@sjcrh/proteinpaint-client 2.204.0 → 2.205.0

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

@@ -1,198 +0,0 @@
-import {
-  hg38
-} from "./chunk-7VB2BKXW.js";
-import {
-  SearchHandler
-} from "./chunk-ONXYJWY6.js";
-import {
-  sleep
-} from "./chunk-FYXIK6Y6.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import {
-  vocabInit
-} from "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import {
-  TermTypes
-} from "./chunk-S5SOLLGM.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.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";
-
-// 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-NRJOIDRD.js.map

package/dist/dofetch-MLAEV3A2.js

@@ -1,48 +0,0 @@
-import {
-  clearServerDataCache,
-  dofetch,
-  dofetch2,
-  dofetch3,
-  getRequiredAuth,
-  getSavedToken,
-  includeEmbedder,
-  isInSession,
-  mayAddJwtToRequest,
-  mayShowAuthUi,
-  namedFetch,
-  processFormData,
-  setAuth,
-  setDsAuthOk,
-  setTokenByDsRoute
-} from "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import "./chunk-S5SOLLGM.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.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,
-  mayShowAuthUi,
-  namedFetch,
-  processFormData,
-  setAuth,
-  setDsAuthOk,
-  setTokenByDsRoute
-};
-//# sourceMappingURL=dofetch-MLAEV3A2.js.map

package/dist/e2pca-F3TGJOMW.js

@@ -1,344 +0,0 @@
-import {
-  axisstyle,
-  make_table_2col,
-  newpane,
-  sayerror,
-  to_svg
-} from "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import "./chunk-S5SOLLGM.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import {
-  axisBottom,
-  axisLeft,
-  json_default,
-  plasma
-} from "./chunk-YLJOZP4P.js";
-import {
-  linear
-} from "./chunk-HDTFYTEL.js";
-import "./chunk-FXQXCOII.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-DQC5FFGV.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-F3TGJOMW.js.map