@sjcrh/proteinpaint-client 2.205.0 → 2.206.1

package/dist/rememberedGvQ.unit.spec-GVRFRVSO.js

@@ -1,211 +0,0 @@
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import {
-  mayShowRememberedGvQ
-} from "./chunk-EEB5VE2A.js";
-import {
-  dtcnv,
-  dtfusionrna,
-  dtsnvindel
-} from "./chunk-IK2BO37K.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.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/rememberedGvQ.unit.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-var term = { type: "geneVariant", name: "BCR", genes: [{ kind: "gene", gene: "BCR", name: "BCR" }] };
-var lst = [
-  { label: "BCR-ABL1 fusion / Others", q: { type: "custom-groupset", customset: { groups: [{ name: "BCR-ABL1" }] } } },
-  { label: "BCR-JAK2 fusion / Others", q: { type: "custom-groupset", customset: { groups: [{ name: "BCR-JAK2" }] } } }
-];
-function getQ(dtTerms) {
-  return {
-    type: "custom-groupset",
-    customset: {
-      groups: [
-        {
-          name: "Group 1",
-          filter: {
-            type: "tvslst",
-            join: "and",
-            in: true,
-            lst: dtTerms.map((t) => ({ type: "tvs", tvs: { term: { id: "dt", ...t }, values: [] } }))
-          }
-        }
-      ]
-    }
-  };
-}
-function getVocabApi(remembered) {
-  return remembered ? { getGvQLst: () => structuredClone(remembered) } : {};
-}
-function getHolder() {
-  return select_default("body").append("div");
-}
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- termdb/handlers/rememberedGvQ -***-");
-  test.end();
-});
-(0, import_tape.default)("renders the remembered settings of a term", (test) => {
-  const holder = getHolder();
-  const shown = mayShowRememberedGvQ({
-    holder,
-    vocabApi: getVocabApi(lst),
-    term,
-    skipLabel: "Continue without one",
-    callback: () => {
-    }
-  });
-  test.equal(shown, true, "should report that the caller must wait for a choice");
-  test.equal(holder.style("display"), "block", "should show the holder");
-  const options = holder.selectAll(".sja_menuoption").nodes();
-  test.deepEqual(
-    options.map((n) => n.textContent),
-    ["BCR-ABL1 fusion / Others", "BCR-JAK2 fusion / Others", "Continue without one"],
-    "should offer each setting, then the way to decline them"
-  );
-  test.equal(
-    holder.selectAll('[data-testid="sjpp-genevariant-rememberedQ"]').size(),
-    2,
-    "should mark only the remembered settings"
-  );
-  test.ok(
-    options.every((n) => n.getAttribute("tabindex") == "0" && n.getAttribute("role") == "button"),
-    "should make every option keyboard operable"
-  );
-  test.equal(document.activeElement, options[0], "should focus the most recent setting");
-  options[0].dispatchEvent(new KeyboardEvent("keydown", { key: "ArrowUp", bubbles: true }));
-  test.equal(document.activeElement, options[2], "should wrap when arrowing past the first option");
-  holder.remove();
-  test.end();
-});
-(0, import_tape.default)("orders the settings by the selected mutation type", (test) => {
-  const cnvEntry = { label: "CNV groups", q: getQ([{ dt: dtcnv }]) };
-  const snvindelEntry = { label: "Somatic SNV/indel groups", q: getQ([{ dt: dtsnvindel, origin: "somatic" }]) };
-  const allelicEntry = { label: "Bi-allelic / Mono-allelic", q: getQ([{ dt: dtsnvindel }, { dt: dtcnv }]) };
-  const remembered = [cnvEntry, snvindelEntry, allelicEntry];
-  const getLabels = (holder) => holder.selectAll(".sja_menuoption").nodes().map((n) => n.textContent);
-  {
-    const holder = getHolder();
-    mayShowRememberedGvQ({
-      holder,
-      vocabApi: getVocabApi(remembered),
-      term,
-      mutationType: { dt: dtsnvindel, origin: "somatic" },
-      skipLabel: "Continue with SNV/indel (somatic)",
-      callback: () => {
-      }
-    });
-    test.deepEqual(
-      getLabels(holder),
-      ["Somatic SNV/indel groups", "CNV groups", "Bi-allelic / Mono-allelic", "Continue with SNV/indel (somatic)"],
-      "should lead with the setting built for the selected mutation type, keeping the rest in order"
-    );
-    test.equal(
-      document.activeElement,
-      holder.selectAll(".sja_menuoption").nodes()[0],
-      "should focus the leading setting"
-    );
-    holder.remove();
-  }
-  {
-    const holder = getHolder();
-    mayShowRememberedGvQ({
-      holder,
-      vocabApi: getVocabApi(remembered),
-      term,
-      mutationType: { dts: [dtsnvindel, dtcnv] },
-      skipLabel: "Continue with Bi/mono-allelic",
-      callback: () => {
-      }
-    });
-    test.deepEqual(
-      getLabels(holder)[0],
-      "Bi-allelic / Mono-allelic",
-      "should lead with the setting filtering by the same dts as a multi-dt mutation type"
-    );
-    holder.remove();
-  }
-  {
-    const holder = getHolder();
-    mayShowRememberedGvQ({
-      holder,
-      vocabApi: getVocabApi(remembered),
-      term,
-      mutationType: { dt: dtfusionrna },
-      skipLabel: "Continue with Fusion RNA",
-      callback: () => {
-      }
-    });
-    test.deepEqual(
-      getLabels(holder),
-      ["Continue with Fusion RNA", "CNV groups", "Somatic SNV/indel groups", "Bi-allelic / Mono-allelic"],
-      "should lead with the mutation type when nothing was remembered for it"
-    );
-    test.equal(
-      document.activeElement,
-      holder.selectAll(".sja_menuoption").nodes()[0],
-      "should focus the way to continue with the mutation type"
-    );
-    test.equal(
-      holder.selectAll('[data-testid="sjpp-genevariant-rememberedQ"]').size(),
-      3,
-      "should still mark only the remembered settings"
-    );
-    holder.remove();
-  }
-  test.end();
-});
-(0, import_tape.default)("picks a setting, or declines them", (test) => {
-  const picked = [];
-  const holder = getHolder();
-  mayShowRememberedGvQ({
-    holder,
-    vocabApi: getVocabApi(lst),
-    term,
-    skipLabel: "Continue without one",
-    callback: (q) => {
-      picked.push(q);
-    }
-  });
-  const options = holder.selectAll(".sja_menuoption").nodes();
-  options[1].dispatchEvent(new KeyboardEvent("keydown", { key: "Enter", bubbles: true }));
-  test.deepEqual(picked[0], lst[1].q, "should call back with the q of the picked setting");
-  options[2].click();
-  test.equal(picked[1], void 0, "should call back with nothing when the settings are declined");
-  holder.remove();
-  test.end();
-});
-(0, import_tape.default)("renders nothing when there is nothing to offer", (test) => {
-  const holder = getHolder();
-  test.equal(
-    mayShowRememberedGvQ({ holder, vocabApi: getVocabApi(), term, skipLabel: "x", callback: () => {
-    } }),
-    false,
-    "should offer nothing in a host app that does not remember settings"
-  );
-  test.equal(
-    mayShowRememberedGvQ({ holder, vocabApi: getVocabApi([]), term, skipLabel: "x", callback: () => {
-    } }),
-    false,
-    "should offer nothing when the term has none remembered"
-  );
-  mayShowRememberedGvQ({ holder, vocabApi: getVocabApi(lst), term, skipLabel: "x", callback: () => {
-  } });
-  mayShowRememberedGvQ({ holder, vocabApi: getVocabApi(), term, skipLabel: "x", callback: () => {
-  } });
-  test.equal(holder.selectAll(".sja_menuoption").size(), 0, "should clear options left from a previous gene");
-  test.equal(holder.style("display"), "none", "should hide the holder again");
-  holder.remove();
-  test.end();
-});
-//# sourceMappingURL=rememberedGvQ.unit.spec-GVRFRVSO.js.map

package/dist/render-G7V6R4PV.js

@@ -1,33 +0,0 @@
-import {
-  renderGeomap
-} from "./chunk-UM5NWVMA.js";
-import "./chunk-J7JDCNLU.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-N635HDJ4.js";
-import "./chunk-T46FA72N.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-JYOIO5UY.js";
-import "./chunk-YN5NY3D3.js";
-import "./chunk-RN4BOWRH.js";
-import "./chunk-IK2BO37K.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 "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  renderGeomap
-};
-//# sourceMappingURL=render-G7V6R4PV.js.map

package/dist/report-O7D46EKQ.js

@@ -1,217 +0,0 @@
-import {
-  PlotBase,
-  controlsInit,
-  downloadSVGsAsPdf
-} from "./chunk-J7JDCNLU.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import {
-  importPlot
-} from "./chunk-N635HDJ4.js";
-import "./chunk-T46FA72N.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import {
-  icons
-} from "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-JYOIO5UY.js";
-import "./chunk-YN5NY3D3.js";
-import "./chunk-RN4BOWRH.js";
-import "./chunk-IK2BO37K.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./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 "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.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-O7D46EKQ.js.map

package/dist/sampleView-6Y3OOOMW.js

@@ -1,43 +0,0 @@
-import {
-  componentInit,
-  getPlotConfig,
-  getSamplesRelated,
-  getTermValue,
-  sampleViewInit,
-  searchSampleInput
-} from "./chunk-L743GRJE.js";
-import "./chunk-J7JDCNLU.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-N635HDJ4.js";
-import "./chunk-T46FA72N.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-JYOIO5UY.js";
-import "./chunk-YN5NY3D3.js";
-import "./chunk-RN4BOWRH.js";
-import "./chunk-IK2BO37K.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 "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  componentInit,
-  getPlotConfig,
-  getSamplesRelated,
-  getTermValue,
-  sampleViewInit,
-  searchSampleInput
-};
-//# sourceMappingURL=sampleView-6Y3OOOMW.js.map

package/dist/samplelst-JRVC4GYC.js

@@ -1,106 +0,0 @@
-import {
-  getPillNameDefault,
-  renderTable
-} from "./chunk-J7JDCNLU.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-N635HDJ4.js";
-import "./chunk-T46FA72N.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-JYOIO5UY.js";
-import "./chunk-YN5NY3D3.js";
-import "./chunk-RN4BOWRH.js";
-import "./chunk-IK2BO37K.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 "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.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 : `${group.name} will exclude these samples`;
-          addTable(groupDiv, name, group, noButtonCallback);
-        }
-        div.append("div").style("padding", "6px").append("button").attr("data-testid", "sjpp-ts-samplelst-apply").text("Apply").on("click", () => {
-          for (const group of groups)
-            group.values = group.values.filter((value) => !("checked" in value) || value.checked);
-          self.api.runCallback();
-        });
-      } else {
-        const e = self.vocabApi.tokenVerificationPayload;
-        const missingAccess = e?.error == "Missing access" && self.vocabApi.termdbConfig.dataDownloadCatch?.missingAccess;
-        const message = e && missingAccess?.message?.replace("MISSING-ACCESS-LINK", missingAccess?.links[e.linkKey || ""]);
-        const helpLink = self.vocabApi.termdbConfig?.dataDownloadCatch?.helpLink;
-        div.append("div").style("color", "#e44").style("padding", "10px").html(
-          message || (self.vocabApi.tokenVerificationMessage || "Requires sign-in") + (helpLink ? ` <a href='${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-JRVC4GYC.js.map