@sjcrh/proteinpaint-client 2.219.1 → 2.221.0

package/dist/dnaMethylation.integration.spec-PJLIRGN5.js

@@ -0,0 +1,194 @@
+import {
+  hg38
+} from "./chunk-7VB2BKXW.js";
+import {
+  SearchHandler
+} from "./chunk-CUCP2GMT.js";
+import {
+  sleep
+} from "./chunk-WA3C3A2M.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import {
+  vocabInit
+} from "./chunk-WD7FZ5EE.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-WXSMUSU7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import {
+  TermTypes
+} from "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import {
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// termdb/handlers/test/dnaMethylation.integration.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+var vocabApi = await getVocabApi();
+var handler = new SearchHandler();
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- dnaMethylation search handler -***-");
+  test.end();
+});
+(0, import_tape.default)("Search handler layout", async (test) => {
+  const holder = getHolder();
+  await initializeSearchHandler({ holder });
+  const geneSearchInput = holder.select(".sja_genesearchinput").node();
+  test.ok(geneSearchInput, "should display gene search input");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Coordinate search", async (test) => {
+  let term;
+  const callback = (_term) => {
+    term = _term;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const geneSearchInput = holder.select(".sja_genesearchinput").node();
+  const chr = "chr17";
+  const start = 7661778;
+  const stop = 7687537;
+  const coord = `${chr}:${start}-${stop}`;
+  geneSearchInput.value = coord;
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(term.chr, chr, "term.chr should equal input chr");
+  test.equal(term.start, start, "term.start should equal input start");
+  test.equal(term.stop, stop, "term.stop should equal input stop");
+  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Single position search (chr:pos format)", async (test) => {
+  let term;
+  const callback = (_term) => {
+    term = _term;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const geneSearchInput = holder.select(".sja_genesearchinput").node();
+  geneSearchInput.value = "chr17:7669073";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(term.chr, "chr17", "term.chr should equal input chr");
+  test.equal(term.start, 7669073, "term.start should be exact position, not 400bp-expanded");
+  test.equal(term.stop, 7669074, "term.stop should be start+1 for a single CpG site");
+  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Single position search (chr:pos-pos format)", async (test) => {
+  let term;
+  const callback = (_term) => {
+    term = _term;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const geneSearchInput = holder.select(".sja_genesearchinput").node();
+  geneSearchInput.value = "chr17:7669073-7669073";
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  test.equal(term.chr, "chr17", "term.chr should equal input chr");
+  test.equal(term.start, 7669073, "term.start should be exact position, not 400bp-expanded");
+  test.equal(term.stop, 7669074, "term.stop should be start+1 for a single CpG site");
+  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Gene search", async (test) => {
+  let term;
+  const callback = (_term) => {
+    term = _term;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const geneSearchInput = holder.select(".sja_genesearchinput").node();
+  const geneSymbol = "TP53";
+  geneSearchInput.value = geneSymbol;
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(100);
+  const blockSvg = holder.select('[data-testid="sjpp_block_svg"]').node();
+  test.ok(blockSvg, "should render block svg");
+  const submitBtn = holder.select('[data-testid="sjpp-dnaMethylation-submitDiv"]').select("button").node();
+  submitBtn.click();
+  await sleep(100);
+  test.equal(term.chr, "chr17", "term.chr should be TP53 chr");
+  test.equal(term.start, 7661778, "term.start should be TP53 start");
+  test.equal(term.stop, 7687537, "term.stop should be TP53 stop");
+  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("Gene search with navigation", async (test) => {
+  let term;
+  const callback = (_term) => {
+    term = _term;
+  };
+  const holder = getHolder();
+  await initializeSearchHandler({ holder, callback });
+  const geneSearchInput = holder.select(".sja_genesearchinput").node();
+  const geneSymbol = "TP53";
+  geneSearchInput.value = geneSymbol;
+  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(1e3);
+  const blockCoordInput = holder.select(".sja_Block_div").select("input").node();
+  const chr = "chr17";
+  const start = 7682350;
+  const stop = 7684350;
+  const coord = `${chr}:${start}-${stop}`;
+  blockCoordInput.value = coord;
+  blockCoordInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
+  await sleep(1e3);
+  const submitBtn = holder.select('[data-testid="sjpp-dnaMethylation-submitDiv"]').select("button").node();
+  submitBtn.click();
+  await sleep(100);
+  test.equal(term.chr, chr, "term.chr should equal input chr");
+  test.equal(term.start, 7682349, "term.start should equal input start");
+  test.equal(term.stop, 7684349, "term.stop should equal input stop");
+  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+async function getVocabApi() {
+  const vocabApi2 = vocabInit({ state: { vocab: { genome: "hg38-test", dslabel: "TermdbTest" } } });
+  if (!vocabApi2) throw "vocabApi is missing";
+  await vocabApi2.getTermdbConfig();
+  return vocabApi2;
+}
+function getHolder() {
+  const holder = select_default("body").append("div");
+  return holder;
+}
+async function initializeSearchHandler(opts) {
+  const callback = opts.callback || (() => {
+  });
+  const hg38_copy = structuredClone(hg38);
+  hg38_copy.hasSNP = false;
+  await handler.init({
+    holder: opts.holder,
+    app: { vocabApi },
+    genomeObj: hg38_copy,
+    callback
+  });
+}
+//# sourceMappingURL=dnaMethylation.integration.spec-PJLIRGN5.js.map

package/dist/dofetch-KBTN6OW4.js

@@ -0,0 +1,49 @@
+import {
+  clearServerDataCache,
+  dofetch,
+  dofetch2,
+  dofetch3,
+  getRequiredAuth,
+  getSavedToken,
+  includeEmbedder,
+  isInSession,
+  mayAddJwtToRequest,
+  mayAdjustCredentials,
+  mayShowAuthUi,
+  namedFetch,
+  processFormData,
+  setAuth,
+  setDsAuthOk,
+  setTokenByDsRoute
+} from "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  clearServerDataCache,
+  dofetch,
+  dofetch2,
+  dofetch3,
+  getRequiredAuth,
+  getSavedToken,
+  includeEmbedder,
+  isInSession,
+  mayAddJwtToRequest,
+  mayAdjustCredentials,
+  mayShowAuthUi,
+  namedFetch,
+  processFormData,
+  setAuth,
+  setDsAuthOk,
+  setTokenByDsRoute
+};
+//# sourceMappingURL=dofetch-KBTN6OW4.js.map

package/dist/e2pca-O7SNMJGB.js

@@ -0,0 +1,340 @@
+import {
+  axisstyle,
+  make_table_2col,
+  newpane,
+  sayerror,
+  to_svg
+} from "./chunk-WD7FZ5EE.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-WXSMUSU7.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import {
+  axisBottom,
+  axisLeft,
+  json_default,
+  plasma
+} from "./chunk-WJLRU5OF.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import {
+  linear
+} from "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import {
+  rgb_default
+} from "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// src/e2pca.js
+var dullcolor = "#ccc";
+function e2pca_inputui(hostURL, jwt) {
+  const pane = newpane({ x: 100, y: 100 });
+  pane.header.text("PCA - expression plot");
+  const butrow = pane.body.append("div").style("margin", "20px");
+  const div = pane.body.append("div").style("margin", "20px");
+  const ta_pca = butrow.append("input").attr("size", 30).attr("placeholder", "PCA/SNE matrix file path").style("margin", "10px").property("value", "xiang/sep20/set1");
+  const ta_db = butrow.append("input").attr("size", 30).attr("placeholder", "numerical db file path").style("margin", "10px").property("value", "xiang/sep20/set1.db");
+  butrow.append("button").text("Submit").on("click", () => {
+    div.selectAll("*").remove();
+    const filepca = ta_pca.property("value");
+    if (filepca == "") {
+      div.text("No PCA file");
+      return;
+    }
+    const filedb = ta_db.property("value");
+    if (filedb == "") {
+      div.text("No db file");
+      return;
+    }
+    json_default(hostURL + "/textfile").post(JSON.stringify({ file: filepca, jwt }), (data) => {
+      if (data.error) {
+        div.text("Error getting file: " + data.error);
+        return;
+      }
+      const [err, numdata2plot] = e2pca_plot({
+        holder: div,
+        text: data.text
+      });
+      if (err) {
+        sayerror(div, err);
+        return;
+      }
+      e2pca_genesearchui({
+        holder: div.append("div"),
+        numdata2plot,
+        hostURL,
+        jwt,
+        obj: {
+          dbfile: filedb
+        }
+      });
+    });
+  });
+  butrow.append("button").text("Clear").on("click", () => {
+    ta_pca.property("value", "");
+    ta_db.property("value", "");
+  });
+  butrow.append("span").style("padding-left", "10px").html(
+    "<a href=https://docs.google.com/document/d/1Midt0rYs1iIJveUMjeng9si3q31YelcNe_PI3Njce9E/edit?usp=sharing target=_blank>Help</a>"
+  );
+}
+function e2pca_plot(arg) {
+  const samples = [];
+  const lines = arg.text.split(/\r?\n/);
+  for (let i = 0; i < lines.length; i++) {
+    const line = lines[i];
+    if (!line) continue;
+    const l = line.split("	");
+    const samplename = l[0];
+    const x = Number.parseFloat(l[1]);
+    const y = Number.parseFloat(l[2]);
+    if (Number.isNaN(x)) {
+      return ["invalid x value at line " + (i + 1)];
+    }
+    if (Number.isNaN(y)) {
+      return ["invalid y value at line " + (i + 1)];
+    }
+    const s = {
+      sample: samplename,
+      x,
+      y
+    };
+    if (arg.mdanno) {
+      if (arg.mdanno.annotation[samplename]) {
+        s.attr = [];
+        for (const termkey in arg.mdanno.annotation[samplename]) {
+          if (arg.mdanno.mdh[termkey]) {
+            const valuekey = arg.mdanno.annotation[samplename][termkey];
+            if (arg.mdanno.mdh[termkey].values[valuekey]) {
+              s.attr.push({
+                k: arg.mdanno.mdh[termkey].label,
+                v: arg.mdanno.mdh[termkey].values[valuekey].label
+              });
+            } else {
+              s.attr.push({
+                k: arg.mdanno.mdh[termkey].label,
+                v: valuekey
+              });
+            }
+          } else {
+            s.attr.push({
+              k: termkey,
+              v: "unknown term key"
+            });
+          }
+        }
+      }
+    }
+    samples.push(s);
+  }
+  if (samples.length == 0) {
+    return ["no samples"];
+  }
+  let value2color;
+  if (arg.obj && arg.obj.colorscale && arg.obj.colorscale.from && arg.obj.colorscale.to) {
+    value2color = rgb_default(arg.obj.colorscale.from, arg.obj.colorscale.to);
+  } else {
+    value2color = plasma;
+  }
+  let minx = samples[0].x, maxx = samples[0].x, miny = samples[0].y, maxy = samples[0].y;
+  for (const s of samples) {
+    minx = Math.min(minx, s.x);
+    maxx = Math.max(maxx, s.x);
+    miny = Math.min(miny, s.y);
+    maxy = Math.max(maxy, s.y);
+  }
+  const svgholder = arg.holder.append("div").style("display", "inline-block");
+  const menu = new Menu({ padding: "5px" });
+  const svg = svgholder.append("svg");
+  let toppad = 30, bottompad = 50, leftpad = 100, rightpad = 30, vpad = 20, width = 500, height = 500;
+  const xaxisg = svg.append("g");
+  const yaxisg = svg.append("g");
+  const dotg = svg.append("g");
+  const dots = dotg.selectAll().data(samples).enter().append("g");
+  const circles = dots.append("circle").attr("fill", "#aaa").attr("stroke", "none").on("mouseover", (event, d) => {
+    event.target.setAttribute("stroke", "white");
+    menu.clear();
+    menu.show(event.clientX, event.clientY);
+    const lst = [{ k: "name", v: d.sample }];
+    if (d.value != void 0) {
+      lst.push({ k: "value", v: d.value });
+    }
+    if (d.attr) {
+      for (const v of d.attr) {
+        lst.push(v);
+      }
+    }
+    make_table_2col(menu.d, lst);
+  }).on("mouseout", (event, d) => {
+    event.target.setAttribute("stroke", "none");
+    menu.hide();
+  });
+  if (arg.obj) {
+    arg.obj.circles = circles;
+  }
+  const xscale = linear().domain([minx, maxx]);
+  const yscale = linear().domain([miny, maxy]);
+  function resize() {
+    const radius = 3;
+    bottompad = width / 20 + 20;
+    svg.attr("width", leftpad + vpad + width + rightpad).attr("height", toppad + height + vpad + bottompad);
+    xaxisg.attr("transform", "translate(" + (leftpad + vpad) + "," + (toppad + height + vpad) + ")");
+    yaxisg.attr("transform", "translate(" + leftpad + "," + toppad + ")");
+    dotg.attr("transform", "translate(" + (leftpad + vpad) + "," + toppad + ")");
+    xscale.range([0, width]);
+    yscale.range([height, 0]);
+    axisstyle({
+      axis: xaxisg.call(axisBottom().scale(xscale)),
+      color: "black",
+      fontsize: width / 40,
+      showline: true
+    });
+    axisstyle({
+      axis: yaxisg.call(axisLeft().scale(yscale)),
+      color: "black",
+      fontsize: height / 40,
+      showline: true
+    });
+    dots.attr("transform", (d) => "translate(" + xscale(d.x) + "," + yscale(d.y) + ")");
+    circles.attr("r", radius);
+  }
+  resize();
+  const underdiv = svgholder.append("div").style("position", "relative");
+  {
+    const row = arg.toprow || underdiv;
+    row.append("button").style("margin-right", "20px").text("SVG").on("click", () => to_svg(svg.node(), "plot"));
+  }
+  const legendholder = underdiv.append("div").style("margin", "10px 10px 10px 30px");
+  if (arg.obj) {
+    arg.obj.legendholder = legendholder;
+  }
+  underdiv.append("div").style("position", "absolute").style("right", "0px").style("top", "0px").attr("class", "sja_clbtext").text("drag to resize").on("mousedown", (event) => {
+    event.preventDefault();
+    const b = select_default(document.body);
+    const x = event.clientX;
+    const y = event.clientY;
+    const w0 = width;
+    const h0 = height;
+    b.on("mousemove", (event2) => {
+      width = w0 + event2.clientX - x;
+      height = h0 + event2.clientY - y;
+      resize();
+    });
+    b.on("mouseup", (event2) => {
+      b.on("mousemove", null).on("mouseup", null);
+    });
+  });
+  let usezscore = false;
+  const numdata2plot = (data, genename) => {
+    const sample2data = /* @__PURE__ */ new Map();
+    let maxv = data[0].value, minv = data[0].value;
+    for (const i of data) {
+      sample2data.set(i.sample, i.value);
+      maxv = Math.max(maxv, i.value);
+      minv = Math.min(minv, i.value);
+    }
+    let mean, std;
+    if (usezscore) {
+      mean = data.reduce((i, j) => i + j.value, 0) / data.length;
+      std = Math.sqrt(data.reduce((i, j) => i + Math.pow(j.value - mean, 2), 0) / data.length);
+      console.log(mean, std);
+      minv = maxv = 0;
+      data.forEach((i) => {
+        const zscore = (i.value - mean) / std;
+        minv = Math.min(minv, zscore);
+        maxv = Math.max(maxv, zscore);
+      });
+    }
+    circles.attr("fill", (d) => {
+      if (sample2data.has(d.sample)) {
+        let v = sample2data.get(d.sample);
+        d.value = v;
+        if (usezscore) {
+          v = (v - mean) / std;
+          d.value = v;
+        }
+        const scalev = (v - minv) / (maxv - minv);
+        return value2color(scalev);
+      }
+      d.value = void 0;
+      return dullcolor;
+    });
+    dots.each(function(d) {
+      if (d.value != void 0) {
+        this.parentNode.appendChild(this);
+      }
+    });
+    legendholder.selectAll("*").remove();
+    legendholder.append("span").html(genename + "&nbsp;");
+    legendholder.append("span").html("min: " + minv + "&nbsp;");
+    const colorlst = [];
+    for (let i = 0; i <= 1; i += 0.1) {
+      colorlst.push(value2color(i));
+    }
+    legendholder.append("div").style("display", "inline-block").style("width", "150px").style("height", "20px").style("background", "linear-gradient(to right," + colorlst.join(",") + ")").style("border", "solid 1px " + dullcolor);
+    legendholder.append("span").html("&nbsp;max: " + maxv);
+    const row = legendholder.append("div").style("margin-top", "10px");
+    const id = Math.random().toString();
+    row.append("input").attr("type", "checkbox").style("margin-right", "10px").property("checked", usezscore).attr("id", id).on("change", () => {
+      usezscore = !usezscore;
+      numdata2plot(data, genename);
+    });
+    row.append("label").attr("for", id).text("apply Z-score");
+  };
+  return [null, numdata2plot];
+}
+function e2pca_genesearchui(arg) {
+  const geneta = arg.holder.append("input").attr("placeholder", "search gene").attr("padding-right", "20px");
+  const genesearchsays = arg.holder.append("span");
+  geneta.on("keyup", (event) => {
+    genesearchsays.text("");
+    if (event.code != "Enter") return;
+    const gene = geneta.property("value");
+    if (!gene) return;
+    geneta.property("value", "");
+    json_default(arg.hostURL + "/dbdata").post(
+      JSON.stringify({ db: arg.obj.dbfile, tablename: "data", keyname: "gene", key: gene.toLowerCase(), jwt: arg.jwt }),
+      (data) => {
+        if (data.error) {
+          genesearchsays.text("error getting data: " + data.error);
+          return;
+        }
+        if (!data.rows) {
+          genesearchsays.text(".rows missing");
+          return;
+        }
+        if (data.rows.length == 0) {
+          genesearchsays.text("no match for " + gene);
+          return;
+        }
+        arg.obj.expressiondata = data.rows;
+        arg.obj.searchedgene = gene;
+        arg.numdata2plot(data.rows, gene);
+        if (arg.callback) {
+          arg.callback();
+        }
+      }
+    );
+  });
+}
+export {
+  e2pca_genesearchui,
+  e2pca_inputui,
+  e2pca_plot
+};
+//# sourceMappingURL=e2pca-O7SNMJGB.js.map