@sjcrh/proteinpaint-client 2.183.0 → 2.183.1

package/dist/chunk-APOHXHKH.js

@@ -1,526 +0,0 @@
-import {
-  setComputedConfig
-} from "./chunk-77ZJGPK2.js";
-import {
-  MatrixControls
-} from "./chunk-ZGT4XP5J.js";
-import {
-  matrix_data_exports
-} from "./chunk-WPHOEG56.js";
-import {
-  matrix_layout_exports
-} from "./chunk-36DYWBU7.js";
-import {
-  matrix_serieses_exports
-} from "./chunk-D4QFQQWJ.js";
-import {
-  matrix_legend_exports
-} from "./chunk-DNCSPTOQ.js";
-import {
-  matrix_groups_exports
-} from "./chunk-QRIRWDIW.js";
-import {
-  setMatrixDom
-} from "./chunk-VYIO7T6J.js";
-import {
-  setInteractivity
-} from "./chunk-DTDQKGIQ.js";
-import {
-  setRenderers
-} from "./chunk-YALAQWX4.js";
-import {
-  MatrixCluster
-} from "./chunk-A5TSPTYC.js";
-import {
-  PlotBase,
-  TwRouter,
-  getCombinedTermFilter,
-  rebaseGroupFilter,
-  routedTermTypes,
-  sayerror,
-  svgLegend
-} from "./chunk-OXJ2TWDO.js";
-import {
-  copyMerge,
-  deepEqual,
-  getCompInit
-} from "./chunk-MVTCBVSX.js";
-import {
-  dt2label,
-  mclass,
-  morigin
-} from "./chunk-XYFDBYOY.js";
-import {
-  convertUnits
-} from "./chunk-TV74I3Y5.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-
-// plots/matrix/matrix.xtw.ts
-var addons;
-async function getTermGroups(termgroups, app) {
-  const termGroups = structuredClone(termgroups);
-  if (!addons)
-    addons = {
-      QualTWValues: discreteAddons,
-      QualTWPredefinedGS: discreteAddons,
-      QualTWCustomGS: discreteAddons,
-      NumTWRegularBin: discreteAddons,
-      NumTWCustomBin: discreteAddons,
-      NumTWCont: continuousAddons,
-      TermCollectionTWCont: TermCollectionContAddons
-    };
-  const opts = {
-    vocabApi: app.vocabApi,
-    addons
-  };
-  for (const [origIndex, tG] of termGroups.entries()) {
-    tG.origIndex = origIndex;
-    if (tG.type == "hierCluster") continue;
-    const xtwlst = [];
-    for (const tw of tG.lst) {
-      const inputTw = tw.getTw?.() || tw;
-      xtwlst.push(
-        inputTw.type in opts.addons && routedTermTypes.has(inputTw.term.type) ? await TwRouter.init(inputTw, opts) : inputTw
-      );
-    }
-    tG.lst = xtwlst;
-  }
-  return termGroups;
-}
-var discreteAddons = {
-  setCellProps: {
-    value: function(cell, anno, value, s, t, self2, width, height, dx, dy, i) {
-      const tw = this.getTw();
-      const key = anno.key;
-      const values = tw.term.values || {};
-      cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
-      const tw$id = tw.$id;
-      cell.fill = self2.config.settings.matrix.twSpecificSettings?.[tw$id]?.[key]?.color || anno.color || values[anno.key]?.color || self2.data.refs.byTermId?.[tw$id]?.bins?.find((b) => anno.key == b.name)?.color;
-      cell.order = t.ref.bins ? t.ref.bins.findIndex((bin) => bin.name == key) : 0;
-      cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-      cell.y = height * i;
-      const group = tw.legend?.group || tw$id;
-      return { ref: t.ref, group, value: key, entry: { key, label: cell.label, fill: cell.fill } };
-    }
-  }
-};
-var continuousAddons = {
-  setCellProps: {
-    value: function(cell, anno, value, s, t, self2, width, height, dx, dy, i) {
-      const tw = this.getTw();
-      const key = anno.key;
-      const values = tw.term.values || {};
-      cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : key;
-      cell.fill = anno.color || values[anno.key]?.color;
-      const tw$id = tw.$id;
-      const twSpecificSettings = self2.config.settings.matrix.twSpecificSettings;
-      if (!twSpecificSettings[tw$id]) twSpecificSettings[tw$id] = {};
-      const twSettings = twSpecificSettings[tw$id];
-      if (!twSettings.contBarH) twSettings.contBarH = s.barh;
-      if (!("gap" in twSettings)) twSettings.contBarGap = 4;
-      const specialValue = tw.term.values?.[cell.key];
-      if (specialValue?.uncomputable) {
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        cell.y = height * i;
-        cell.height = twSettings.contBarH;
-        cell.fill = "transparent";
-        cell.label = specialValue.label;
-        const group = tw.legend?.group || tw.$id;
-        return {
-          ref: t.ref,
-          group,
-          value: specialValue.label || specialValue.key,
-          entry: { key, label: cell.label, fill: cell.fill }
-        };
-      }
-      cell.fill = self2.config.settings.matrix.twSpecificSettings?.[tw$id]?.contBarColor || "#555";
-      if (s.transpose) {
-        cell.height = t.scale(cell.key);
-        cell.x = twSettings.contBarGap;
-      } else {
-        const vc = cell.term.valueConversion;
-        let renderV = vc ? cell.key * vc.scaleFactor : cell.key;
-        if (this.q.convert2ZScore) {
-          renderV = (renderV - t.mean) / t.std;
-          cell.fill = renderV > 0 ? "#FF6666" : "#6666FF";
-          cell.zscoreLabel = ` (Z-score: ${renderV.toFixed(2)})`;
-        }
-        cell.label = "label" in anno ? anno.label : values[key]?.label ? values[key].label : this.term.unit ? `${cell.key.toFixed(2)} ${this.term.unit}` : cell.key.toFixed(2);
-        cell.height = renderV >= 0 ? t.scales.pos(renderV) : t.scales.neg(renderV);
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        cell.y = renderV >= 0 ? t.counts.posMaxHt + twSettings.contBarGap - cell.height : t.counts.posMaxHt + twSettings.contBarGap;
-        cell.convertedValueLabel = !vc ? "" : convertUnits(cell.key, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-      }
-    }
-  }
-};
-var TermCollectionContAddons = {
-  setCellProps: {
-    value: function(cell, anno, value, s, t, self2, width, height, dx, _dy, _i) {
-      const tw = this.getTw();
-      const twSpecificSettings = self2.config.settings.matrix.twSpecificSettings;
-      if (!twSpecificSettings[tw.$id]) twSpecificSettings[tw.$id] = {};
-      const twSettings = twSpecificSettings[tw.$id];
-      if (!twSettings.contBarH) twSettings.contBarH = s.barh;
-      if (!("gap" in twSettings)) twSettings.contBarGap = 4;
-      const isNegative = value.value < 0;
-      if (isNegative) {
-        cell.height = t.scales.neg ? t.scales.neg(value.value) - t.scales.neg(0) : 0;
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        const cumulativeHeight = t.scales.neg ? t.scales.neg(value.pre_val_sum) - t.scales.neg(0) : 0;
-        cell.y = t.counts.posMaxHt + twSettings.contBarGap + (t.scales.neg ? t.scales.neg(0) : 0) + cumulativeHeight;
-      } else {
-        cell.height = t.scales.pos(value.value) - t.scales.pos(0);
-        cell.x = cell.totalIndex * dx + cell.grpIndex * s.colgspace;
-        const cumulativeHeight = t.scales.pos(value.pre_val_sum) - t.scales.pos(0);
-        cell.y = t.counts.posMaxHt + twSettings.contBarGap - t.scales.pos(0) - cumulativeHeight - cell.height;
-      }
-      cell.label = value.label;
-      cell.fill = twSettings[value.label]?.color || value.color || tw.term.propsByTermId?.[value.label]?.color;
-      cell.value = value.value;
-      return {
-        ref: t.ref,
-        group: tw.$id,
-        value: value.label,
-        order: -1,
-        entry: { key: value.label, label: value.label, fill: cell.fill }
-      };
-    }
-  }
-};
-
-// plots/matrix/matrix.js
-var Matrix = class _Matrix extends PlotBase {
-  static type = "matrix";
-  configTermKeys = ["termgroups.lst", "divideBy"];
-  constructor(opts) {
-    super(opts);
-    this.type = _Matrix.type;
-    this.holderTitle = "Sample Matrix";
-    this.optionalFeatures = JSON.parse(sessionStorage.getItem("optionalFeatures") || `{}`)?.matrix || [];
-    setInteractivity(this);
-    setRenderers(this);
-  }
-  async init(appState) {
-    const opts = this.opts;
-    if (opts.reactsTo) this.reactsTo = opts.reactsTo;
-    this.setDom = setMatrixDom;
-    this.setDom(opts);
-    this.config = appState.plots.find((p) => p.id === this.id);
-    this.settings = Object.assign({}, this.config.settings.matrix);
-    this.computed = {};
-    if (this.dom.header) this.dom.header.html(this.config.preBuiltPlotTitle || this.holderTitle);
-    this.setControls(appState);
-    this.clusterRenderer = new MatrixCluster({ holder: this.dom.cluster, app: this.app, parent: this });
-    this.legendRenderer = svgLegend({
-      holder: this.dom.legendG,
-      rectFillFxn: (d) => d.color,
-      iconStroke: "#aaa",
-      handlers: {
-        legend: {
-          click: this.legendClick
-        }
-      },
-      settings: {
-        isExcludedAttr: "isExcluded"
-      },
-      note: "CLICK A ROW LABEL OR ITEM TO APPLY FILTERING"
-    });
-    this.customTipApi = this.dom.tip.getCustomApi({
-      d: this.dom.menubody,
-      clear: (event) => {
-        if (event?.target) this.dom.menutop.style("display", "none");
-        this.dom.menubody.selectAll("*").remove();
-        return this.customTipApi;
-      },
-      show: () => {
-        this.dom.menubody.style("display", "block");
-      },
-      hide: () => {
-      }
-    });
-    this.setPill(appState);
-    const commonKeys = { mclass, dt2label, morigin };
-    for (const k in commonKeys) {
-      const v = commonKeys[k];
-      this[k] = copyMerge({}, v, appState.termdbConfig[k] || {}, appState.termdbConfig.matrix?.[k] || {});
-    }
-  }
-  setControls(appState) {
-    this.controlsRenderer = new MatrixControls(
-      {
-        app: this.app,
-        id: this.id,
-        parent: this,
-        holder: this.dom.controls,
-        getSvg: () => this.dom.svg.node()
-      },
-      appState
-    );
-  }
-  // reactsTo(action) {
-  // 	// note: a parent app or 'plot' component is expected to already have
-  // 	// a comprehensive reactsTo() call to filter the actions for this component,
-  // 	// so only farther selective action filters should be applied here as needed
-  // 	return true
-  // }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    const filter0 = appState.termfilter.filter0;
-    this.prevFilter0 = this.state?.filter0;
-    const parentConfig = appState.plots.find((p) => p.id === this.parentId);
-    const termfilter = getCombinedTermFilter(appState, config.filter || parentConfig?.filter);
-    return {
-      isVisible: true,
-      config,
-      filter: termfilter.filter,
-      filter0,
-      // read-only, invisible filter currently only used for gdc dataset
-      hasVerifiedToken: this.app.vocabApi.hasVerifiedToken(),
-      tokenVerificationMessage: this.app.vocabApi.tokenVerificationMessage,
-      vocab: appState.vocab,
-      termdbConfig: appState.termdbConfig,
-      clusterMethod: config.settings.hierCluster?.clusterMethod,
-      distanceMethod: config.settings.hierCluster?.distanceMethod,
-      clusterSamples: config.settings.hierCluster?.clusterSamples,
-      clusterRows: config.settings.hierCluster?.clusterRows,
-      zScoreTransformation: config.settings.hierCluster?.zScoreTransformation,
-      nav: appState.nav,
-      groups: rebaseGroupFilter(appState)
-    };
-  }
-  async main() {
-    try {
-      this.config = await this.getMutableConfig();
-      if (this.mayRequireToken()) return;
-      const termGroups = await getTermGroups(this.config.termgroups, this.app);
-      const prevTranspose = this.settings.transpose;
-      Object.assign(this.settings, structuredClone(this.config.settings), this.controlsRenderer.getSettings());
-      this.dom.loadingDiv.selectAll("*").remove();
-      this.dom.loadingDiv.html("").style("display", "").style("position", "relative").style("left", "45%");
-      this.dom.svg.style("opacity", 0.1).style("pointer-events", "none");
-      delete this.clickedClusterIds;
-      delete this.clickedLeftClusterIds;
-      try {
-        setComputedConfig(this.config);
-        const promises = [];
-        if (this.setHierClusterData) promises.push(this.setHierClusterData());
-        promises.push(this.setData());
-        this.dom.loadingDiv.html("Processing data ...");
-        await Promise.all(promises);
-        const warnings = this.data.warnings.join("\n");
-        this.dom.warningDiv.style("display", warnings.length ? "" : "none").html(warnings);
-        this.applyLegendValueFilter();
-        if (this.combineData) this.combineData();
-        this.app.save({ type: "plot_edit", id: this.id, config: this.config });
-      } catch (e) {
-        if (e == "no data") {
-          this.showNoMatchingDataMessage();
-          return;
-        } else if (this.app.isAbortError(e)) {
-          return;
-        } else {
-          this.dom.svg.style("display", "none");
-          throw e;
-        }
-      }
-      this.termGroups = termGroups;
-      this.dom.loadingDiv.html("Updating ...").style("display", "");
-      this.termOrder = this.getTermOrder(this.data);
-      this.sampleGroups = this.getSampleGroups(this.hierClusterSamples || this.data);
-      this.sampleOrder = this.getSampleOrder(this.data);
-      this.setLayout();
-      if (this.setHierColorScale) this.setHierColorScale(this.hierClusterData.clustering);
-      if (!this.sampleOrder?.length) {
-        this.showNoMatchingDataMessage();
-      }
-      this.controlsRenderer.main();
-      this.serieses = this.getSerieses(this.data);
-      this.dom.loadingDiv.html("Rendering ...");
-      if (this.plotDendrogramHclust) this.plotDendrogramHclust();
-      this.render();
-      this.mayDisplayCohortMessage();
-      this.dom.svg.style("display", "").style("opacity", 1).style("pointer-events", "");
-      const [xGrps, yGrps] = !this.settings.matrix.transpose ? ["sampleGrps", "termGrps"] : ["termGrps", "sampleGrps"];
-      const d = this.dimensions;
-      this.clusterRenderer.main({
-        settings: this.settings.matrix,
-        xGrps: this[xGrps],
-        yGrps: this[yGrps],
-        dimensions: d
-      });
-      this.legendRenderer(this.legendData, {
-        settings: Object.assign({}, this.settings.legend, {
-          svgw: Math.max(400, d.mainw + d.xOffset - this.settings.matrix.margin.right),
-          svgh: d.mainh + d.yOffset,
-          dimensions: d,
-          padleft: this.settings.legend.padleft
-          //+ d.xOffset
-        })
-      });
-      await this.adjustSvgDimensions(prevTranspose);
-      this.controlsRenderer.main();
-      if (this.data.removedHierClusterTerms) {
-        for (const r of this.data.removedHierClusterTerms) {
-          sayerror(this.dom.errorDiv, r.text + ": " + r.lst.join(", "));
-        }
-      }
-    } catch (e) {
-      const message = this.app.vocabApi.tokenVerificationMessage;
-      this.mayRequireToken(message);
-      if (!message) {
-        this.app.tip.hide();
-        this.dom.loadingDiv.style("display", "none");
-        throw e;
-      }
-    }
-    this.resetInteractions();
-  }
-  showNoMatchingDataMessage() {
-    this.forcedSampleCount = 0;
-    this.dom.svg.style("opacity", 1e-3).style("display", "none");
-    if (this.termOrder && this.dimensions) this.controlsRenderer.main({ sampleCount: 0 });
-    this.dom.loadingDiv.html("");
-    const div = this.dom.loadingDiv.append("div").style("display", "inline-block").style("text-align", "center").style("position", "relative").style("left", "-150px");
-    div.append("div").style("margin", "5px 10px").html("No matching cohort sample data for the current gene list.");
-    if (this.settings.matrix.showHints?.includes("genesetEdit")) {
-      const div1 = div.append("div").style("margin", "5px 10px");
-      div1.append("span").html("You may change the selected cohort,");
-      if (this.config.legendGrpFilter?.lst.length || this.config.legendValueFilter?.lst.length) {
-        const cnvBtn = this.controlsRenderer.btns.filter((d) => d.label == "CNV")?.node();
-        if (cnvBtn) {
-          div1.append("br");
-          div1.append("span").html("show hidden ");
-          div1.append("span").html("CNV").style("cursor", "pointer").style("text-decoration", "underline").on("click", () => {
-            cnvBtn.click();
-          });
-        }
-        const mutationBtn = this.controlsRenderer.btns.filter((d) => d.label == "Mutation")?.node();
-        if (cnvBtn && mutationBtn) div1.append("span").html(" or ");
-        if (mutationBtn) {
-          div1.append("span").style("cursor", "pointer").style("text-decoration", "underline").html("Mutation").on("click", () => {
-            mutationBtn.click();
-          });
-        }
-        if (cnvBtn || mutationBtn) div1.append("span").html(" data,");
-      }
-      div1.append("br");
-      div1.append("span").html("or edit the gene list from the ");
-      div1.append("span").style("cursor", "pointer").style("text-decoration", "underline").html("Gene Set Edit Group menu.").on("click", () => {
-        const GenesBtn = this.controlsRenderer.btns.filter((d) => d.label == "Genes")?.node().click();
-        const i = setInterval(() => {
-          const editBtn = this.app.tip.d.selectAll("button").filter(function() {
-            return this.innerHTML == "Edit Group";
-          }).node();
-          if (editBtn) {
-            editBtn.click();
-            clearInterval(i);
-          }
-        }, 100);
-      });
-    }
-    this.dom.svg.style("display", "none");
-  }
-  mayDisplayCohortMessage() {
-    const msg = deepEqual(this.state.filter0, this.prevFilter0) ? "" : "The gene list is persisted across cohorts.";
-    if (msg) {
-      this.dom.loadingDiv.html("");
-      const div = this.dom.loadingDiv.append("div").style("display", "inline-block").style("text-align", "center").style("position", "relative").style("left", "-150px");
-      div.append("div").html(msg);
-      if (this.settings.matrix.showHints?.includes("genesetEdit")) {
-        const div1 = div.append("div");
-        div1.append("span").html(" You may edit the gene list from the ");
-        div1.append("span").style("cursor", "pointer").style("text-decoration", "underline").html("Gene Set Edit Group menu.").on("click", () => {
-          const GenesBtn = this.controlsRenderer.btns.filter((d) => d.label == "Genes")?.node().click();
-          const i = setInterval(() => {
-            const editBtn = this.app.tip.d.selectAll("button").filter(function() {
-              return this.innerHTML == "Edit Group";
-            }).node();
-            if (editBtn) {
-              editBtn.click();
-              clearInterval(i);
-            }
-          }, 100);
-        });
-      }
-    }
-    this.dom.loadingDiv.style("display", msg ? "" : "none");
-  }
-  sampleKey(s) {
-    return s.row.sample;
-  }
-  sampleLabel(s) {
-    return s.label || s.row._ref_.label || "";
-  }
-  sampleGrpKey(s) {
-    return s.grp.name;
-  }
-  sampleGrpLabel(s) {
-    return s.grp.label || s.grp.name || "";
-  }
-  termKey(t) {
-    return t.tw.$id;
-  }
-  termLabel(t) {
-    return t.label;
-  }
-  termGrpKey(t) {
-    return t.grp.name;
-  }
-  termGrpLabel(t) {
-    return t.grp.label || t.grp.name || [{ text: "\u22EE", dx: 3, cls: "sjpp-exclude-svg-download" }];
-  }
-  destroy() {
-    select_default(window).on(`resize.sjpp-${self.id}`, null);
-  }
-};
-for (const m of [matrix_data_exports, matrix_groups_exports, matrix_layout_exports, matrix_serieses_exports, matrix_legend_exports]) {
-  for (const methodName in m) {
-    Matrix.prototype[methodName] = m[methodName];
-  }
-}
-var matrixInit = getCompInit(Matrix);
-var componentInit = matrixInit;
-function makeChartBtnMenu(holder, chartsInstance) {
-  chartsInstance.dom.tip.clear();
-  const menuDiv = holder.append("div");
-  if (chartsInstance.state.termdbConfig.matrixplots) {
-    for (const plot of chartsInstance.state.termdbConfig.matrixplots) {
-      menuDiv.append("button").style("margin", "10px").style("padding", "10px 15px").style("border-radius", "20px").style("border-color", "#ededed").style("display", "inline-block").text(plot.name).on("click", async () => {
-        chartsInstance.dom.tip.hide();
-        const config = await chartsInstance.app.vocabApi.getMatrixByName(plot.name);
-        config.preBuiltPlotTitle = plot.name;
-        chartsInstance.app.dispatch({
-          type: "plot_create",
-          config
-        });
-      });
-    }
-  }
-  const chart = {
-    clickTo: chartsInstance.showTree_selectlst,
-    chartType: "matrix",
-    usecase: { target: "matrix", detail: "termgroups" },
-    processSelection: (lst) => {
-      return [
-        {
-          name: "",
-          lst: lst.map((term) => {
-            return { term };
-          })
-        }
-      ];
-    }
-  };
-  chartsInstance.showTree_selectlst(chart);
-}
-
-export {
-  Matrix,
-  matrixInit,
-  componentInit,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=chunk-APOHXHKH.js.map

package/dist/chunk-AQ4OP4GR.js

@@ -1,39 +0,0 @@
-import {
-  isNumeric
-} from "./chunk-TV74I3Y5.js";
-
-// common/urlmap.js
-function urlmap_default(search = "", log = console.warn) {
-  const location = search ? { search } : window.location;
-  const urlp = /* @__PURE__ */ new Map();
-  for (const s of location.search.substr(1).split("&")) {
-    if (!s) continue;
-    const l = s.split("=");
-    if (l.length == 2 && l[0] != "" && l[1] != "") {
-      let value = decodeURIComponent(l[1]);
-      if (
-        // assume JSON encoding when the string is enclosed by matching characters below
-        value.startsWith('"') && value.endsWith('"') || value.startsWith("{") && value.endsWith("}") || value.startsWith("[") && value.endsWith("]")
-      ) {
-        try {
-          value = JSON.parse(value);
-        } catch (e) {
-          log(e);
-        }
-      } else if (isNumeric(value)) {
-        value = Number(value);
-      }
-      urlp.set(l[0].toLowerCase(), value);
-    } else if (l.length > 2) {
-      log(`unexpected '=' character in the URL parameter value for '${l[0]}'`);
-    } else {
-      log(`Invalid url parameter: '${s}'`);
-    }
-  }
-  return urlp;
-}
-
-export {
-  urlmap_default
-};
-//# sourceMappingURL=chunk-AQ4OP4GR.js.map