@sjcrh/proteinpaint-client 2.220.0 → 2.221.0

package/dist/report-KB4K7ZXC.js

@@ -1,213 +0,0 @@
-import {
-  PlotBase,
-  controlsInit,
-  downloadSVGsAsPdf
-} from "./chunk-PEKCVKJK.js";
-import "./chunk-HJ6L54YS.js";
-import {
-  importPlot
-} from "./chunk-YR6EXI2K.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import {
-  icons
-} from "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import "./chunk-WJLRU5OF.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.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-KB4K7ZXC.js.map

package/dist/sampleView-QD2JLZ4T.js

@@ -1,39 +0,0 @@
-import {
-  componentInit,
-  getPlotConfig,
-  getSamplesRelated,
-  getTermValue,
-  sampleViewInit,
-  searchSampleInput
-} from "./chunk-67MD4UES.js";
-import "./chunk-PEKCVKJK.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-YR6EXI2K.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 "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  componentInit,
-  getPlotConfig,
-  getSamplesRelated,
-  getTermValue,
-  sampleViewInit,
-  searchSampleInput
-};
-//# sourceMappingURL=sampleView-QD2JLZ4T.js.map

package/dist/samplelst-6R5RYHNV.js

@@ -1,114 +0,0 @@
-import {
-  getPillNameDefault,
-  renderTable
-} from "./chunk-PEKCVKJK.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-YR6EXI2K.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 "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// termsetting/handlers/samplelst.ts
-function getHandler(self) {
-  return {
-    showEditMenu(div) {
-      div.selectAll("*").remove();
-      const q = self.q;
-      const groups = q.groups.filter((g) => Array.isArray(g.values));
-      for (const group of q.groups) {
-        if (groups.includes(group)) continue;
-        const row = div.append("div").style("padding", "6px 10px").style("font-size", "0.8rem");
-        row.append("b").text(group.name);
-        if (Number.isFinite(group.sampleCount)) row.append("span").text(`, n=${group.sampleCount}`);
-      }
-      if (!groups.length) return;
-      if (self.vocabApi.termdbConfig?.displaySampleIds && self.vocabApi.hasVerifiedToken()) {
-        for (const group of groups) {
-          const groupDiv = div.append("div").style("display", "inline-block").style("vertical-align", "top");
-          const noButtonCallback = (i, node) => {
-            group.values[i].checked = node.checked;
-          };
-          const name = group.in ? group.name : `${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
-  });
-}
-async function fillTW(tw, vocabApi) {
-  if (!tw.q.groups) tw.q.groups = [];
-  if (tw.q.groups.length == 0 && Object.values(tw.term.values || {}).some((v) => !Array.isArray(v.list))) {
-    const customTws = await vocabApi?.getCustomTerms?.() || [];
-    const customTw = customTws.find((t) => t.term.type == "samplelst" && t.term.name == tw.term.name);
-    if (customTw?.q?.groups?.length) tw.q.groups = structuredClone(customTw.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-6R5RYHNV.js.map