@sjcrh/proteinpaint-client 2.196.0 → 2.198.0

package/dist/report-JEJFCWUU.js

@@ -1,222 +0,0 @@
-import {
-  PlotBase,
-  controlsInit,
-  downloadSVGsAsPdf
-} from "./chunk-WY2PGUVX.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import {
-  importPlot
-} from "./chunk-MBUQ34CF.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-LQJMCE7G.js";
-import "./chunk-FN5XPUPH.js";
-import {
-  icons
-} from "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-OVSKJROY.js";
-import "./chunk-A3URBFXN.js";
-import "./chunk-LYVLF6HO.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import "./chunk-NNFAUP2I.js";
-import "./chunk-7KRS7L4U.js";
-import "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./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/report/view/reportView.ts
-var ReportView = class {
-  constructor(report) {
-    this.opts = report.opts;
-    this.report = report;
-    const leftDiv = this.opts.holder.insert("div").style("display", "inline-block");
-    const controlsHolder = leftDiv.insert("div").style("display", "inline-block");
-    const mainDiv = this.opts.holder.insert("div").style("display", "inline-block").style("vertical-align", "top").style("padding", "20px");
-    const headerDiv = mainDiv.append("div").style("padding", "10px");
-    const downloadDiv = headerDiv.append("div").style("display", "inline-block").style("padding-left", "10px").style("vertical-align", "middle");
-    icons["pdf"](downloadDiv, {
-      handler: () => this.report.downloadReport(),
-      title: "Download the report",
-      width: 20,
-      height: 20
-    });
-    const plotsDiv = mainDiv.append("div");
-    this.dom = {
-      headerDiv,
-      plotsDiv,
-      header: this.opts.header,
-      //holder,
-      controlsHolder
-    };
-    if (this.dom.header) {
-      this.dom.header.html(this.report.config.name || "Summary Report");
-    }
-  }
-  getControlInputs() {
-    const inputs = [];
-    return inputs;
-  }
-};
-
-// plots/report/report.ts
-var Report = class _Report extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.components = {};
-    this.type = _Report.type;
-  }
-  static {
-    this.type = "report";
-  }
-  async init(appState) {
-    this.config = appState.plots.find((p) => p.id === this.id);
-    this.view = new ReportView(this);
-    this.components = { plots: {} };
-    const state = this.getState(appState);
-    for (const section of state.config.sections) {
-      const div = this.view.dom.plotsDiv.append("div");
-      const headerIcon = div.append("span").style("margin-right", "10px").style("cursor", "pointer").text("\u25BC");
-      div.append("div").style("display", "inline-block").style("font-size", "1.2em").style("margin", "10px 0px").style("font-weight", "bold").text(section.name);
-      const sectionDiv = div.append("div").style("margin", "10px").style("display", "flex").style("flex-direction", "row").style("flex-wrap", "wrap").style("width", "100vw");
-      headerIcon.on("click", () => {
-        const display = sectionDiv.style("display");
-        headerIcon.text(display === "none" ? "\u25BC" : "\u25B2");
-        sectionDiv.style("display", display === "none" ? "flex" : "none");
-      });
-      for (const plot of section.plots) {
-        if (this.components.plots[plot.id]) continue;
-        await this.setPlot(plot, sectionDiv);
-      }
-    }
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      config,
-      plots: appState.plots.filter((p) => p.parentId === this.id),
-      //this property is needed to indicate that child plots need to be added to the appState plots
-      termfilter: appState.termfilter,
-      vocab: appState.vocab,
-      termdbConfig: appState.termdbConfig
-    };
-  }
-  async main() {
-    this.config = structuredClone(this.state.config);
-    this.settings = this.config.settings.report;
-  }
-  async setPlot(plot, sectionDiv) {
-    const plotDiv = sectionDiv.append("div").style("display", "inline-block").style("margin", "10px");
-    const headerDiv = plotDiv.append("div");
-    const headerIcon = headerDiv.append("span").style("margin", "10px").style("cursor", "pointer").text("\u25BC");
-    const header = headerDiv.append("div").style("display", "inline-block").style("font-size", "1.1em").style("margin-top", "10px");
-    headerIcon.on("click", () => {
-      const display = holder.style("display");
-      headerIcon.text(display === "none" ? "\u25BC" : "\u25B2");
-      holder.style("display", display === "none" ? "block" : "none");
-    });
-    const holder = plotDiv.append("div");
-    const opts = structuredClone(plot);
-    opts.header = header;
-    opts.holder = holder;
-    opts.app = this.app;
-    opts.parentId = this.id;
-    const { componentInit: componentInit2 } = await importPlot(opts.chartType);
-    this.components.plots[opts.id] = await componentInit2(opts);
-  }
-  async setControls() {
-    this.view.dom.controlsHolder.selectAll("*").remove();
-    const inputs = this.view.getControlInputs();
-    this.components = {
-      controls: await controlsInit({
-        app: this.app,
-        id: this.id,
-        holder: this.view.dom.controlsHolder,
-        inputs
-      })
-    };
-  }
-  getChartImages() {
-    const chartImagesAll = [];
-    for (const section of this.config.sections) {
-      for (const plotConfig of section.plots) {
-        const plot = this.components.plots[plotConfig.id];
-        if (plot?.getChartImages) {
-          const chartImages = plot.getChartImages();
-          for (const chartImage of chartImages) {
-            if (chartImage.name.trim()) chartImage.name = `${section.name} / ${chartImage.name}`;
-            else chartImage.name = section.name;
-            chartImagesAll.push(chartImage);
-          }
-        }
-      }
-    }
-    return chartImagesAll;
-  }
-  async downloadReport() {
-    const chartImagesAll = this.getChartImages();
-    const globalFilterImg = await this.app.getComponents("nav.filter").getFilterImage();
-    const filterImg = await this.opts.getFilterImage();
-    const filterImgs = [];
-    if (globalFilterImg) filterImgs.push(globalFilterImg);
-    if (filterImg) filterImgs.push(filterImg);
-    downloadSVGsAsPdf(chartImagesAll, "report", "landscape", filterImgs);
-  }
-};
-async function getPlotConfig(opts, app) {
-  const settings = getDefaultReportSettings();
-  const plot = {
-    settings: {
-      controls: {
-        isOpen: false
-        // control panel is hidden by default
-      },
-      report: settings,
-      startColor: {},
-      //dict to store the start color of the gradient for each chart when using continuous color
-      stopColor: {}
-      //dict to store the stop color of the gradient for each chart when using continuous color
-    }
-  };
-  try {
-    const config = app.vocabApi?.termdbConfig?.plotConfigByCohort?.default?.report;
-    opts.filter = app.vocabApi?.termdbConfig?.authFilter;
-    copyMerge(plot, config, opts);
-    return plot;
-  } catch (e) {
-    console.log(e);
-    throw `${e} [sampleScatter getPlotConfig()]`;
-  }
-}
-var reportInit = getCompInit(Report);
-var componentInit = reportInit;
-function getDefaultReportSettings() {
-  return {};
-}
-export {
-  Report,
-  componentInit,
-  getDefaultReportSettings,
-  getPlotConfig,
-  reportInit
-};
-//# sourceMappingURL=report-JEJFCWUU.js.map

package/dist/sampleScatter.spec-LBAZBDYA.js

@@ -1,202 +0,0 @@
-import {
-  getRunPp
-} from "./chunk-OF5FE6GT.js";
-import {
-  require_tape
-} from "./chunk-TUMA63WX.js";
-import "./chunk-WQCQWUUP.js";
-import "./chunk-7D3WX34I.js";
-import "./chunk-PU2Q4SZR.js";
-import "./chunk-QMXCK4Y5.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-GE4NJDV4.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-WKNI3HRQ.js";
-import "./chunk-53JJ7SXN.js";
-import "./chunk-CDJAHMAN.js";
-import "./chunk-WY2PGUVX.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-MBUQ34CF.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-OVSKJROY.js";
-import "./chunk-A3URBFXN.js";
-import "./chunk-LYVLF6HO.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import "./chunk-NNFAUP2I.js";
-import "./chunk-7KRS7L4U.js";
-import "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-TJYRBEBK.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-SOTB4FRE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  selectAll_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// plots/test/sampleScatter.spec.js
-var import_tape = __toESM(require_tape(), 1);
-var runpp = getRunPp("mass", {
-  state: {
-    vocab: {
-      dslabel: "PNET",
-      genome: "hg19"
-    }
-  },
-  debug: 1
-});
-function sleep(ms) {
-  return new Promise((resolve) => setTimeout(resolve, ms));
-}
-var state = {
-  plots: [
-    {
-      chartType: "sampleScatter",
-      colorTW: { id: "TSNE Category" },
-      name: "Methylome TSNE"
-    }
-  ]
-};
-var open_state = {
-  nav: { header_mode: "hide_search" },
-  plots: [
-    {
-      chartType: "sampleScatter",
-      colorTW: { id: "TSNE Category" },
-      name: "Methylome TSNE"
-    }
-  ]
-};
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- mass/sampleScatter -***-");
-  test.end();
-});
-(0, import_tape.default)("PNET plot + filter + colorTW=gene", function(test) {
-  test.timeoutAfter(3e3);
-  test.plan(1);
-  const s2 = JSON.parse(JSON.stringify(state));
-  s2.termfilter = {
-    filter: {
-      type: "tvslst",
-      join: "",
-      in: true,
-      lst: [{ type: "tvs", tvs: { term: { id: "Gender" }, values: [{ key: "M", label: "Male" }] } }]
-    }
-  };
-  s2.plots[0].colorTW = { term: { type: "geneVariant", name: "TP53", gene: "TP53" } };
-  runpp({
-    state: s2,
-    sampleScatter: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  function runTests(scatter) {
-    testPlot();
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-    function testPlot() {
-      const scatterDiv = scatter.Inner.model.charts[0].chartDiv;
-      const serieG = scatterDiv.select(".sjpcb-scatter-series");
-      const numSymbols = serieG.selectAll("path").size();
-      console.log(numSymbols == scatter.Inner.model.charts[0].data.samples.length);
-      test.true(
-        numSymbols == scatter.Inner.model.charts[0].data.samples.length,
-        `Should be ${scatter.Inner.model.charts[0].data.samples.length}. Rendered ${numSymbols} symbols.`
-      );
-    }
-  }
-});
-import_tape.default.skip("Add shape, clicking term and replace by search", function(test) {
-  test.timeoutAfter(8e3);
-  runpp({
-    state: open_state,
-    sampleScatter: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  const origTerm = "TSNE Category";
-  const testTerm = "Mutational Burden";
-  async function runTests(scatter) {
-    scatter.on("postRender.test", null);
-    await sleep(500);
-    triggerAddBtn(scatter);
-    await sleep(300);
-    triggerPillChange();
-    await sleep(100);
-    testShapeRendering(scatter, testTerm);
-    await sleep(500);
-    triggerShapeReplace();
-    await sleep(300);
-    changeShapeBySearch();
-    await sleep(100);
-    testShapeRendering(scatter, origTerm);
-    if (test._ok) scatter.Inner.app.destroy();
-    test.end();
-  }
-  function triggerAddBtn(scatter) {
-    const addBtn = scatter.Inner.view.dom.controls.selectAll("div").nodes().find((c) => c.style.display == "block" && c?.childNodes[1]?.innerHTML == "+");
-    addBtn.dispatchEvent(new Event("click"));
-  }
-  function triggerPillChange() {
-    selectAll_default(".ts_pill").filter((d) => d.name == testTerm).node().click();
-  }
-  function testShapeRendering(scatter, term) {
-    const shapeLegend = scatter.Inner.model.charts[0].chartDiv.selectAll("g").nodes().find((c) => c?.childNodes[0].innerHTML == term);
-    let groups = [];
-    for (const [i, group] of shapeLegend.childNodes.entries()) {
-      if (i == 0) continue;
-      const label = group.childNodes[1].innerHTML.split(",");
-      groups.push({
-        label: label[0],
-        samples: label[1].match(/[\d\.]+/g)
-        //Maybe test all samples rendered?
-      });
-    }
-    test.ok(
-      scatter.Inner.shapeLegend.size == groups.length + 1,
-      `Legend categories (# = ${groups.length + 1}) should equal size of shapeLegend (# = ${scatter.Inner.shapeLegend.size}) `
-    );
-    compareData2DOMLegend(scatter, groups);
-  }
-  function compareData2DOMLegend(scatter, groups) {
-    for (const group of groups) {
-      const mapLeg = scatter.Inner.shapeLegend.get(group.label);
-      test.ok(
-        mapLeg.sampleCount == group.samples[0],
-        `Should show matching n = ${mapLeg.sampleCount} for ${group.label}. Legend: n = ${group.samples[0]}`
-      );
-    }
-  }
-  function triggerShapeReplace() {
-    selectAll_default(".ts_pill").filter((d) => d.name == testTerm).node().click();
-    selectAll_default(".sja_sharp_border").filter((d) => d.label == "Replace").node().click();
-  }
-  async function changeShapeBySearch() {
-    const termSearchDiv = selectAll_default(".tree_search").nodes().find((e) => e.placeholder.endsWith("genes"));
-    termSearchDiv.value = origTerm;
-    termSearchDiv.dispatchEvent(new Event("input"));
-    await sleep(1e3);
-    selectAll_default(".sja_tree_click_term").filter((d) => d.name == origTerm).node().click();
-  }
-});
-//# sourceMappingURL=sampleScatter.spec-LBAZBDYA.js.map

package/dist/sampleView-WKZT5ZFE.js

@@ -1,48 +0,0 @@
-import {
-  componentInit,
-  getPlotConfig,
-  getSamplesRelated,
-  getTermValue,
-  sampleViewInit,
-  searchSampleInput
-} from "./chunk-QKR3ZD3S.js";
-import "./chunk-WY2PGUVX.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-MBUQ34CF.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-OVSKJROY.js";
-import "./chunk-A3URBFXN.js";
-import "./chunk-LYVLF6HO.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import "./chunk-NNFAUP2I.js";
-import "./chunk-7KRS7L4U.js";
-import "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./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";
-export {
-  componentInit,
-  getPlotConfig,
-  getSamplesRelated,
-  getTermValue,
-  sampleViewInit,
-  searchSampleInput
-};
-//# sourceMappingURL=sampleView-WKZT5ZFE.js.map

package/dist/samplelst-HXM3H6M4.js

@@ -1,111 +0,0 @@
-import {
-  getPillNameDefault,
-  renderTable
-} from "./chunk-WY2PGUVX.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-MBUQ34CF.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-OVSKJROY.js";
-import "./chunk-A3URBFXN.js";
-import "./chunk-LYVLF6HO.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import "./chunk-NNFAUP2I.js";
-import "./chunk-7KRS7L4U.js";
-import "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./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";
-
-// termsetting/handlers/samplelst.ts
-function getHandler(self) {
-  return {
-    showEditMenu(div) {
-      div.selectAll("*").remove();
-      const q = self.q;
-      if (self.vocabApi.termdbConfig?.displaySampleIds && self.vocabApi.hasVerifiedToken()) {
-        const groups = q.groups;
-        for (const group of groups) {
-          const groupDiv = div.append("div").style("display", "inline-block").style("vertical-align", "top");
-          const noButtonCallback = (i, node) => {
-            group.values[i].checked = node.checked;
-          };
-          const name = group.in ? group.name : `${group.name} will exclude these samples`;
-          addTable(groupDiv, name, group, noButtonCallback);
-        }
-        div.append("div").append("div").style("display", "inline-block").style("float", "right").style("padding", "6px 20px").append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn").text("Apply").on("click", () => {
-          for (const group of groups)
-            group.values = group.values.filter((value) => !("checked" in value) || value.checked);
-          self.api.runCallback();
-        });
-      } else {
-        const e = self.vocabApi.tokenVerificationPayload;
-        const missingAccess = e?.error == "Missing access" && self.vocabApi.termdbConfig.dataDownloadCatch?.missingAccess;
-        const message = e && missingAccess?.message?.replace("MISSING-ACCESS-LINK", missingAccess?.links[e.linkKey || ""]);
-        const helpLink = self.vocabApi.termdbConfig?.dataDownloadCatch?.helpLink;
-        div.append("div").style("color", "#e44").style("padding", "10px").html(
-          message || (self.vocabApi.tokenVerificationMessage || "Requires sign-in") + (helpLink ? ` <a href='${helpLink}' target=_blank>Tutorial</a>` : "")
-        );
-      }
-    },
-    getPillStatus() {
-    },
-    getPillName(d) {
-      return getPillNameDefault(self, d);
-    }
-  };
-}
-function addTable(div, name, group, noButtonCallback) {
-  div.style("padding", "6px").append("div").style("margin", "10px").style("font-size", "0.8rem").html(`<b> ${name}</b>.`);
-  const rows = [];
-  for (const value of group.values) rows.push([{ value: value.sample }]);
-  const columns = [{ label: "Sample" }];
-  renderTable({
-    rows,
-    columns,
-    div,
-    maxWidth: "30vw",
-    maxHeight: "40vh",
-    noButtonCallback,
-    striped: false,
-    showHeader: false,
-    selectAll: true,
-    columnButtons: void 0,
-    //Leave until table.js is typed
-    buttons: void 0
-  });
-}
-function fillTW(tw) {
-  if (!tw.q.groups) tw.q.groups = [];
-  if (tw.q.groups.length == 0) {
-    for (const k in tw.term.values) {
-      const v = tw.term.values[k];
-      tw.q.groups.push({
-        name: k,
-        inuse: v.inuse,
-        values: v.list
-      });
-    }
-  }
-}
-export {
-  fillTW,
-  getHandler
-};
-//# sourceMappingURL=samplelst-HXM3H6M4.js.map