@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/radarFacility2-HXUUTRYO.js

@@ -1,323 +0,0 @@
-import {
-  getDefaultProfilePlotSettings,
-  getProfilePlotConfig,
-  makeChartBtnMenu,
-  profilePlot
-} from "./chunk-4JVNATQR.js";
-import {
-  fillTwLst,
-  renderTable
-} from "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import {
-  dofetch3
-} from "./chunk-6ZCHECOT.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import {
-  arc_default,
-  line_default
-} from "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/profile/radarFacility2.ts
-var ProfileRadarFacility2 = class extends profilePlot {
-  static {
-    this.type = "profileRadarFacility2";
-  }
-  constructor(opts) {
-    super(opts, "profileRadarFacility2");
-    this.radius = 200;
-    this.isRadarFacility = true;
-    this.lineGenerator = line_default().defined((d) => d !== null);
-    this.arcGenerator = arc_default().innerRadius(0);
-  }
-  async init(appState) {
-    await super.init(appState);
-    const config = structuredClone(appState.plots.find((p) => p.id === this.id));
-    for (const row of config.terms) {
-      this.scoreTerms.push(row);
-    }
-    this.angle = Math.PI * 2 / config.terms.length;
-  }
-  async main() {
-    await super.main();
-    await this.setControls();
-    this.plot();
-  }
-  /**
-   * Called by the base class's setControls() in place of the shared
-   * getProfileScores fetch AND the second facility-site fetch — both are
-   * covered by this single dedicated-route call. Sets `this.data` (aggregate)
-   * and `this.sampleData` (single-site) from one response.
-   */
-  async fetchRadarFacility2Scores() {
-    const response = await dofetch3("termdb/profileRadarFacility2Scores", {
-      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 }
-        })),
-        filter: this.filter,
-        filterByUserSites: this.settings?.filterByUserSites,
-        facilitySite: this.settings?.facilitySite || null
-      }
-    });
-    if (response && "error" in response) throw response.error;
-    this.sampleData = response.sampleData;
-    return response;
-  }
-  plot() {
-    const hasFacilityData = !!this.sampleData?.site;
-    const { radarG, rows, data, data2 } = this.createSvgAndGrid(hasFacilityData);
-    this.drawLines(radarG, data, data2, hasFacilityData);
-    this.drawPercentLabels(radarG);
-    this.drawTableAndLegend(rows, hasFacilityData);
-  }
-  createSvgAndGrid(hasFacilityData) {
-    const width = this.isComparison ? 1e3 : 1100;
-    const height = 630;
-    this.dom.svg = this.dom.plotDiv.append("div").style("display", "inline-block").append("svg").attr("width", width).attr("height", height);
-    const rightDiv = this.dom.plotDiv.append("div").style("display", "inline-block").style("vertical-align", "top").style("margin-top", "80px").style("margin-right", "20px");
-    this.dom.tableDiv = rightDiv.append("div").attr("data-testid", "sjpp-profileRadarFacility2-data-table");
-    this.dom.svg.append("text").attr("transform", `translate(90, 30)`).attr("font-weight", "bold").text(`${this.config.title} (v2)`);
-    const x = 300;
-    const y = 330;
-    const radarG = this.dom.svg.append("g").attr("transform", `translate(${x},${y})`);
-    this.radarG = radarG;
-    this.legendG = this.dom.svg.append("g").attr("data-testid", "sjpp-profileRadarFacility2-legend").attr("font-size", "0.9em").attr("transform", `translate(${x + 320},${y - 150})`);
-    this.filterG = this.dom.svg.append("g").attr("transform", `translate(${x + 320},${y - 50})`);
-    for (let i2 = 0; i2 <= 10; i2++) this.drawPolygon(i2 * 10);
-    const rows = [];
-    const data = [];
-    const data2 = [];
-    const angle = this.angle;
-    let i = 0;
-    for (const item of this.config.terms) {
-      const iangle = i * angle - Math.PI / 2;
-      const rawFacility = this.getSamplePercentage(item);
-      const rawGlobal = this.getPercentage(item);
-      const p1 = hasFacilityData && Number.isFinite(rawFacility) ? rawFacility : null;
-      const p2 = Number.isFinite(rawGlobal) ? rawGlobal : null;
-      const tooltipDatum = { module: item.module, percentage1: p1, percentage2: p2 };
-      this.radarG.append("path").datum(tooltipDatum).attr("fill", "transparent").attr(
-        "d",
-        this.arcGenerator({
-          outerRadius: this.radius,
-          startAngle: i * angle - angle / 2,
-          endAngle: (i + 1) * angle - angle / 2
-        })
-      ).on("click", (event) => this.onMouseOver(event));
-      if (p2 !== null) this.addDataPoint(iangle, data2, p2, false, tooltipDatum);
-      else data2.push(null);
-      if (p1 !== null) this.addDataPoint(iangle, data, p1, true, tooltipDatum);
-      else data.push(null);
-      const color = item.score.term.color;
-      const bothPresent = p1 !== null && p2 !== null;
-      const diff = bothPresent ? Math.abs(p1 - p2) : null;
-      const diffRow = diff !== null ? { value: diff } : { value: "\u2014" };
-      if (diff !== null && diff >= 20) diffRow.color = p2 > p1 ? "red" : "blue";
-      rows.push([
-        { color, disabled: true },
-        { value: item.module },
-        { value: p1 !== null ? p1 : "\u2014" },
-        { value: p2 !== null ? p2 : "\u2014" },
-        diffRow
-      ]);
-      this.drawModuleLabel(item.module, iangle);
-      i++;
-    }
-    return { radarG, rows, data, data2 };
-  }
-  drawLines(radarG, data, data2, hasFacilityData) {
-    const closePolygon = (arr) => {
-      const firstDefined = arr.find((v) => v !== null);
-      if (firstDefined) arr.push(firstDefined);
-    };
-    closePolygon(data2);
-    const color1 = "blue";
-    const color2 = "gray";
-    if (hasFacilityData) {
-      closePolygon(data);
-      radarG.append("g").append("path").style("stroke", color1).attr("fill", "none").attr("stroke-width", "2px").attr("d", this.lineGenerator(data));
-    }
-    if (this.state.logged) {
-      radarG.append("g").append("path").style("stroke", color2).attr("fill", "none").style("stroke-dasharray", "5, 5").attr("d", this.lineGenerator(data2));
-    }
-  }
-  drawPercentLabels(radarG) {
-    for (let i = 0; i <= 10; i++) {
-      const percent = i * 10;
-      radarG.append("text").attr("transform", `translate(0, ${-percent / 100 * this.radius - 2})`).attr("text-anchor", "end").style("font-size", "0.8rem").text(`${percent}%`).attr("pointer-events", "none");
-    }
-  }
-  drawTableAndLegend(rows, hasFacilityData) {
-    const columns = [
-      { label: "Color" },
-      { label: "Module" },
-      { label: "Facility" },
-      { label: "Global" },
-      {
-        label: "Difference*",
-        tooltip: `* Difference between site and aggregated scores. If bigger than 20 and positive shown in blue, if negative shown in red.`
-      }
-    ];
-    if (!this.isComparison) {
-      renderTable({
-        rows,
-        columns,
-        div: this.dom.tableDiv,
-        showLines: true,
-        resize: true
-      });
-    }
-    this.addFilterLegend();
-    this.legendG.append("text").attr("text-anchor", "left").style("font-weight", "bold").text("Legend");
-    if (hasFacilityData) {
-      const site = this.sampleData.site;
-      this.addFacilityLegendItem(`${site.label} / ${site.value}`, "blue", 0, "none");
-      this.addFacilityLegendItem(this.config.score, "gray", 1, "5, 5");
-    } else {
-      this.legendG.append("text").attr("text-anchor", "start").style("font-style", "italic").style("font-size", "0.85em").attr("transform", "translate(0, 25)").text("No institutional data available for the current filter.");
-      if (this.state.logged) {
-        this.addFacilityLegendItem(this.config.score, "gray", 2, "5, 5");
-      }
-    }
-  }
-  drawModuleLabel(module, iangle) {
-    const radius = this.radius;
-    const leftSide = iangle > Math.PI / 2 && iangle <= 3 / 2 * Math.PI;
-    const dx = radius * 1.1 * Math.cos(iangle);
-    let dy = radius * 1.1 * Math.sin(iangle) - 10;
-    const textElem = this.radarG.append("text").attr("x", `${dx}px`).attr("y", `${dy}px`).attr("font-size", "0.9em");
-    const texts = module.split(" ");
-    let span;
-    for (const text of texts) {
-      if (text != "and") {
-        dy += 15;
-        span = textElem.append("tspan").attr("x", `${dx}px`).attr("y", `${dy}px`).text(text);
-      } else span.append("tspan").text(" and");
-    }
-    if (leftSide) textElem.attr("text-anchor", "end");
-  }
-  addDataPoint(iangle, data, percentage, isFacility, tooltipDatum) {
-    const iradius = percentage / 100 * this.radius;
-    const x = iradius * Math.cos(iangle);
-    const y = iradius * Math.sin(iangle);
-    const color = isFacility ? "blue" : "#aaa";
-    this.radarG.append("g").attr("transform", `translate(${x}, ${y})`).append("circle").attr("r", 4).attr("fill", color).datum(tooltipDatum).on("click", (event) => this.onMouseOver(event));
-    data.push([x, y]);
-  }
-  drawPolygon(percent) {
-    const data = [];
-    for (let i = 0; i < this.config.terms.length; i++) {
-      const iangle = i * this.angle - Math.PI / 2;
-      const iradius = percent / 100 * this.radius;
-      const x = iradius * Math.cos(iangle);
-      const y = iradius * Math.sin(iangle);
-      data.push([x, y]);
-    }
-    data.push(data[0]);
-    this.radarG.append("g").append("path").style("stroke", "#aaa").attr("fill", "none").attr("d", this.lineGenerator(data)).style("opacity", "0.5");
-  }
-  addFacilityLegendItem(text, color, index, strokeDash) {
-    const step = 25;
-    const y = step + index * step;
-    const x = 35;
-    this.legendG.append("path").attr("stroke", color).style("stroke-dasharray", strokeDash).attr("stroke-width", "2px").attr(
-      "d",
-      this.lineGenerator([
-        [0, y - 5],
-        [x, y - 5]
-      ])
-    );
-    this.legendG.append("g").attr("transform", `translate(0, ${y - 5})`).append("circle").attr("r", 4).attr("fill", color);
-    this.legendG.append("text").attr("font-size", "0.9em").attr("transform", `translate(${x + 5}, ${y})`).attr("text-anchor", "left").append("tspan").text(text);
-  }
-  onMouseOver(event) {
-    const d = event.target.__data__;
-    if (d?.module) {
-      const label1 = "Facility";
-      const label2 = this.config.score;
-      const menu = this.tip.clear();
-      menu.d.append("div").style("font-weight", "bold").text(d.module);
-      const table = menu.d.append("table");
-      let tr = table.append("tr");
-      tr.append("td").text(label1);
-      tr.append("td").text(d.percentage1 ?? "\u2014");
-      tr = table.append("tr");
-      tr.append("td").text(label2);
-      tr.append("td").text(d.percentage2 ?? "\u2014");
-      menu.show(event.clientX, event.clientY, true, true);
-    } else this.onMouseOut(event);
-  }
-  /**
-   * Returns the single-site percentage for term `d` — or `undefined` when the
-   * server omitted the term (no eligible data) OR when `sampleData` is absent.
-   * Callers must treat `undefined` as missing and NOT participate in arithmetic
-   * or coordinate math — coercing to 0 would conflate missing with a real 0 score.
-   */
-  getSamplePercentage(d) {
-    if (!d) return void 0;
-    return this.sampleData?.term2Score?.[d.score.term.id];
-  }
-};
-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.profileRadarFacility2";
-    const config = copyMerge(structuredClone(defaults), opts);
-    const settings = getDefaultProfilePlotSettings();
-    config.settings = {
-      profileRadarFacility2: settings,
-      controls: { isOpen: false }
-    };
-    const twlst = [];
-    for (const row of config.terms) {
-      row.score.q = row.maxScore.q = { mode: "continuous" };
-      twlst.push(row.score);
-      twlst.push(row.maxScore);
-    }
-    await fillTwLst(twlst, app.vocabApi);
-    return config;
-  } catch (e) {
-    throw `${e} [profileRadarFacility2 getPlotConfig()]`;
-  }
-}
-var profileRadarFacility2Init = getCompInit(ProfileRadarFacility2);
-var componentInit = profileRadarFacility2Init;
-export {
-  componentInit,
-  getPlotConfig,
-  makeChartBtnMenu,
-  profileRadarFacility2Init
-};
-//# sourceMappingURL=radarFacility2-HXUUTRYO.js.map

package/dist/regression-Y4NYGZSA.js

@@ -1,54 +0,0 @@
-import {
-  componentInit,
-  getPlotConfig,
-  get_defaultQ4fillTW,
-  makeChartBtnMenu,
-  regressionInit
-} from "./chunk-O4WJSZC3.js";
-import "./chunk-W35IOI74.js";
-import "./chunk-K7XWZSQA.js";
-import "./chunk-JMJW3ERE.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-YQVEBFGT.js";
-import "./chunk-3JAC5CHL.js";
-import "./chunk-EBGX226R.js";
-import "./chunk-HZETQJGD.js";
-import "./chunk-PXYYICV7.js";
-import "./chunk-7OYOC7XY.js";
-import "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  componentInit,
-  getPlotConfig,
-  get_defaultQ4fillTW,
-  makeChartBtnMenu,
-  regressionInit
-};
-//# sourceMappingURL=regression-Y4NYGZSA.js.map

package/dist/regression.inputs-RWFIJLNF.js

@@ -1,46 +0,0 @@
-import {
-  RegressionInputs
-} from "./chunk-O4WJSZC3.js";
-import "./chunk-W35IOI74.js";
-import "./chunk-K7XWZSQA.js";
-import "./chunk-JMJW3ERE.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-YQVEBFGT.js";
-import "./chunk-3JAC5CHL.js";
-import "./chunk-EBGX226R.js";
-import "./chunk-HZETQJGD.js";
-import "./chunk-PXYYICV7.js";
-import "./chunk-7OYOC7XY.js";
-import "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  RegressionInputs
-};
-//# sourceMappingURL=regression.inputs-RWFIJLNF.js.map

package/dist/regression.inputs.term-QIU5SHTN.js

@@ -1,46 +0,0 @@
-import {
-  InputTerm
-} from "./chunk-O4WJSZC3.js";
-import "./chunk-W35IOI74.js";
-import "./chunk-K7XWZSQA.js";
-import "./chunk-JMJW3ERE.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-YQVEBFGT.js";
-import "./chunk-3JAC5CHL.js";
-import "./chunk-EBGX226R.js";
-import "./chunk-HZETQJGD.js";
-import "./chunk-PXYYICV7.js";
-import "./chunk-7OYOC7XY.js";
-import "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  InputTerm
-};
-//# sourceMappingURL=regression.inputs.term-QIU5SHTN.js.map

package/dist/regression.inputs.values.table-FM6QTSEV.js

@@ -1,43 +0,0 @@
-import {
-  InputValuesTable
-} from "./chunk-W35IOI74.js";
-import "./chunk-K7XWZSQA.js";
-import "./chunk-JMJW3ERE.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-YQVEBFGT.js";
-import "./chunk-3JAC5CHL.js";
-import "./chunk-EBGX226R.js";
-import "./chunk-HZETQJGD.js";
-import "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  InputValuesTable
-};
-//# sourceMappingURL=regression.inputs.values.table-FM6QTSEV.js.map