@sjcrh/proteinpaint-client 2.201.0 → 2.202.0

package/dist/NumSplineEditor-2DCORF5E.js

@@ -0,0 +1,215 @@
+import {
+  keyupEnter
+} from "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import {
+  HandlerBase
+} from "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import {
+  toStoredUnit,
+  toUserUnit
+} from "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.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-HFNDKYVF.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-2DCORF5E.js.map

package/dist/NumSplineEditor.unit.spec-TTNB5IXX.js

@@ -0,0 +1,229 @@
+import {
+  agedx
+} from "./chunk-32AI7I4C.js";
+import {
+  NumericHandler
+} from "./chunk-W2WOZNEN.js";
+import "./chunk-MKPU5TWN.js";
+import {
+  termjson
+} from "./chunk-2TZITKMT.js";
+import {
+  sleep
+} from "./chunk-Z2TA7NML.js";
+import {
+  require_tape
+} from "./chunk-TUMA63WX.js";
+import {
+  TwRouter
+} from "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.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-HFNDKYVF.js";
+
+// termsetting/handlers/test/NumSplineEditor.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 };
+  return term;
+}
+async function getNumericHandler(opts = {}) {
+  const term = opts.term || JSON.parse(JSON.stringify(termjson.agedx));
+  const rawTw = {
+    term,
+    q: opts.q || {
+      mode: "spline",
+      //[{value: 0.04}, {value: 3.13}, {value: 8.16}, {value: 17.87}]
+      knots: [{ value: 10 }, { value: 100 }, { value: 500 }, { value: 1e3 }]
+    }
+  };
+  let handler = {};
+  const vocabApi = {
+    state: {
+      termfilter: { filter: { type: "tvslst", in: "", lst: [] } }
+    },
+    getViolinBox() {
+      return agedx;
+    },
+    getPercentile() {
+      return {
+        values: [0.03537315665, 3.13072460515, 8.164619357749999, 17.8726813385]
+      };
+    }
+  };
+  const tw = await TwRouter.initRaw(rawTw, { vocabApi });
+  handler = new NumericHandler({
+    termsetting: {
+      tw,
+      term: rawTw.term,
+      q: rawTw.q,
+      opts: {
+        numericEditMenuVersion: ["spline"],
+        usecase: opts.usecase
+      },
+      api: {
+        runCallback() {
+        }
+      },
+      dom: {
+        tip: {
+          hide() {
+          }
+        }
+      },
+      vocabApi
+    }
+  });
+  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]);
+  return {
+    rawTw,
+    tw,
+    handler,
+    editHandler: handler.editHandler,
+    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("-***- NumBinaryEditor.unit.spec -***-");
+  test.end();
+});
+(0, import_tape.default)("handler methods", async (test) => {
+  const { editHandler, destroy } = await getNumericHandler();
+  test.deepEqual(editHandler.getPillStatus(), { text: "cubic spline" }, "should give the expected status");
+  editHandler.termsetting.tw.q = { mode: "discrete" };
+  test.deepEqual(
+    await editHandler.getDefaultQ(),
+    { mode: "spline", knots: [{ value: "0.04" }, { value: "3.13" }, { value: "8.16" }, { value: "17.87" }] },
+    "should give the expected defaultQ"
+  );
+  if (test._ok) destroy();
+  test.end();
+});
+(0, import_tape.default)("initial rendered UI", async (test) => {
+  const { editHandler, holder, destroy } = await getNumericHandler();
+  await editHandler.showEditMenu(holder);
+  test.equal(editHandler.dom?.density_div.selectAll("svg").size(), 1, `should render a density plot svg`);
+  const lines = [...editHandler.handler.density.dom.binsize_g.node().querySelectorAll("line")];
+  test.equal(lines.length, 4, `should render 4 draggable lines in the density plot`);
+  test.deepEqual(
+    lines.map((l) => l.getAttribute("x1")),
+    ["11", "21", "63", "116"],
+    `should render the draggable lines in the expected x-positions`
+  );
+  test.equal(
+    editHandler.dom.customKnotsInput.property("value"),
+    "10\n100\n500\n1000",
+    "should display line-separated values in the knots inputs"
+  );
+  test.equal(editHandler.dom.knot_select_div.selectAll("select").size(), 1, `should render an auto-compute dropdown`);
+  test.equal(
+    editHandler.dom.knot_select_div.select("select").property("value"),
+    "4",
+    `should default to 4 knots for auto-compute`
+  );
+  const density_div = editHandler.dom.density_div.node();
+  await editHandler.showEditMenu(holder);
+  test.equal(
+    density_div,
+    editHandler.dom.density_div.node(),
+    `should not re-render the menu when the holder has not changed`
+  );
+  if (test._ok) destroy();
+  test.end();
+});
+(0, import_tape.default)("knots interactivity", async (test) => {
+  const { editHandler, holder, destroy } = await getNumericHandler();
+  await editHandler.showEditMenu(holder);
+  const newKnots = [10, 200, 600, 3e3];
+  editHandler.dom.customKnotsInput.property("value", newKnots.join("\n"));
+  editHandler.dom.customKnotsInput.node().dispatchEvent(new Event("change", { bubbles: true }));
+  const lines = [...editHandler.handler.density.dom.binsize_g.node().querySelectorAll("line")];
+  test.deepEqual(
+    lines.map((l) => l.getAttribute("x1")),
+    ["11", "31", "74", "328"],
+    `should re-render the draggable lines in the updated x-positions`
+  );
+  test.deepEqual(
+    editHandler.getEditedQ(false),
+    { mode: "spline", knots: newKnots.map((value) => ({ value })) },
+    `should give the expected edited q object`
+  );
+  editHandler.undoEdits();
+  await sleep(0);
+  {
+    const lines2 = [...editHandler.handler.density.dom.binsize_g.node().querySelectorAll("line")];
+    test.equal(lines2.length, 4, `should render 4 draggable lines in the density plot`);
+    test.deepEqual(
+      lines2.map((l) => l.getAttribute("x1")),
+      ["11", "21", "63", "116"],
+      `should render the draggable lines in the expected x-positions`
+    );
+  }
+  if (test._ok) destroy();
+  test.end();
+});
+(0, import_tape.default)("converted term", async (test) => {
+  const q = { mode: "spline", knots: [365.25, 1826.25, 2922, 3652.5].map((value) => ({ value })) };
+  const { editHandler, holder, destroy } = await getNumericHandler({ term: getConvertedTerm(), q });
+  await editHandler.showEditMenu(holder);
+  test.equal(
+    editHandler.dom.customKnotsInput.property("value"),
+    "1\n5\n8\n10",
+    `should fill the knots textarea in years`
+  );
+  test.equal(
+    editHandler.dom.density_div.node().nextSibling.firstChild.innerText.includes("unit of year"),
+    true,
+    `should note the unit immediately under the density plot`
+  );
+  editHandler.dom.customKnotsInput.property("value", [2, 6].join("\n"));
+  editHandler.dom.customKnotsInput.node().dispatchEvent(new Event("change", { bubbles: true }));
+  test.deepEqual(
+    editHandler.getEditedQ(false),
+    { mode: "spline", knots: [{ value: 730.5 }, { value: 2191.5 }] },
+    `should give an edited q whose knots are in days`
+  );
+  if (test._ok) destroy();
+  test.end();
+});
+//# sourceMappingURL=NumSplineEditor.unit.spec-TTNB5IXX.js.map

package/dist/NumericDensity-3A7KTA7Y.js

@@ -0,0 +1,38 @@
+import {
+  NumericDensity
+} from "./chunk-MKPU5TWN.js";
+import "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.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-HFNDKYVF.js";
+export {
+  NumericDensity
+};
+//# sourceMappingURL=NumericDensity-3A7KTA7Y.js.map