@sjcrh/proteinpaint-client 2.210.1 → 2.211.0

package/dist/NumRegularBinEditor.unit.spec-RGV3EUPC.js

@@ -1,278 +0,0 @@
-import {
-  agedx
-} from "./chunk-32AI7I4C.js";
-import {
-  NumericHandler
-} from "./chunk-XQLOEZ7T.js";
-import "./chunk-F4DM3WS4.js";
-import {
-  termjson
-} from "./chunk-FQYXNCZI.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import {
-  TwRouter
-} from "./chunk-CSAS3PVJ.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-T4RYLTR3.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-Y3SDMRDX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VTHZGUSZ.js";
-import "./chunk-3TV5WWUN.js";
-import "./chunk-4Y5W26UF.js";
-import "./chunk-UYKJOBRO.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 {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.js";
-
-// termsetting/handlers/test/NumRegularBinEditor.unit.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-var DAY_TO_YEAR = 1 / 365.25;
-function getConvertedTerm() {
-  const term = JSON.parse(JSON.stringify(termjson.agedx));
-  term.valueConversion = { fromUnit: "day", toUnit: "year", scaleFactor: DAY_TO_YEAR };
-  term.bins.default = {
-    type: "regular-bin",
-    label_offset: 1,
-    bin_size: 365.25,
-    first_bin: { startunbounded: true, stop: 365.25 }
-  };
-  return term;
-}
-async function getNumericHandler(opts = {}) {
-  const term = opts.term || JSON.parse(JSON.stringify(termjson.agedx));
-  if (term.bins.default.type == "regular-bin" && !opts.term) term.bins.default.bin_size = 500;
-  const rawTw = {
-    term,
-    q: term.bins.default
-  };
-  let handler = {};
-  const vocabApi = {
-    state: {
-      termfilter: { filter: { type: "tvslst", in: "", lst: [] } }
-    },
-    getViolinBox() {
-      return agedx;
-    }
-  };
-  const tw = await TwRouter.initRaw(rawTw, { vocabApi });
-  handler = new NumericHandler({
-    termsetting: {
-      tw,
-      term: rawTw.term,
-      q: rawTw.q,
-      opts: {
-        numericEditMenuVersion: ["discrete"],
-        usecase: opts.usecase
-      },
-      api: {
-        runCallback() {
-        }
-      },
-      dom: {
-        tip: {
-          hide() {
-          }
-        }
-      },
-      vocabApi
-    }
-  });
-  handler.density_data = { min: agedx.min, max: agedx.max };
-  const holder = select_default("body").append("div").style("position", "relative").style("width", "fit-content").style("margin", "20px").style("padding", "5px").style("border", "1px solid #000");
-  handler.dom.editDiv = holder;
-  await handler.setEditHandler(handler.tabs[0]);
-  const binsEditor = handler.editHandler.editorsByType["regular-bin"];
-  return {
-    rawTw,
-    tw,
-    handler,
-    editHandler: handler.editHandler,
-    binsEditor,
-    holder,
-    destroy: () => {
-      if ("destroy" in handler.editHandler) handler.editHandler.destroy();
-      if (typeof handler.destroy == "function") handler.destroy();
-      holder.remove();
-    }
-  };
-}
-(0, import_tape.default)("\n", (test) => {
-  test.comment("-***- NumRegularBinEditor.unit.spec -***-");
-  test.end();
-});
-(0, import_tape.default)("handler methods", async (test) => {
-  const { binsEditor, destroy } = await getNumericHandler();
-  test.deepEqual(
-    binsEditor.getDefaultQ(),
-    {
-      type: "regular-bin",
-      label_offset: 1,
-      bin_size: 500,
-      first_bin: { startunbounded: true, stop: 2 },
-      isAtomic: true,
-      mode: "discrete",
-      hiddenValues: {}
-    },
-    `should give the expected default tw.q object`
-  );
-  binsEditor.tw.q = { mode: "continuous" };
-  test.deepEqual(
-    binsEditor.getDefaultQ(),
-    {
-      type: "regular-bin",
-      label_offset: 1,
-      bin_size: 500,
-      first_bin: { startunbounded: true, stop: 2 },
-      isAtomic: true,
-      mode: "discrete",
-      hiddenValues: {}
-    },
-    `should give the expected default tw.q object if the mode is not discrete`
-  );
-  if (test._ok) destroy();
-  test.end();
-});
-(0, import_tape.default)("initial rendered UI", async (test) => {
-  const { editHandler, binsEditor, holder, destroy } = await getNumericHandler();
-  await editHandler.showEditMenu(holder);
-  test.equal(binsEditor.dom.binsTable.selectAll("tr").size(), 3, `should render a boundary inputs table with 3 rows`);
-  const numberInputs = binsEditor.dom.binsTable.node().querySelectorAll(`input[type='number']`);
-  test.equal(
-    numberInputs.length,
-    3,
-    `should render 3 number inputs for bin size, first bin stop, and optional last bin start`
-  );
-  test.equal(
-    numberInputs[2].parentNode?.style.display,
-    "none",
-    `should hide the input for last bin start, if not specified in q`
-  );
-  const radios = binsEditor.dom.binsTable.node().querySelectorAll(`input[type='radio']`);
-  test.equal(radios.length, 2, `should render 2 radio inputs for optional last bin`);
-  test.equal(radios[0].checked, true, `should checked the automatic last bin start radio`);
-  test.equal(radios[1].checked, false, `should not check the fixed last bin start radio`);
-  if (test._ok) destroy();
-  test.end();
-});
-(0, import_tape.default)("edit interactivity", async (test) => {
-  const { editHandler, binsEditor, holder, destroy } = await getNumericHandler();
-  await editHandler.showEditMenu(holder);
-  binsEditor.dom.bin_size_input.property("value", 300);
-  binsEditor.dom.bin_size_input.node().dispatchEvent(new Event("change", { bubbles: true }));
-  binsEditor.dom.first_stop_input.property("value", 100);
-  binsEditor.dom.first_stop_input.node().dispatchEvent(new Event("change", { bubbles: true }));
-  binsEditor.dom.fixed_radio.property("checked", true);
-  binsEditor.dom.fixed_radio.node().dispatchEvent(new Event("input", { bubbles: true }));
-  binsEditor.dom.last_start_input.property("value", 1e3);
-  binsEditor.dom.last_start_input.node().dispatchEvent(new Event("change", { bubbles: true }));
-  test.equal(
-    binsEditor.dom.last_start_input.style("display"),
-    "inline-block",
-    `should display the last start input when fixed stop option is selected`
-  );
-  test.deepEqual(
-    editHandler.getEditedQ(false),
-    {
-      mode: "discrete",
-      type: "regular-bin",
-      startinclusive: false,
-      stopinclusive: true,
-      bin_size: 300,
-      first_bin: { startunbounded: true, stop: 100 },
-      rounding: ".0f",
-      last_bin: { start: 1e3, stopunbounded: true }
-    },
-    `should give the expected edited tw.q object`
-  );
-  {
-    const lines = [...editHandler.handler.density.dom.binsize_g.node().querySelectorAll("line")];
-    test.deepEqual(
-      lines.filter((l) => l.style.display !== "none").map((l) => l.getAttribute("x1")),
-      ["21", "52", "84", "116"],
-      `should render 4 lines in the expected x-positions of the density plot`
-    );
-  }
-  const binsTable = binsEditor.dom.binsTable.node();
-  await binsEditor.render(editHandler.dom.binsDiv.node().firstChild);
-  test.equal(
-    binsTable,
-    binsEditor.dom.binsTable.node(),
-    `should not re-render the menu when the holder has not changed`
-  );
-  await editHandler.undoEdits();
-  {
-    const lines = [...editHandler.handler.density.dom.binsize_g.node().querySelectorAll("line")];
-    test.deepEqual(
-      lines.map((l) => l.getAttribute("x1")),
-      ["10", "63", "116", "169", "223", "276", "329", "382", "435", "488"],
-      `should render a draggable line in the expected x-position`
-    );
-  }
-  if (test._ok) destroy();
-  test.end();
-});
-(0, import_tape.default)("converted term", async (test) => {
-  const alerts = [];
-  const origAlert = window.alert;
-  window.alert = (msg) => alerts.push(msg);
-  const { editHandler, binsEditor, holder, destroy } = await getNumericHandler({ term: getConvertedTerm() });
-  await editHandler.showEditMenu(holder);
-  test.equal(binsEditor.dom.bin_size_input.property("value"), "1", `should fill the bin size input in years`);
-  test.equal(binsEditor.dom.first_stop_input.property("value"), "1", `should fill the first bin stop input in years`);
-  test.equal(binsEditor.q.bin_size, 365.25, `should keep the bin size of q in days`);
-  const note = editHandler.dom.density_div.node().nextSibling;
-  test.equal(note?.innerText.includes("unit of year"), true, `should note the unit immediately under the density plot`);
-  test.equal(
-    editHandler.dom.boundaryInclusionDiv.node().previousSibling,
-    note,
-    `should note the unit above the boundary inclusion row`
-  );
-  binsEditor.dom.bin_size_input.property("value", 2.5);
-  binsEditor.dom.bin_size_input.node().dispatchEvent(new Event("change", { bubbles: true }));
-  test.equal(binsEditor.q.bin_size, 913.125, `should store a bin size typed in years as days`);
-  binsEditor.dom.first_stop_input.property("value", 3);
-  binsEditor.dom.first_stop_input.node().dispatchEvent(new Event("change", { bubbles: true }));
-  binsEditor.dom.fixed_radio.property("checked", true);
-  binsEditor.dom.fixed_radio.node().dispatchEvent(new Event("input", { bubbles: true }));
-  binsEditor.dom.last_start_input.property("value", 10);
-  binsEditor.dom.last_start_input.node().dispatchEvent(new Event("change", { bubbles: true }));
-  test.deepEqual(
-    editHandler.getEditedQ(false),
-    {
-      mode: "discrete",
-      type: "regular-bin",
-      startinclusive: false,
-      stopinclusive: true,
-      bin_size: 913.125,
-      first_bin: { startunbounded: true, stop: 1095.75 },
-      rounding: ".0f",
-      last_bin: { start: 3652.5, stopunbounded: true }
-    },
-    `should give an edited q in the stored unit, rounding the bin labels as whole days`
-  );
-  test.deepEqual(alerts, [], `should not alert for a value that the editor filled in itself`);
-  window.alert = origAlert;
-  if (test._ok) destroy();
-  test.end();
-});
-//# sourceMappingURL=NumRegularBinEditor.unit.spec-RGV3EUPC.js.map

package/dist/NumSplineEditor-PC5X7AUJ.js

@@ -1,210 +0,0 @@
-import {
-  keyupEnter
-} from "./chunk-CSAS3PVJ.js";
-import "./chunk-HJ6L54YS.js";
-import {
-  HandlerBase
-} from "./chunk-KV4W2ACA.js";
-import "./chunk-T4RYLTR3.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-Y3SDMRDX.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VTHZGUSZ.js";
-import "./chunk-3TV5WWUN.js";
-import "./chunk-4Y5W26UF.js";
-import "./chunk-UYKJOBRO.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import {
-  toStoredUnit,
-  toUserUnit
-} from "./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";
-
-// termsetting/handlers/NumSplineEditor.ts
-var NumSplineEditor = class extends HandlerBase {
-  constructor(opts, handler) {
-    super(opts);
-    this.dom = {};
-    this.default_knots_count = 4;
-    this.opts = opts;
-    this.handler = handler;
-    this.tw = handler.tw;
-  }
-  /* q.knots are stored in the term's own unit, matching the values they are knots of, but are
-  entered and shown in its user-facing one. see makeRinput() in server/src/routes/termdb.regression.ts,
-  which converts them alongside the values before fitting.
-  both are identity functions unless the term declares valueConversion{} */
-  toDisplay(v) {
-    return toUserUnit(v, this.tw.term);
-  }
-  toStored(v) {
-    return toStoredUnit(v, this.tw.term);
-  }
-  async getDefaultQ() {
-    const tw = this.termsetting.tw;
-    if (tw.q.mode == "spline") {
-      return JSON.parse(JSON.stringify(tw.q));
-    }
-    return await this.getKnots(this.default_knots_count);
-  }
-  async getKnots(knot_count) {
-    const middle_knot_count = knot_count - 2;
-    const t = this.tw.term;
-    const knots = [];
-    const percentile_lst = [5];
-    const second_knot_perc = (90 / (middle_knot_count + 1)).toFixed(0);
-    for (let i = 1; i < middle_knot_count + 1; i++) {
-      percentile_lst.push(i * second_knot_perc);
-    }
-    percentile_lst.push(95);
-    const values = await this.getPercentile2Value(percentile_lst);
-    for (const val of values) {
-      knots.push({ value: val.toFixed(t.type == "integer" ? 0 : 2) });
-    }
-    return {
-      mode: "spline",
-      knots
-    };
-  }
-  async getPercentile2Value(percentile_lst) {
-    const vocabApi = this.termsetting.vocabApi;
-    const data = await vocabApi.getPercentile(this.tw.term, percentile_lst, vocabApi.state?.termfilter);
-    if (data.error || !data.values.length || !data.values.every((v) => Number.isFinite(v)))
-      throw "cannot get median value: " + (data.error || "no data");
-    const perc_values = [...new Set(data.values)];
-    return perc_values;
-  }
-  async showEditMenu(div) {
-    this.tw = this.handler.tw;
-    const isRemounting = !!this.dom.density_div && this.handler.dom.editDiv?.node().contains(this.dom.density_div.node());
-    if (!isRemounting) this.q = await this.getDefaultQ();
-    if (this.dom.density_div) {
-      if (isRemounting) {
-        await this.handler.density.showViolin(this.dom.density_div, this.getBoundaryOpts());
-        return;
-      } else {
-        this.dom.density_div.remove();
-        delete this.dom.density_div;
-      }
-    }
-    this.dom.density_div = div.append("div");
-    await this.handler.density.showViolin(this.dom.density_div);
-    await this.handler.density.setBinLines(this.getBoundaryOpts());
-    this.dom.knots_div = div.append("div").style("padding", "5px");
-    this.mayShowValueconversionMsg(this.dom.knots_div);
-    this.renderCustomSplineInputs();
-    this.renderAutoSplineInputs();
-  }
-  getBoundaryOpts() {
-    return {
-      values: this.q.knots.map((k) => {
-        return {
-          //this.q.lst[0].map(bin => ({ x: bin.startunbounded ? bin.stop : bin.start, isDraggable: true })),
-          x: this.toDisplay(k.value),
-          isDraggable: true
-        };
-      }),
-      // the dragged value arrives in display units, matching what the textarea holds
-      callback: (d, value) => {
-        this.q.knots[d.index].value = this.toStored(value);
-        this.dom.customKnotsInput.property("value", this.q.knots.map((k) => this.toDisplay(k.value)).join("\n"));
-      }
-    };
-  }
-  /******************* Functions for Custom Spline knots *******************/
-  renderCustomSplineInputs() {
-    this.dom.custom_knots_div = this.dom.knots_div.append("div");
-    this.dom.custom_knots_div.append("div").style("display", "inline-block").style("vertical-align", "top").style("padding", "3px 15px").style("font-weight", "normal").style("color", "rgb(136, 136, 136)").html("Knots");
-    this.dom.customKnotsInput = this.dom.custom_knots_div.append("div").style("display", "inline-block").style("padding", "3px 15px").style("padding-left", "5px").append("textarea").style("height", "100px").style("width", "100px").text(this.q.knots.map((d) => this.toDisplay(d.value)).join("\n")).on("change", () => {
-      this.q.knots = this.processKnotsInputs();
-      this.handler.density.setBinLines(this.getBoundaryOpts());
-    }).on("keyup", async (event) => {
-      if (!keyupEnter(event) && event.key != 8) return;
-      this.q.knots = this.processKnotsInputs();
-      this.handler.density.setBinLines(this.getBoundaryOpts());
-    });
-    this.dom.custom_knots_div.append("div").style("display", "inline-block").style("vertical-align", "top").style("font-size", ".7em").style("padding", "3px 15px").style("padding-left", "5px").style("color", "rgb(136, 136, 136)").html(`Enter knot values, one knot per line.</br> 
-				Adjust knot by dragging on the vertical line.</br>
-			 	Or autocompute knots from below.`);
-  }
-  // apply custom knots if changed from density plot to textarea
-  updateCustomSplineInputs() {
-    this.dom.customKnotsInput.property("value", this.q.knots.map((d) => this.toDisplay(d.value)).join("\n"));
-  }
-  // apply custom knots to this.q.knots
-  processKnotsInputs() {
-    const data = this.dom.customKnotsInput.property("value").split("\n").filter((d) => d != "").map((d) => +d).sort((a, b) => a - b).map((d) => {
-      const knot = {
-        value: this.toStored(+d)
-      };
-      return knot;
-    });
-    return data;
-  }
-  /******************* Functions for Auto Spline knots *******************/
-  renderAutoSplineInputs() {
-    const div = this.dom.knots_div;
-    const knot_count = 4;
-    const default_knot_count = knot_count;
-    this.dom.knot_select_div = div.append("div");
-    this.dom.knot_select_div.append("div").style("display", "inline-block").style("margin-left", "15px").style("color", "rgb(136, 136, 136)").html("Autocompute");
-    const knot_ct_select = this.dom.knot_select_div.append("select").attr("data-testid", "num-spline-editor-num-knots").style("margin-left", "10px").style("margin-bottom", "7px");
-    for (let i = default_knot_count - 1; i < default_knot_count + 5; i++) {
-      knot_ct_select.append("option").attr("value", i).html(i);
-    }
-    knot_ct_select.node().value = this.q.knots?.length || this.default_knots_count;
-    this.dom.knot_select_div.append("div").style("display", "inline-block").style("margin-left", "10px").style("color", "rgb(136, 136, 136)").html("knots");
-    this.dom.knot_select_div.append("button").style("margin", "15px").text("Compute").on("click", async () => {
-      this.dom.knots_div.style("pointer-events", "none").style("opacity", 0.5);
-      const desired_knots_ct = Number.parseInt(knot_ct_select.node().value);
-      let requested_knots_ct = desired_knots_ct;
-      while (this.q.knots.length != desired_knots_ct) {
-        if (requested_knots_ct > 99) break;
-        const result = await this.getKnots(requested_knots_ct);
-        this.q.knots = result.knots;
-        requested_knots_ct = requested_knots_ct + 1;
-      }
-      this.dom.knots_div.style("pointer-events", "auto").style("opacity", 1);
-      this.updateCustomSplineInputs();
-      this.handler.density.setBinLines(this.getBoundaryOpts());
-    });
-    this.dom.knot_select_div.append("div").style("display", "inline-block").style("font-size", ".7em").style("padding", "3px 15px").style("padding-left", "5px").style("color", "rgb(136, 136, 136)").html("Will overwrite existing values.");
-  }
-  getEditedQ(destroyDom = true) {
-    const knots = this.processKnotsInputs();
-    if (destroyDom) {
-      for (const name of Object.keys(this.dom)) {
-        this.dom[name].remove();
-        delete this.dom[name];
-      }
-    }
-    return {
-      mode: "spline",
-      knots
-    };
-  }
-  async undoEdits() {
-    this.q = await this.getDefaultQ();
-    this.dom.knots_div.selectAll("*").remove();
-    await this.handler.density.setBinLines(this.getBoundaryOpts());
-    this.mayShowValueconversionMsg(this.dom.knots_div);
-    this.renderCustomSplineInputs();
-    this.renderAutoSplineInputs();
-  }
-};
-export {
-  NumSplineEditor
-};
-//# sourceMappingURL=NumSplineEditor-PC5X7AUJ.js.map