120, 75, y, "A");
-    this.legendG = this.dom.svg.append("g").attr("data-testid", "sjpp-profileBarchart-legend").attr("transform", `translate(400,${y + 90})`);
-    this.filterG = this.dom.svg.append("g").attr("transform", `translate(0,${y + 90})`);
-    if (!this.isComparison) {
-      this.legendG.append("text").attr("text-anchor", "left").style("font-weight", "bold").text("Overall Score").attr("transform", `translate(0, -5)`);
-      this.addLegendItem("A", "More than 75% of possible scorable items", 1);
-      this.addLegendItem("B", "50-75% of possible scorable items", 2);
-      this.addLegendItem("C", "Less than 50% of possible scorable items", 3);
-      if (this.state.activeCohort == ABBREV_COHORT) {
-        const uiG = this.legendG.append("g");
-        this.addEndUserImpressionNote(uiG);
-      } else this.addPOCNote(this.legendG.append("g"));
-    }
-    this.addFilterLegend();
-    if (!hasSubjectiveData) return;
-    drawLine(910, 120, 50, y, "B");
-    drawLine(910, 120, 75, y, "A");
-    y += 40;
-    x = 600;
-    const lineG = svg.append("g");
-    this.drawLegendRect(x, y, "and", color, lineG);
-    x += 300;
-    this.drawLegendRect(x, y, "or", color, lineG);
-    function drawAxes(x2, y2) {
-      const xAxisScale = linear().domain([0, 100]).range([0, barwidth]);
-      svg.append("g").attr("transform", `translate(${x2}, ${y2})`).call(axisTop(xAxisScale));
-    }
-    function drawLine(x2, y2, percent, y22, text) {
-      const x1 = x2 + percent / 100 * barwidth;
-      svg.append("line").style("stroke", "#aaa").style("stroke-width", 1).style("stroke-dasharray", "5, 5").attr("x1", x1).attr("y1", y2).attr("x2", x1).attr("y2", y22);
-      svg.append("text").attr("transform", `translate(${x1 + 0.125 * barwidth}, ${y22 + 20})`).attr("text-anchor", "middle").text(text).style("font-weight", "bold");
-      if (percent == 50)
-        svg.append("text").attr("transform", `translate(${x1 - 0.25 * barwidth}, ${y22 + 20})`).attr("text-anchor", "middle").text("C").style("font-weight", "bold");
-    }
-  }
-  drawRect(x, y, row, field, g) {
-    const hasSubjectiveData = this.configProfileComponent.hasSubjectiveData;
-    const d = row[field];
-    let subjectiveTerm = false;
-    if ((row.name == "Total Module" || row.name == "End-user Impression*") && !row.term2) subjectiveTerm = true;
-    const termColor = d.score.term.color;
-    const value = this.getPercentage(d);
-    const isFirst = field == "term1" || field == "term2" && !row.term1;
-    const pairValue = field == "term1" ? this.getPercentage(row.term2) : this.getPercentage(row.term1);
-    const width = value ? value / 100 * barwidth : 0;
-    if (value) {
-      const isObjective = this.state.activeCohort == FULL_COHORT && this.settings.profileComponent == "Patients and Outcomes" ? true : !subjectiveTerm && (pairValue || !hasSubjectiveData);
-      const rect = g.append("rect").attr("transform", `translate(${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}, ${y + 15})`).attr("text-anchor", "end").text(row.name).attr("pointer-events", "none");
-  }
-  drawLegendRect(x, y, operator, color, lineG) {
-    const rect = lineG.append("g").attr("transform", `translate(${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}, ${y + 15})`).attr("text-anchor", "start").text("Objective ");
-    text.append("tspan").attr("font-weight", "bold").text(operator);
-    text.append("tspan").text(" Subjective data");
-  }
-};
-async function getPlotConfig(opts, app, _activeCohort) {
-  try {
-    const activeCohort = _activeCohort === void 0 ? app.getState().activeCohort : _activeCohort;
-    const defaults = await getProfilePlotConfig(activeCohort, app, opts);
-    defaults.settings = { profileBarchart: getDefaultProfilePlotSettings() };
-    let config = structuredClone(defaults);
-    config = copyMerge(config, opts);
-    config.settings.controls = { isOpen: false };
-    const twlst = [];
-    for (const profileComponent of config.plotByComponent) {
-      profileComponent.hasSubjectiveData = false;
-      for (const group of profileComponent.groups)
-        for (const row of group.rows) {
-          if (row.term1) {
-            row.term1.score.q = row.term1.maxScore.q = { mode: "continuous" };
-            twlst.push(row.term1.score);
-            twlst.push(row.term1.maxScore);
-          }
-          if (row.term2) {
-            row.term2.score.q = row.term2.maxScore.q = { mode: "continuous" };
-            twlst.push(row.term2.score);
-            twlst.push(row.term2.maxScore);
-          }
-          if (row.term1 && row.term2) profileComponent.hasSubjectiveData = true;
-        }
-    }
-    await fillTwLst(twlst, app.vocabApi);
-    return config;
-  } catch (e) {
-    throw `${e} [profileBarchart getPlotConfig()]`;
-  }
-}
-var profileBarchartInit = getCompInit(profileBarchart);
-var componentInit = profileBarchartInit;
-function getDefaultProfileBarchartSettings() {
-  return {};
-}
-export {
-  componentInit,
-  getDefaultProfileBarchartSettings,
-  getPlotConfig,
-  profileBarchartInit
-};
-//# sourceMappingURL=profileBarchart-EFLPJK2P.js.map