@sjcrh/proteinpaint-client 2.191.4 → 2.193.0

package/dist/polar2-IT3OF5DX.js

@@ -0,0 +1,231 @@
+import {
+  getDefaultProfilePlotSettings,
+  getProfilePlotConfig,
+  profilePlot
+} from "./chunk-JEZUPG4J.js";
+import {
+  fillTwLst,
+  renderTable
+} from "./chunk-L7VDSIM7.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-LSEFWW72.js";
+import "./chunk-UXDVUCXU.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-HBW42TDT.js";
+import "./chunk-LQJMCE7G.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-IIT367QZ.js";
+import "./chunk-RZGEKL77.js";
+import "./chunk-KM4JBR26.js";
+import "./chunk-COYULNJF.js";
+import {
+  dofetch3
+} from "./chunk-6G4YOMWW.js";
+import "./chunk-7IYJZZQI.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-M3J4MINX.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-I73KUUYG.js";
+import "./chunk-IVXCWCKS.js";
+import "./chunk-7KRS7L4U.js";
+import "./chunk-BKPDYW5T.js";
+import "./chunk-JNITUVXP.js";
+import {
+  arc_default
+} from "./chunk-TJYRBEBK.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-SOTB4FRE.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-KYBIQBXE.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-OMR2DT66.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// plots/profile/polar2.ts
+var ProfilePolar2 = class extends profilePlot {
+  constructor(opts) {
+    super(opts, "profilePolar2");
+    this.radius = 250;
+    this.arcGenerator = arc_default().innerRadius(0);
+  }
+  static {
+    this.type = "profilePolar2";
+  }
+  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() {
+    this.dom.loadingDiv.style("display", "");
+    try {
+      await super.main();
+      await this.setControls();
+      this.plot();
+    } finally {
+      this.dom.loadingDiv.style("display", "none");
+    }
+  }
+  /**
+   * Fetches aggregated module scores from termdb/profilePolar2Scores after
+   * super.setControls() builds the filter UI and sets this.filter. The server
+   * derives the facility term from the request term IDs and returns the median
+   * percentage across all eligible sites.
+   */
+  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/profilePolar2Scores", {
+      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) {
+    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);
+      const label = percentage == null ? "N/A" : `${percentage}%`;
+      menu.d.text(`${d.module} ${label}`);
+      menu.show(event.clientX, event.clientY, true, true);
+    } else {
+      this.onMouseOut(event);
+    }
+  }
+  plot() {
+    this.createSvg();
+    const rows = this.drawArcs();
+    this.drawGrid();
+    this.drawTable(rows);
+    this.drawLegend();
+  }
+  createSvg() {
+    const width = this.isComparison ? 800 : 1e3, height = 600;
+    this.dom.svg = this.dom.plotDiv.append("div").style("display", "inline-block").append("svg").attr("width", width).attr("height", height);
+    this.dom.tableDiv = this.dom.plotDiv.append("div").attr("data-testid", "sjpp-profilePolar2-data-table").style("display", "inline-block").style("vertical-align", "top").style("margin", "45px 20px");
+    this.dom.svg.append("text").attr("transform", `translate(130, 40)`).attr("font-weight", "bold").text(this.config.title);
+    const x = 280, y = 330;
+    this.polarG = this.dom.svg.append("g").attr("transform", `translate(${x},${y})`);
+    this.legendG = this.dom.svg.append("g").attr("data-testid", "sjpp-profilePolar2-legend").attr("transform", `translate(${x + 280}, ${y - 200})`);
+    this.filterG = this.dom.svg.append("g").attr("transform", `translate(${x + 280},${y})`);
+  }
+  drawGrid() {
+    for (let i = 0; i <= 10; i++) this.drawGridCircle(i * 10);
+    this.drawGradeCircle(50, "C");
+    this.drawGradeCircle(75, "B");
+    this.drawGradeCircle(100, "A");
+    for (let i = 0; i <= 10; i++) {
+      const percent = i * 10;
+      this.polarG.append("text").attr("transform", `translate(-10, ${-percent / 100 * this.radius + 5})`).attr("text-anchor", "end").style("font-size", "0.8rem").text(`${percent}%`).attr("pointer-events", "none");
+    }
+  }
+  drawGridCircle(percent) {
+    const circle = this.polarG.append("circle").attr("r", percent / 100 * this.radius).style("fill", "none").style("opacity", "0.5");
+    if (percent != 50) circle.style("stroke", "#aaa");
+  }
+  drawGradeCircle(percent, label) {
+    const circle = this.polarG.append("circle").attr("r", percent / 100 * this.radius).style("fill", "none").style("opacity", "0.5");
+    if (percent != 100) circle.style("stroke-dasharray", "5, 5").style("stroke-width", "2").style("stroke", "black");
+    this.polarG.append("text").attr("transform", `translate(15, ${-(percent / 100 - 0.125) * this.radius + 10})`).attr("text-anchor", "middle").text(label).style("font-weight", "bold").style("font-size", "24px").attr("pointer-events", "none");
+  }
+  /** Draws the arc slices and returns table rows for drawTable(). */
+  drawArcs() {
+    const rows = [];
+    let i = 0;
+    for (const d of this.config.terms) {
+      d.i = i;
+      const color = d.score.term.color;
+      const percentage = this.getPercentage(d);
+      rows.push([{ color, disabled: true }, { value: d.module }, { value: percentage ?? "N/A" }]);
+      this.polarG.append("g").append("path").datum(d).attr("fill", color).attr("stroke", "white").attr(
+        "d",
+        this.arcGenerator({
+          outerRadius: percentage / 100 * this.radius,
+          startAngle: i * this.angle,
+          endAngle: (i + 1) * this.angle
+        })
+      ).on("click", (event) => this.onMouseOver(event));
+      i++;
+    }
+    return rows;
+  }
+  drawTable(rows) {
+    const columns = [{ label: "Color" }, { label: "Module" }, { label: "Score", align: "center" }];
+    this.dom.tableDiv.selectAll("*").remove();
+    if (!this.isComparison)
+      renderTable({
+        rows,
+        columns,
+        div: this.dom.tableDiv,
+        showLines: true,
+        resize: true,
+        maxHeight: "50vh"
+      });
+  }
+  drawLegend() {
+    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();
+  }
+};
+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.profilePolar2";
+    const settings = getDefaultProfilePlotSettings();
+    defaults.settings = { profilePolar2: 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 `${e} [profilePolar2 getPlotConfig()]`;
+  }
+}
+var profilePolar2Init = getCompInit(ProfilePolar2);
+var componentInit = profilePolar2Init;
+export {
+  componentInit,
+  getPlotConfig,
+  profilePolar2Init
+};
+//# sourceMappingURL=polar2-IT3OF5DX.js.map

package/dist/polar2-IT3OF5DX.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/profile/polar2.ts"],
+  "sourcesContent": ["import type { MassAppApi, MassState } from '#mass/types/mass'\nimport type { SvgG } from '../../types/d3'\nimport type { ProfilePolarConfig, ProfilePolarDom } from './types/PolarTypes'\nimport type { TableCell } from '#dom'\nimport { getCompInit, copyMerge } from '#rx'\nimport { fillTwLst } from '#termsetting'\nimport { arc } from 'd3'\nimport { profilePlot, getDefaultProfilePlotSettings, getProfilePlotConfig } from './profilePlot.js'\nimport { dofetch3 } from '#common/dofetch'\nimport { renderTable } from '#dom'\n\n/** TODO: profilePlot must extend RxComponent but file not tsc.\n * Work arounds until profilePlot is migrated to ts.\n */\nclass ProfilePolar2 extends profilePlot {\n\tstatic type = 'profilePolar2'\n\treadonly radius = 250\n\treadonly arcGenerator = arc().innerRadius(0)\n\tangle!: number\n\tpolarG!: SvgG\n\tdeclare legendG: SvgG\n\tdeclare filterG: SvgG\n\tdeclare dom: ProfilePolarDom\n\n\tconstructor(opts) {\n\t\tsuper(opts, 'profilePolar2')\n\t}\n\n\tasync init(appState: MassState) {\n\t\tawait super.init(appState)\n\t\tconst config = appState.plots.find(p => p.id === this.id) as ProfilePolarConfig\n\t\tthis.scoreTerms = config.terms\n\t\tthis.angle = (Math.PI * 2) / config.terms.length\n\t}\n\n\tasync main() {\n\t\tthis.dom.loadingDiv.style('display', '')\n\t\ttry {\n\t\t\tawait super.main()\n\t\t\tawait this.setControls()\n\t\t\tthis.plot()\n\t\t} finally {\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t}\n\t}\n\n\t/**\n\t * Fetches aggregated module scores from termdb/profilePolar2Scores after\n\t * super.setControls() builds the filter UI and sets this.filter. The server\n\t * derives the facility term from the request term IDs and returns the median\n\t * percentage across all eligible sites.\n\t */\n\tasync setControls(additionalInputs: any[] = []) {\n\t\tawait super.setControls(additionalInputs)\n\t\tthis.data = await this.fetchAggregatedScores()\n\t\tif (this.data && 'error' in this.data) throw this.data.error\n\t}\n\n\tprivate async fetchAggregatedScores() {\n\t\t// No facilityTW \u2014 the server derives it from term ID prefixes in the request.\n\t\t// scoreTerms stripped to { term: { id }, q } only \u2014 server fills the rest via termjsonByOneid.\n\t\treturn dofetch3('termdb/profilePolar2Scores', {\n\t\t\tbody: {\n\t\t\t\tgenome: this.state.vocab.genome,\n\t\t\t\tdslabel: this.state.vocab.dslabel,\n\t\t\t\tscoreTerms: this.scoreTerms.map((t: any) => ({\n\t\t\t\t\tscore: { term: { id: t.score.term.id }, q: t.score.q },\n\t\t\t\t\tmaxScore: typeof t.maxScore === 'number' ? t.maxScore : { term: { id: t.maxScore.term.id }, q: t.maxScore.q }\n\t\t\t\t})),\n\t\t\t\tfilterByUserSites: this.settings?.filterByUserSites,\n\t\t\t\tfilter: this.filter\n\t\t\t}\n\t\t})\n\t}\n\n\tonMouseOut(event: MouseEvent) {\n\t\tconst target = event.target as HTMLElement\n\t\tif (target.tagName === 'path') {\n\t\t\ttarget.setAttribute('stroke', 'white')\n\t\t\tif (target.getAttribute('stroke-opacity') === '0') {\n\t\t\t\ttarget.setAttribute('stroke-opacity', '1')\n\t\t\t}\n\t\t}\n\t\tthis.tip.hide()\n\t}\n\n\tonMouseOver(event: MouseEvent) {\n\t\tconst target = event.target as HTMLElement\n\t\tif (target.tagName === 'path') {\n\t\t\ttarget.setAttribute('stroke-opacity', '0')\n\t\t\tconst d = (target as any).__data__\n\t\t\tconst menu = this.tip.clear()\n\t\t\tconst percentage = this.getPercentage(d)\n\t\t\tconst label = percentage == null ? 'N/A' : `${percentage}%`\n\t\t\tmenu.d.text(`${d.module} ${label}`)\n\t\t\tmenu.show(event.clientX, event.clientY, true, true)\n\t\t} else {\n\t\t\tthis.onMouseOut(event)\n\t\t}\n\t}\n\n\tplot() {\n\t\tthis.createSvg()\n\t\tconst rows = this.drawArcs()\n\t\tthis.drawGrid()\n\t\tthis.drawTable(rows)\n\t\tthis.drawLegend()\n\t}\n\n\tprivate createSvg() {\n\t\tconst width = this.isComparison ? 800 : 1000,\n\t\t\theight = 600\n\t\tthis.dom.svg = this.dom.plotDiv\n\t\t\t.append('div')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.append('svg')\n\t\t\t.attr('width', width)\n\t\t\t.attr('height', height) as any\n\n\t\tthis.dom.tableDiv = this.dom.plotDiv\n\t\t\t.append('div')\n\t\t\t.attr('data-testid', 'sjpp-profilePolar2-data-table')\n\t\t\t.style('display', 'inline-block')\n\t\t\t.style('vertical-align', 'top')\n\t\t\t.style('margin', '45px 20px') as any\n\n\t\tthis.dom.svg\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(130, 40)`)\n\t\t\t.attr('font-weight', 'bold')\n\t\t\t.text(this.config.title)\n\n\t\tconst x = 280,\n\t\t\ty = 330\n\t\tthis.polarG = this.dom.svg.append('g').attr('transform', `translate(${x},${y})`)\n\t\tthis.legendG = this.dom.svg\n\t\t\t.append('g')\n\t\t\t.attr('data-testid', 'sjpp-profilePolar2-legend')\n\t\t\t.attr('transform', `translate(${x + 280}, ${y - 200})`)\n\t\tthis.filterG = this.dom.svg.append('g').attr('transform', `translate(${x + 280},${y})`)\n\t}\n\n\tprivate drawGrid() {\n\t\t// Background concentric circles at every 10%\n\t\tfor (let i = 0; i <= 10; i++) this.drawGridCircle(i * 10)\n\n\t\t// Grade boundary circles with grade labels\n\t\tthis.drawGradeCircle(50, 'C')\n\t\tthis.drawGradeCircle(75, 'B')\n\t\tthis.drawGradeCircle(100, 'A')\n\n\t\t// Percentage labels along the left axis\n\t\tfor (let i = 0; i <= 10; i++) {\n\t\t\tconst percent = i * 10\n\t\t\tthis.polarG\n\t\t\t\t.append('text')\n\t\t\t\t.attr('transform', `translate(-10, ${(-percent / 100) * this.radius + 5})`)\n\t\t\t\t.attr('text-anchor', 'end')\n\t\t\t\t.style('font-size', '0.8rem')\n\t\t\t\t.text(`${percent}%`)\n\t\t\t\t.attr('pointer-events', 'none')\n\t\t}\n\t}\n\n\tprivate drawGridCircle(percent: number) {\n\t\tconst circle = this.polarG\n\t\t\t.append('circle')\n\t\t\t.attr('r', (percent / 100) * this.radius)\n\t\t\t.style('fill', 'none')\n\t\t\t.style('opacity', '0.5')\n\t\tif (percent != 50) circle.style('stroke', '#aaa')\n\t}\n\n\tprivate drawGradeCircle(percent: number, label: string) {\n\t\tconst circle = this.polarG\n\t\t\t.append('circle')\n\t\t\t.attr('r', (percent / 100) * this.radius)\n\t\t\t.style('fill', 'none')\n\t\t\t.style('opacity', '0.5')\n\n\t\tif (percent != 100) circle.style('stroke-dasharray', '5, 5').style('stroke-width', '2').style('stroke', 'black')\n\n\t\tthis.polarG\n\t\t\t.append('text')\n\t\t\t.attr('transform', `translate(15, ${-(percent / 100 - 0.125) * this.radius + 10})`)\n\t\t\t.attr('text-anchor', 'middle')\n\t\t\t.text(label)\n\t\t\t.style('font-weight', 'bold')\n\t\t\t.style('font-size', '24px')\n\t\t\t.attr('pointer-events', 'none')\n\t}\n\n\t/** Draws the arc slices and returns table rows for drawTable(). */\n\tprivate drawArcs(): TableCell[][] {\n\t\tconst rows: TableCell[][] = []\n\t\tlet i = 0\n\t\tfor (const d of this.config.terms) {\n\t\t\td.i = i\n\t\t\tconst color = d.score.term.color\n\t\t\tconst percentage = this.getPercentage(d)\n\t\t\trows.push([{ color, disabled: true }, { value: d.module }, { value: percentage ?? 'N/A' }])\n\t\t\tthis.polarG\n\t\t\t\t.append('g')\n\t\t\t\t.append('path')\n\t\t\t\t.datum(d)\n\t\t\t\t.attr('fill', color)\n\t\t\t\t.attr('stroke', 'white')\n\t\t\t\t.attr(\n\t\t\t\t\t'd',\n\t\t\t\t\tthis.arcGenerator({\n\t\t\t\t\t\touterRadius: (percentage! / 100) * this.radius,\n\t\t\t\t\t\tstartAngle: i * this.angle,\n\t\t\t\t\t\tendAngle: (i + 1) * this.angle\n\t\t\t\t\t} as any)\n\t\t\t\t)\n\t\t\t\t.on('click', event => this.onMouseOver(event))\n\t\t\ti++\n\t\t}\n\t\treturn rows\n\t}\n\n\tprivate drawTable(rows: TableCell[][]) {\n\t\tconst columns = [{ label: 'Color' }, { label: 'Module' }, { label: 'Score', align: 'center' }]\n\t\tthis.dom.tableDiv.selectAll('*').remove()\n\t\tif (!this.isComparison)\n\t\t\trenderTable({\n\t\t\t\trows,\n\t\t\t\tcolumns,\n\t\t\t\tdiv: this.dom.tableDiv,\n\t\t\t\tshowLines: true,\n\t\t\t\tresize: true,\n\t\t\t\tmaxHeight: '50vh'\n\t\t\t})\n\t}\n\n\tprivate drawLegend() {\n\t\tif (!this.isComparison) {\n\t\t\tthis.legendG\n\t\t\t\t.append('text')\n\t\t\t\t.attr('text-anchor', 'left')\n\t\t\t\t.style('font-weight', 'bold')\n\t\t\t\t.text('Overall Score')\n\t\t\t\t.attr('transform', `translate(0, -5)`)\n\t\t\tthis.addLegendItem('A', 'More than 75% of possible scorable items', 1)\n\t\t\tthis.addLegendItem('B', '50-75% of possible scorable items', 2)\n\t\t\tthis.addLegendItem('C', 'Less than 50% of possible scorable items', 3)\n\t\t}\n\t\tthis.addFilterLegend()\n\t}\n}\n\nexport async function getPlotConfig(opts: any, app: MassAppApi, _activeCohort: number) {\n\ttry {\n\t\tconst activeCohort = _activeCohort === undefined ? app.getState().activeCohort : _activeCohort\n\t\tconst defaults = await getProfilePlotConfig(activeCohort, app, opts)\n\t\tif (!defaults) throw 'default config not found in termdbConfig.plotConfigByCohort.profilePolar2'\n\t\tconst settings = getDefaultProfilePlotSettings()\n\t\tdefaults.settings = { profilePolar2: settings }\n\n\t\tconst config = copyMerge(structuredClone(defaults), opts)\n\t\tconfig.settings.controls = { isOpen: false }\n\t\tconst twlst: any[] = []\n\t\tfor (const data of config.terms) {\n\t\t\tdata.score.q = { mode: 'continuous' }\n\t\t\tdata.maxScore.q = { mode: 'continuous' }\n\t\t\ttwlst.push(data.score, data.maxScore)\n\t\t}\n\t\tawait fillTwLst(twlst, app.vocabApi)\n\n\t\treturn config\n\t} catch (e) {\n\t\tthrow `${e} [profilePolar2 getPlotConfig()]`\n\t}\n}\n\nexport const profilePolar2Init = getCompInit(ProfilePolar2)\nexport const componentInit = profilePolar2Init\n"],
+  "mappings": 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