@sjcrh/proteinpaint-client 2.191.4 → 2.192.0

package/dist/chunk-VV36JRUF.js

@@ -1,381 +0,0 @@
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  copyMerge
-} from "./chunk-M3J4MINX.js";
-import {
-  mclass
-} from "./chunk-4UWS5Y3N.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// plots/matrix/matrix.sorterUi.js
-var alphabet = `ABCDEFGHIJKLMNOPQRSTUVWXYZ`.split("");
-function getSorterUi(opts) {
-  const { controls, holder } = opts;
-  const parent = controls.parent;
-  const s = structuredClone(parent.config.settings.matrix);
-  const l = s.controlLabels;
-  const tip = new Menu({ padding: "", parent_menu: parent.app.tip?.d.node() });
-  let input, theads = [], sectionData, dragged = {};
-  const self = {
-    dom: { tip },
-    opts,
-    highlightColor: "none",
-    label: `Sort ${l.Samples}`,
-    title: `Set how to sort ${l.samples}`,
-    type: "custom",
-    expanded: opts.expanded || false,
-    expandedSection: opts.expandedSection || "",
-    init(overrides = {}, _opts = {}) {
-      tip.clear().hide();
-      if (parent.config.settings.matrix != s) copyMerge(s, parent.config.settings.matrix);
-      if (s !== overrides) copyMerge(s, overrides);
-      self.settings = s;
-      self.activeOption = structuredClone(s.sortOptions[s.sortSamplesBy]);
-      sectionData = [
-        {
-          label: `For each selected row, sort ${l.samples} by matching data`,
-          notDraggable: true,
-          tiebreakers: [],
-          handler: handleSelectedTerms
-        },
-        ...self.activeOption.sortPriority,
-        {
-          label: `Sort ${l.samples} by name, alphabetically`,
-          notDraggable: true,
-          tiebreakers: []
-        }
-      ];
-      Object.assign(opts, _opts);
-      opts.holder.selectAll("*").remove();
-      const topDiv = opts.holder.append("div").style("text-align", "right");
-      topDiv.append("button").html("Apply").on("click", apply);
-      topDiv.append("button").html("Reset").on("click", (event, d) => self.init());
-      const table = opts.holder.append("table");
-      const tr = table.append("thead");
-      tr.append("th").html("Priority").style("text-align", "left").style("max-width", "0px");
-      tr.append("th").html("Description");
-      tr.append("th").html("Action");
-      let i = 0, j = 0;
-      for (const sd of sectionData) {
-        const hasTbOrder = sd.tiebreakers?.[0]?.order || sd.handler;
-        const thead = table.append("thead").datum(sd).property("draggable", !sd.notDraggable).attr("droppable", true).on("dragstart", trackDraggedSection).on("dragover", highlightSection).on("dragleave", unhighlightSection).on("drop", adjustSortPriority);
-        theads.push(select_default(thead));
-        const tr2 = thead.append("tr").style("background-color", "#eee").on("mouseover", undoMouseoverHighlights);
-        tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("font-weight", 400).html(alphabet[j++]).on("click", hasTbOrder ? toggleSection : null);
-        const td2 = tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("text-align", "left").style("cursor", hasTbOrder ? "pointer" : "").on("click", hasTbOrder ? toggleSection : null);
-        td2.append("span").style("margin-right", "12px").style("font-weight", 400).html(sd.label);
-        tr2.append("th").style("padding", "5px").style("vertical-align", "top").style("text-align", "center").style("font-weight", 400).style("cursor", hasTbOrder ? "pointer" : "").append("span").html(hasTbOrder ? "Details" : " ").on("click", hasTbOrder ? toggleSection : null);
-        const tbody = table.append("tbody").datum(sd).style("display", self.expandedSection == "all" || self.expandedSection == sd.label ? "" : "none");
-        for (const tb of sd.tiebreakers) {
-          if (tb.skip) continue;
-          if (!sd.types?.includes("geneVariant")) {
-            continue;
-          }
-          const tr3 = tbody.append("tr").on("mouseover", undoMouseoverHighlights).datum(tb).attr("draggable", !tb.disabled && sd.types?.length !== 0).attr("droppable", !tb.disabled && sd.types?.length !== 0).on("dragstart", trackDraggedTieBreaker).on("dragover", highlightTieBreaker).on("dragleave", unhighlightTieBreaker).on("drop", adjustTieBreakers);
-          if (!tb.disabled) i++;
-          const td1 = tr3.append("td").attr(
-            "title",
-            tb.disabled ? `This tiebreaker is currently not being used to sort ${l.cases}. Check the box to use.` : `The number indicates the order in which this tiebreaker is used. Unched the box to skip.`
-          ).datum(tb);
-          td1.style("padding", "5px").style("vertical-align", "top").style("text-align", "center");
-          td1.append("span").html(!tb.disabled ? i : "");
-          const td22 = tr3.append("td").style("opacity", tb.disabled ? 0.5 : 1).style("padding", "5px").style("vertical-align", "top").style("max-width", "500px");
-          td22.append("span").html(tb.label || "");
-          if (!tb.disabled) {
-            const label = td22.append("label");
-            label.append("span").html("<br>(use data list order ");
-            if (!tb.isOrdered) tb.isOrdered = false;
-            const checkbox = label.append("input").datum(tb).attr("type", "checkbox").property("checked", tb.isOrdered).style("vertical-align", "bottom").on("change", toggleTieBreakerIsOrdered);
-            label.append("span").html(")");
-            const order = tb.order;
-            td22.append("div").attr("class", "sjpp-matrix-sorter-ui-value").selectAll("div").data(
-              order.map((key, index) => ({
-                lstName: "order",
-                key,
-                cls: mclass[key],
-                tb,
-                dragstart: trackDraggedValue,
-                dragover: highlightValue,
-                dragleave: unhighlightValue,
-                drop: adjustValueOrder,
-                filterByClass: s.filterByClass,
-                index
-              }))
-            ).enter().append("div").style("display", tb.isOrdered ? "block" : "inline-block").each(setValueDiv);
-            if (tb.notUsed?.length) {
-              const notUsed = td22.append("div");
-              notUsed.append("div").attr("data-testid", "sjpp-matrix-sorter-ui-hidden-add").style("display", "inline-block").style("padding", "5x").style("vertical-align", "top").style("padding", "3px 5px").style("cursor", "pointer").html(`+Add`).on("click", showNotUsedValues);
-            }
-          }
-          const td3 = tr3.append("td").style("text-align", "center").style("vertical-align", "top");
-          if (tb.mayToggle) {
-            td3.append("button").datum(tb).html(tb.disabled ? "Enable" : "Disable").on("click", toggleTieBreakerDisabled);
-          }
-        }
-        const lastTr = tbody.append("tr").attr("draggable", true).on("mouseover", undoMouseoverHighlights);
-        lastTr.append("td").html("&nbsp;");
-        const tdNew = lastTr.append("td").style("text-align", "left").html(sd.details && !sd.order?.length ? sd.details : "&nbsp;");
-        if (sd.handler) sd.handler(tdNew, lastTr, tbody);
-        lastTr.append("td").html("&nbsp;");
-      }
-    },
-    toggleSection,
-    trackDraggedSection,
-    highlightSection,
-    unhighlightSection,
-    adjustSortPriority,
-    trackDraggedTieBreaker,
-    highlightTieBreaker,
-    unhighlightTieBreaker,
-    adjustTieBreakers,
-    trackDraggedValue,
-    highlightValue,
-    unhighlightValue,
-    adjustValueOrder,
-    apply
-  };
-  function toggleSection(event, d = { label: "all" }) {
-    self.expandedSection = self.expandedSection === d.label ? "" : d.label;
-    self.expanded = !!self.expandedSection;
-    self.init();
-  }
-  function trackDraggedSection(event, d) {
-    dragged.type = "sortPriority";
-    dragged.data = d;
-    dragged.index = self.activeOption.sortPriority.indexOf(d);
-  }
-  function highlightSection(event, d) {
-    if (dragged.type != "sortPriority" || d == dragged.data) return;
-    event.preventDefault();
-    const i = self.activeOption.sortPriority.indexOf(d);
-    const borderSide = i < dragged.index ? "border-top" : i > dragged.index ? "border-bottom" : "";
-    if (!borderSide) return;
-    select_default(this).selectAll("th").style(borderSide, "2px solid blue");
-  }
-  function unhighlightSection(event, d) {
-    if (dragged.type != "sortPriority") return;
-    event.preventDefault();
-    select_default(this).selectAll("th").style("border", "none");
-  }
-  function adjustSortPriority(event, d) {
-    if (d == dragged.data) return;
-    const i = self.activeOption.sortPriority.indexOf(d);
-    const s2 = parent.config.settings.matrix;
-    self.activeOption.sortPriority.splice(dragged.index, 1);
-    self.activeOption.sortPriority.splice(i, 0, dragged.data);
-    self.init({
-      sortOptions: {
-        [s2.sortSamplesBy]: self.activeOption
-      }
-    });
-  }
-  function trackDraggedTieBreaker(event, d) {
-    dragged.type = "tiebreaker";
-    dragged.data = d;
-    dragged.sectionData = event.target.closest("tbody").__data__;
-    dragged.priorityIndex = self.activeOption.sortPriority.indexOf(dragged.sectionData);
-    dragged.index = dragged.sectionData.tiebreakers.indexOf(d);
-  }
-  function highlightTieBreaker(event, d) {
-    if (dragged.type != "tiebreaker" || d == dragged.data) return;
-    event.preventDefault();
-    const i = dragged.sectionData.tiebreakers.indexOf(d);
-    const borderSide = i < dragged.index ? "border-top" : i > dragged.index ? "border-bottom" : "";
-    if (!borderSide) return;
-    select_default(this).selectAll("td:nth-child(2)").style(borderSide, "2px solid blue");
-  }
-  function unhighlightTieBreaker(event, d) {
-    if (dragged.type != "tiebreaker") return;
-    event.preventDefault();
-    select_default(this).selectAll("td:nth-child(2)").style("border", "none");
-  }
-  function toggleTieBreakerIsOrdered(event, tb) {
-    event.stopPropagation();
-    tb.isOrdered = !tb.isOrdered;
-    self.init({
-      sortOptions: {
-        [s.sortSamplesBy]: self.activeOption
-      }
-    });
-  }
-  function toggleTieBreakerDisabled(event, tb) {
-    event.stopPropagation();
-    tb.disabled = !tb.disabled;
-    self.init({
-      sortOptions: {
-        [s.sortSamplesBy]: self.activeOption
-      }
-    });
-  }
-  function adjustTieBreakers(event, d) {
-    if (dragged.type != "tiebreaker" || d == dragged.data) return;
-    event.preventDefault();
-    const i = dragged.sectionData.tiebreakers.indexOf(d);
-    const s2 = parent.config.settings.matrix;
-    dragged.sectionData.tiebreakers.splice(dragged.index, 1);
-    dragged.sectionData.tiebreakers.splice(i, 0, dragged.data);
-    self.init({
-      sortOptions: {
-        [s2.sortSamplesBy]: self.activeOption
-      }
-    });
-  }
-  function setValueDiv(d) {
-    const title = [];
-    if (d.tb.notUsed?.includes(d.key)) title.push(`- Click on this label to include in used data values.`);
-    if (d.filterByClass[d.key])
-      title.unshift("- Click on the corresponding entry in the matrix legend or Mutation/CNV menus to unhide");
-    if (title.length) title.unshift(`To use this data value for sorting ${l.samples}:`);
-    const skipped = d.tb.notUsed?.includes(d.key);
-    const opacity = d.filterByClass[d.key] == "value" ? 0.5 : 1;
-    const div = select_default(this).attr("aria-label", title.length ? title.join("\n") : `Click to not use this data value to sort ${l.samples}`).attr("draggable", d.tb.isOrdered ? true : false).attr("droppable", d.tb.isOrdered ? true : false).style("width", "fit-content").style("margin-right", "10px").style("overflow", "hidden").style("white-space", "nowrap").style("opacity", opacity).style("cursor", "pointer").on("dragstart", d.dragstart).on("dragover", d.dragover).on("dragleave", d.dragleave).on("drop", d.drop).on("mouseenter", () => toggle.style("opacity", 1)).on("mouseleave", () => toggle.style("opacity", 0)).on("click", () => {
-      if (title.length) {
-        const cls = "sjpp-matrix-sorter-value-note";
-        div.selectAll(`.${cls}`).remove();
-        const note = div.append("div").attr("class", cls).style("max-width", "200px").style("padding", "5px");
-        note.html(title.join("<br>"));
-        if (d.filterByClass[d.key]) return;
-      }
-      const targetLstName = d.lstName == "order" ? "notUsed" : "order";
-      if (!d.tb[targetLstName]) d.tb[targetLstName] = [];
-      const targetLst = d.tb[targetLstName];
-      d.tb[d.lstName].splice(d.index, 1);
-      if (d.lstName == "order") targetLst.unshift(d.key);
-      else targetLst.push(d.key);
-      self.init({
-        sortOptions: {
-          [s.sortSamplesBy]: self.activeOption
-        }
-      });
-    });
-    div.append("div").style("display", "inline-block").style("cursor", "pointer").style("width", "12px").style("height", "12px").style("margin-right", "3px").style("background-color", d.cls.color);
-    div.append("span").style("cursor", "pointer").style("text-decoration", d.filterByClass[d.key] == "case" ? "line-through" : "").html(d.cls.label + (d.filterByClass[d.key] ? " (<i>not used since this value is hidden</i>)" : ""));
-    const toggle = div.append("div").style("display", "inline-block").style("width", "12px").style("cursor", "pointer").style("opacity", 0).style("color", d.lstName == "order" ? "red" : "green").html(d.lstName == "order" ? "&cross;" : "&check;");
-  }
-  function trackDraggedValue(event, d) {
-    event.stopPropagation?.();
-    dragged.type = "value";
-    dragged.data = d;
-    dragged.sectionData = event.target.closest("tbody").__data__;
-    dragged.priorityIndex = self.activeOption.sortPriority.indexOf(dragged.sectionData);
-    dragged.tiebreaker = event.target.closest("tr").__data__;
-    dragged.tbIndex = dragged.sectionData.tiebreakers.indexOf(dragged.priorityIndex);
-    dragged.order = dragged.tiebreaker.order;
-  }
-  function highlightValue(event, d) {
-    event.stopPropagation?.();
-    if (dragged.type != "value" || d == dragged.data) return;
-    if (d.tb != dragged.data.tb) return;
-    event.preventDefault();
-    const i = dragged.order.indexOf(d);
-    select_default(this).style("border", "2px solid blue");
-  }
-  function unhighlightValue(event, d) {
-    event.stopPropagation?.();
-    if (dragged.type != "value") return;
-    event.preventDefault();
-    select_default(this).style("border", "none");
-  }
-  function adjustValueOrder(event, d) {
-    event.stopPropagation?.();
-    if (dragged.type != "value" || d == dragged.data) return;
-    event.preventDefault();
-    const s2 = self.settings;
-    dragged.data.tb[dragged.data.lstName].splice(dragged.data.index, 1);
-    d.tb[d.lstName].splice(d.index, 0, dragged.data.key);
-    const j = s2.hiddenVariants.indexOf(dragged.data.key);
-    const hiddenVariants = structuredClone(s2.hiddenVariants);
-    const filterByClass = structuredClone(s2.filterByClass);
-    if (j != -1) {
-      hiddenVariants.splice(j, 1);
-      filterByClass[dragged.data.key] = false;
-    }
-    self.init({
-      hiddenVariants,
-      filterByClass,
-      sortOptions: {
-        [s2.sortSamplesBy]: self.activeOption
-      }
-    });
-  }
-  function showNotUsedValues(event, tb) {
-    event?.stopPropagation();
-    const availDiv = tip.clear().d.append("div").attr("data-testid", "sjpp-matrix-sorter-ui-hidden-vals").style("margin-top", "3px").style("vertical-align", "top").style("padding-left", "12px");
-    availDiv.selectAll("div").data(
-      tb.notUsed.map((key, index) => ({
-        lstName: "notUsed",
-        key,
-        cls: mclass[key],
-        tb,
-        dragstart: trackDraggedValue,
-        dragover: highlightValue,
-        dragleave: unhighlightValue,
-        drop: adjustValueOrder,
-        filterByClass: s.filterByClass,
-        index
-      }))
-    ).enter().append("div").style("display", "block").each(setValueDiv);
-    tip.showunder(event.target);
-  }
-  function apply() {
-    parent.app.tip?.hide();
-    parent.app.dispatch({
-      type: "plot_edit",
-      id: parent.id,
-      config: {
-        settings: {
-          matrix: {
-            sortOptions: {
-              [s.sortSamplesBy]: self.activeOption
-            }
-          }
-        }
-      }
-    });
-  }
-  function undoMouseoverHighlights() {
-  }
-  function handleSelectedTerms(td, tr) {
-    if (!parent.selectedTermsToSortAgainst?.length) {
-      td.html(`Click on a matrix row label and the left triangle to add an entry here`);
-      return;
-    }
-    const selectedTerms = parent.selectedTermsToSortAgainst.map((t) => {
-      return {
-        t,
-        label: t.tw.term.name + (t.tw.term.type == "geneVariant" ? " alterations" : " values")
-      };
-    });
-    const tbody = select_default(tr.node().parentNode);
-    tbody.selectAll("tr").remove();
-    tbody.selectAll("tr").data(selectedTerms).enter().append("tr").selectAll("td").data((d, i) => [
-      { label: i + 1, textAlign: "center", cursor: "", t: d.t },
-      { label: d.label, textAlign: "left", cursor: "" },
-      {
-        label: "Delete",
-        textAlign: "center",
-        cursor: "pointer",
-        click: parent.unsortSamplesAgainstTerm,
-        data: d
-      }
-    ]).enter().append("td").style("text-align", (d) => d.textAlign).style("cursor", (d) => d.cursor).html((d) => d.label).on("click", (event, d) => d.click?.(event, d));
-  }
-  self.init();
-  self.api = {
-    main: self.init,
-    destroy: () => {
-      opts.holder.selectAll("*").remove();
-    }
-  };
-  if (opts.debug) self.api.Inner = self;
-  return self.api;
-}
-
-export {
-  getSorterUi
-};
-//# sourceMappingURL=chunk-VV36JRUF.js.map

package/dist/chunk-W55XSG6K.js

@@ -1,142 +0,0 @@
-import {
-  runproteinpaint
-} from "./chunk-74ZU4BT6.js";
-
-// test/front.helpers.js
-var serverData = /* @__PURE__ */ Object.create(null);
-function getRunPp(appname = "", defaultArgs = {}, _host = "http://localhost:3000") {
-  const host = window.testHost || _host;
-  const arg = {
-    host: window.testHost || _host,
-    noheader: 1,
-    nobox: true,
-    debug: 1,
-    norecover: true
-  };
-  if (appname == "mass" || appname == "termdb") {
-    defaultArgs.debounceInterval = 0;
-  }
-  if (appname) arg[appname] = defaultArgs;
-  else copyMerge(arg, defaultArgs);
-  const argStr = JSON.stringify(arg);
-  return function runpp(overrides = {}) {
-    const argCopy = JSON.parse(argStr);
-    if (appname) copyMerge(argCopy[appname], overrides);
-    else copyMerge(argCopy, overrides);
-    if (appname && defaultArgs.fetchOpts) {
-      argCopy[appname].fetchOpts = defaultArgs.fetchOpts;
-    }
-    return runproteinpaint(Object.assign(argCopy, { serverData }));
-  };
-}
-function copyMerge(base, ...args) {
-  const target = typeof base == "string" ? JSON.parse(base) : base;
-  for (const arg of args) {
-    if (arg) {
-      const source = typeof base == "string" ? JSON.parse(JSON.stringify(arg)) : arg;
-      for (const key in source) {
-        if (!target[key] || Array.isArray(target[key]) || typeof target[key] !== "object") target[key] = source[key];
-        else copyMerge(target[key], source[key]);
-      }
-    }
-  }
-  return target;
-}
-function rideInit(opts = {}) {
-  const self = new Ride(opts);
-  const rideApi = {
-    // ride on the default event bus
-    to(callback, sub = {}) {
-      self.addToThen(callback, Object.assign({}, opts, sub));
-      return rideApi;
-    },
-    use(triggerFxn, sub = {}) {
-      self.addUseThen(triggerFxn, Object.assign({}, opts, sub));
-      return rideApi;
-    },
-    change(sub = {}) {
-      Object.assign(opts, sub);
-      return rideApi;
-    },
-    // run callback without using bus, with or without timeout
-    run(callback, after = 0) {
-      self.addRunThen(callback, after, opts);
-      return rideApi;
-    },
-    // close the event bus
-    done(test) {
-      if (opts.bus) self.resolved.then(() => opts.bus.on(opts.eventType, null));
-      self.resolved.then(() => {
-        test.end();
-        if (!opts.preserve && test._ok && opts.arg.Inner.app && typeof opts.arg.Inner.app.destroy == "function") {
-          opts.arg.Inner.app.destroy();
-        }
-      }).catch(console.log);
-      return rideApi;
-    }
-  };
-  return Object.freeze(rideApi);
-}
-var Ride = class {
-  // mutable but private access props and methods
-  // when used inside rideInit()
-  constructor(opts) {
-    this.validateOpts(opts);
-    this.resolved = Promise.resolve();
-  }
-  validateOpts(opts) {
-    try {
-      if (opts.eventType && !opts.bus) {
-        if (!opts.arg) throw "must specify opts.bus or opts.arg for rideInit() argument";
-        opts.bus = opts.arg;
-      }
-      if (opts.bus) {
-        if (typeof opts.eventType !== "string") throw "invalid default.eventType";
-        opts.bus.on(opts.eventType, null);
-        return opts;
-      }
-    } catch (e) {
-      console.log(e);
-    }
-  }
-  addToThen(callback, opts) {
-    this.resolved = this.resolved.then(async (triggerFxn) => {
-      opts.bus.on(opts.eventType, null);
-      return new Promise(async (resolve, reject) => {
-        opts.bus.on(opts.eventType, async () => {
-          await sleep(opts.wait);
-          callback(opts.arg);
-          resolve();
-        });
-        if (triggerFxn) await triggerFxn();
-      });
-    });
-  }
-  // prepare a trigger function for use in the pattern
-  // rideInit().use(triggerFxn).to(...)
-  //
-  // .use() enables setting a different opts.arg to be used for triggerFxn
-  //
-  addUseThen(triggerFxn, opts) {
-    this.resolved = this.resolved.then(async (prevTriggerFxn) => {
-      if (typeof prevTriggerFxn == "function") await prevTriggerFxn();
-      await sleep(isNaN(opts.wait) ? 0 : opts.wait);
-      return () => triggerFxn(opts.arg);
-    });
-  }
-  addRunThen(callback, after, opts) {
-    this.resolved = this.resolved.then(async () => {
-      await sleep(typeof after == "number" ? after : 0);
-      callback(opts.arg);
-    });
-  }
-};
-function sleep(ms) {
-  return new Promise((resolve) => setTimeout(resolve, ms));
-}
-
-export {
-  getRunPp,
-  rideInit
-};
-//# sourceMappingURL=chunk-W55XSG6K.js.map

package/dist/chunk-W6ME65LV.js

@@ -1,34 +0,0 @@
-import {
-  appInit
-} from "./chunk-SA7APTJR.js";
-import {
-  TermTypes
-} from "./chunk-NOEAT6CX.js";
-
-// termdb/handlers/ssGSEA.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const genesetDbName = Object.keys(opts.genomeObj.termdbs || {})[0];
-    if (!genesetDbName) throw "genesetDbName missing";
-    await appInit({
-      holder: opts.holder,
-      state: {
-        dslabel: genesetDbName,
-        genome: opts.genomeObj.name,
-        nav: { header_mode: "search_only" }
-      },
-      tree: {
-        click_term: (term) => {
-          this.callback({ id: term.id, type: TermTypes.SSGSEA, name: term.name });
-        }
-      }
-    });
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-W6ME65LV.js.map