@sjcrh/proteinpaint-client 2.182.1 → 2.183.1

package/dist/chunk-IQ25XHGX.js

@@ -0,0 +1,335 @@
+import {
+  storeInit
+} from "./chunk-OKIJIYSP.js";
+import {
+  summaryInit
+} from "./chunk-QTGTMFHM.js";
+import {
+  navInit
+} from "./chunk-54P7H5GL.js";
+import {
+  AppBase,
+  downloadSVGsAsPdf,
+  filterRxCompInit,
+  newSandboxDiv,
+  sayerror,
+  vocabInit
+} from "./chunk-2LCTMDCS.js";
+import {
+  importPlot
+} from "./chunk-E5JQ3PN6.js";
+import {
+  Menu
+} from "./chunk-A6TQGNDQ.js";
+import {
+  AppApi,
+  getCompInit,
+  multiInit
+} from "./chunk-MVTCBVSX.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+
+// mass/plot.js
+var MassPlot = class _MassPlot {
+  static type = "plot";
+  constructor(opts) {
+    this.type = _MassPlot.type;
+    setRenderers(this);
+    this.initUi(opts);
+  }
+  reactsTo(action) {
+    if (action.type.includes("cache_termq")) return true;
+    if (action.type.endsWith("_group")) return true;
+    if (action.type.startsWith("plot_")) {
+      return action.id === this.id || action.id == this.parentId || action.config?.parentId === this.id || action.parentId === this.id;
+    }
+    if (action.type.startsWith("filter")) return true;
+    if (action.type.startsWith("cohort")) return true;
+    if (action.type == "app_refresh") return true;
+    if (action.type.endsWith("customTerm")) return true;
+  }
+  // !!! NOTE: This getState() method is reused by the plot-specific recover component.
+  // When logging something within getState, it may have been called by either the plot or recover instance
+  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 {
+      termfilter: appState.termfilter,
+      config,
+      groups: appState.groups,
+      // quick fix to skip history tracking as needed
+      _scope_: appState._scope_
+    };
+  }
+  async main() {
+    this.dom.errdiv.style("display", "none").style("background-color", "rgba(255,100,100,0.2)").html("");
+    if (!this.components) await this.setComponents(this.opts);
+  }
+  async setComponents(opts) {
+    const _ = await importPlot(opts.chartType);
+    const promises = {
+      // recover: recoverInit({
+      // 	app: this.app,
+      // 	holder: this.dom.localRecoverDiv,
+      // 	getState: appState => this.getState(appState),
+      // 	reactsTo: action =>
+      // 		action.id == this.id &&
+      // 		(action.type == 'plot_edit' || action.type == 'plot_nestedEdits') &&
+      // 		action._track_ != 'none',
+      // 	plot_id: this.id,
+      // 	maxHistoryLen: 10,
+      // 	hideLabel: true
+      // }),
+      chart: _.componentInit({
+        app: this.app,
+        holder: this.dom.viz,
+        header: this.dom.paneTitleDiv,
+        id: this.id,
+        plotDiv: select_default(this.dom.holder.app_div.node().parentNode),
+        /******* reason for passing plotDiv to chart ********
+        				- this plot instance may allow to launch a new plot as a persistent sandbox
+        				  inside mass plotDiv, maintaining the uniform plot appearance despite it's ad-hoc
+        				  the new plot is not a formal mass plot type, and cannot be done via app.dispatch()
+        				  thus the need to directly access plotDiv
+        				- example: mds3 tk from genome browser can launch disco etc
+        				- having access to plotDiv may offer flexibility for the plot to do stuff
+        
+        				since plot.js has no access to mass app .dom.plotDiv in which all apps are shown,
+        				this workarounds gets the parent node of sandbox.app_div which is app.dom.plotDiv
+        				*/
+        getFilterImage: async () => this.components.filter.getFilterImage()
+      })
+    };
+    if (!this.state.config.hidePlotFilter)
+      promises.filter = filterRxCompInit({
+        app: this.app,
+        vocabApi: this.app.vocabApi,
+        parentId: this.id,
+        holder: this.dom.filterDiv,
+        hideLabel: true,
+        emptyLabel: "+Add new filter",
+        callback: (filter) => {
+          this.app.dispatch({
+            id: this.id,
+            type: "plot_edit",
+            config: { filter }
+          });
+        }
+      });
+    this.components = await multiInit(promises);
+  }
+  destroy() {
+    this.dom.holder.app_div.selectAll("*").remove();
+    this.dom.holder.app_div.remove();
+    for (const key in this.dom) {
+      delete this.dom[key];
+    }
+  }
+};
+var plotInit = getCompInit(MassPlot);
+function setRenderers(self) {
+  self.initUi = function(opts) {
+    const holder = opts.holder;
+    opts.holder.app_div.attr("data-testid", "sjpp-massplot-sandbox-" + opts.chartType);
+    holder.header.style("padding", 0);
+    try {
+      self.dom = {
+        tip: new Menu({ padding: "0px" }),
+        holder,
+        paneTitleDiv: holder.header.append("div").style("display", "inline-block").style("color", "#555").style("padding-left", "7px").style("vertical-align", "sub"),
+        localRecoverDiv: holder.header.append("div").style("display", "inline-block"),
+        filterDiv: holder.header.append("div").style("display", "inline-block").style("zoom", 0.9),
+        body: holder.body.style("white-space", "nowrap").style("overflow-x", "auto"),
+        // will hold no data notice or the page title in multichart views
+        errdiv: holder.body.append("div").style("display", "none").style("padding", "5px").style("background-color", "rgba(255,100,100,0.2)"),
+        // dom.viz will hold the rendered view
+        viz: holder.body.append("div")
+      };
+    } catch (e) {
+      self.dom.errdiv.style("display", "none").text(e);
+    }
+  };
+}
+
+// mass/app.ts
+var MassApp = class extends AppBase {
+  // expected class-specific props
+  constructor(opts, api) {
+    super(opts);
+    this.components = {};
+    this.wasDestroyed = false;
+    this.api = api;
+    if (opts.addLoginCallback) {
+      opts.addLoginCallback(() => this.api.dispatch({ type: "app_refresh" }));
+    }
+    this.type = "app";
+    this.dom = {
+      holder: opts.holder,
+      // do not modify holder style
+      topbar: opts.holder.append("div"),
+      errdiv: opts.holder.append("div"),
+      plotDiv: opts.holder.append("div")
+    };
+    this.plotIdToSandboxId = {};
+  }
+  static {
+    this.type = "app";
+  }
+  async preApiFreeze(api) {
+    try {
+      api.tip = new Menu({ padding: "5px" });
+      api.tip.d.on("keyup", (event) => {
+        if (event.key == "Escape") api.tip.hide();
+      });
+      api.printError = (e) => this.printError(e);
+      api.vocabApi = await vocabInit({
+        app: api,
+        state: { vocab: this.opts.state.vocab },
+        fetchOpts: this.opts.fetchOpts,
+        getDatasetAccessToken: this.opts.getDatasetAccessToken
+      });
+      api.hasWebGL = function() {
+        try {
+          const canvas = document.createElement("canvas");
+          return !!(window.WebGLRenderingContext && (canvas.getContext("webgl") || canvas.getContext("experimental-webgl")));
+        } catch (_) {
+          return false;
+        }
+      };
+      this.opts.state.vocab = api.vocabApi.vocab;
+    } catch (e) {
+      console.log(`preApiFreeze error`, e);
+      throw e;
+    }
+  }
+  async init() {
+    try {
+      const debounceInterval = "debounceInterval" in this.opts ? this.opts.debounceInterval : 0;
+      const embeddedSessionState = this.opts.embeddedSessionState;
+      if (embeddedSessionState) {
+        Object.assign(this.opts.state, embeddedSessionState);
+      }
+      this.store = await storeInit({ app: this.api, state: this.opts.state, debounceInterval });
+      this.state = await this.store.copyState();
+      this.components = {};
+      if (this.state.nav.header_mode != "hidden") {
+        this.components.nav = await navInit({
+          app: this.api,
+          holder: this.dom.topbar,
+          header_mode: this.state && this.state.nav && this.state.nav.header_mode,
+          vocab: this.state.vocab,
+          massSessionDuration: this.state.termdbConfig.massSessionDuration,
+          // this.opts.massSessionDuration
+          pkgver: this.opts.pkgver,
+          downloadPlots: () => {
+            this.downloadPlots();
+          }
+        });
+      }
+      this.components.plots = {};
+      if (this.opts.app?.doNotAwaitInitRender) {
+        this.api.dispatch();
+      } else {
+        await this.api.dispatch();
+      }
+    } catch (e) {
+      this.printError(e);
+      throw e;
+    }
+  }
+  async main() {
+    await this.api.vocabApi.main();
+    this.dom.plotDiv?.style(
+      "display",
+      this.state.nav?.header_mode != "hidden" && this.state.nav?.activeTab == 0 ? "none" : "block"
+    );
+    const newPlots = {};
+    let sandbox;
+    for (const plot of this.state.plots) {
+      if (plot.parentId) continue;
+      if (this.components.plots && !(plot.id in this.components.plots)) {
+        sandbox = newSandboxDiv(this.dom.plotDiv, {
+          close: () => {
+            this.api.dispatch({
+              type: "plot_delete",
+              id: plot.id
+            });
+          },
+          plotId: plot.id,
+          beforePlotId: plot.insertBefore || null,
+          style: {
+            width: "98.5%"
+          }
+        });
+        if (plot.chartType == "summary")
+          newPlots[plot.id] = summaryInit(Object.assign({ app: this.api, holder: sandbox }, plot));
+        else newPlots[plot.id] = plotInit(Object.assign({ app: this.api, holder: sandbox }, plot));
+      }
+    }
+    const numNewPlots = Object.keys(newPlots).length;
+    if (numNewPlots) {
+      await Promise.all(Object.values(newPlots));
+      for (const plotId in newPlots) {
+        this.components.plots[plotId] = await newPlots[plotId];
+      }
+    }
+    for (const plotId in this.components.plots) {
+      if (!this.state.plots.find((p) => p.id === plotId)) {
+        this.components.plots[plotId].destroy();
+        delete this.components.plots[plotId];
+      }
+    }
+  }
+  printError(e) {
+    const errdiv = e.errdiv || this.dom.errdiv;
+    if (errdiv) errdiv.style("display", "").html("").style("background-color", "");
+    sayerror(errdiv || this.opts.holder, "Error: " + (e.message || e.error || e));
+    if (e.stack) console.log(e.stack);
+    this.bus.emit("error");
+    if (this.opts?.debug) console.trace("Trace from MassApp.printError() call");
+  }
+  skipPrevActionAbort(action) {
+    if (!action) return false;
+    if (action.type.startsWith("filter")) return false;
+    if (action.type.startsWith("cohort")) return false;
+    if (action.type == "app_refresh") {
+      if (action.subactions) {
+        return action.subactions.find((a) => a.type.startsWith("filter") || a.type.startsWith("cohort")) ? false : true;
+      }
+    }
+    return true;
+  }
+  async downloadPlots() {
+    const chartImagesAll = [];
+    let i = 1;
+    const values = Object.values(this.components.plots);
+    for (const plot of values) {
+      const chart = plot.type == "plot" ? plot.getComponents("chart") : plot;
+      const chartImages = chart.getChartImages ? chart.getChartImages() : null;
+      if (!chartImages) {
+        console.log(`The ${chart.type} does not support downloading images yet`);
+        continue;
+      }
+      for (const chartImage of chartImages) {
+        if (values.length > 1) chartImage.name = `${i}. ${chartImage.name}`;
+        chartImagesAll.push(chartImage);
+      }
+      i++;
+    }
+    if (chartImagesAll.length > 0) {
+      const filters = [];
+      const globalFilterImg = await this.components.nav.getComponents("filter").getFilterImage();
+      if (globalFilterImg) filters.push(globalFilterImg);
+      downloadSVGsAsPdf(chartImagesAll, "plots", "landscape", filters);
+    } else alert("No chart images available for download");
+  }
+};
+var appInit = AppApi.getInitFxn(MassApp);
+
+export {
+  appInit
+};
+//# sourceMappingURL=chunk-IQ25XHGX.js.map

package/dist/chunk-IQIXGTQV.js

@@ -0,0 +1,84 @@
+// ../shared/utils/src/tree.js
+var hardcode_root = "root";
+var hierarchy_spacer = "...";
+function stratinput(lst, levels) {
+  const lp = /* @__PURE__ */ Object.create(null);
+  const nodes = /* @__PURE__ */ Object.create(null);
+  const size = /* @__PURE__ */ Object.create(null);
+  for (const m of lst) {
+    for (const [i, lev] of levels.entries()) {
+      const thisv = getkey(m, i, levels);
+      const pav = getkey(m, i - 1, levels);
+      if (!m[lev.k]) {
+        if (i > 0) {
+          size[pav] += 1;
+        }
+        break;
+      }
+      lp[thisv] = pav;
+      if (!(thisv in size)) {
+        size[thisv] = 0;
+      }
+      if (!(thisv in nodes)) {
+        const n = {
+          lst: []
+        };
+        if (lev.full) {
+          n.full = m[lev.full];
+        }
+        n.id0 = levels[0].k;
+        n.v0 = m[levels[0].k];
+        if (i == 1) {
+          n.id1 = levels[1].k;
+          n.v1 = m[levels[1].k];
+        }
+        if (i == 2) {
+          n.id2 = levels[2].k;
+          n.v1 = m[levels[2].k];
+        }
+        nodes[thisv] = n;
+      }
+      nodes[thisv].lst.push(m);
+      if (i == levels.length - 1) {
+        size[thisv] += 1;
+      }
+    }
+  }
+  const nlst = [{ id: hardcode_root, name: hardcode_root }];
+  for (const chid in lp) {
+    const paid = lp[chid];
+    const n = nodes[chid];
+    const fields = chid.split(hierarchy_spacer);
+    nlst.push({
+      id: chid,
+      parentId: paid,
+      lst: n.lst,
+      value: size[chid],
+      name: fields[fields.length - 1],
+      // show this instead of chid
+      full: n.full,
+      id0: n.id0,
+      v0: n.v0,
+      id1: n.id1,
+      v1: n.v1,
+      id2: n.id2,
+      v2: n.v2
+    });
+  }
+  return nlst;
+}
+function getkey(m, i, levels) {
+  const klst = [hardcode_root];
+  for (let j = 0; j < i; j++) {
+    klst.push(m[levels[j].k]);
+  }
+  if (i >= 0) {
+    klst.push(m[levels[i].k]);
+  }
+  return klst.join(hierarchy_spacer);
+}
+
+export {
+  stratinput
+};
+//# sourceMappingURL=chunk-IQIXGTQV.js.map

package/dist/chunk-IQIXGTQV.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/utils/src/tree.js"],
+  "sourcesContent": ["/*\ninput:\n1. list of leaf nodes, e.g. mutation cases, each with a set of key-value pairs\n2. levels of hierarchy in an ordered list\n   each item: { k, full }\n   \"k\" and \"full\" are two attribute keys\n\noutput:\na list of items, as input for d3-hierarchy.stratify\none item for each child-parent relationship in the hierarchy\n{\n\tid:\n\tparentId:\n\tlst:\n\tvalue:\n\tname:\n\tfull:\n\tid0:\n\tv0:\n\tid1:\n\tv1:\n\tid2:\n\tv2:\n}\n\nstrange issue: https://github.com/stjude/proteinpaint/commit/c36004d47d4374d2ade719c6ef9e2b848f0850dc\nusing Map for lp, nodes etc will cause memory issue, thus the use of simple objects\n\nto-do: verify this works after a reorg\n*/\n\nconst hardcode_root = 'root'\nconst hierarchy_spacer = '...'\n\nexport function stratinput(lst, levels) {\n\tconst lp = Object.create(null)\n\t// leaf to parent\n\t// k: HM...BALL...sub\n\t// v: HM...BALL\n\n\tconst nodes = Object.create(null)\n\t/*\n\tk: string id of node, e.g. HM...BALL\n\tv: node\n\t\t.full\n\t\t.lst[]\n\t\t\titems from input\n\t*/\n\n\tconst size = Object.create(null)\n\t// only increment size to leaf nodes, so that root.sum() will work\n\t// k: string id of a node, e.g. HM...BALL\n\t// v: number of items\n\n\tfor (const m of lst) {\n\t\tfor (const [i, lev] of levels.entries()) {\n\t\t\tconst thisv = getkey(m, i, levels)\n\t\t\tconst pav = getkey(m, i - 1, levels)\n\n\t\t\t// as mutations can come as {\"subtype\":\"\"}\n\t\t\t// in the sunburst chart at the subtype level, this mutation should not be counted\n\t\t\t// thus the test with !m[lev.k] rather than !(lev.k in m)\n\t\t\tif (!m[lev.k]) {\n\t\t\t\t// stop at this level\n\t\t\t\t// add count to prev level\n\t\t\t\tif (i > 0) {\n\t\t\t\t\tsize[pav] += 1\n\t\t\t\t}\n\t\t\t\tbreak\n\t\t\t}\n\n\t\t\tlp[thisv] = pav\n\t\t\tif (!(thisv in size)) {\n\t\t\t\tsize[thisv] = 0\n\t\t\t}\n\t\t\tif (!(thisv in nodes)) {\n\t\t\t\tconst n = {\n\t\t\t\t\tlst: []\n\t\t\t\t}\n\t\t\t\tif (lev.full) {\n\t\t\t\t\tn.full = m[lev.full]\n\t\t\t\t}\n\n\t\t\t\tn.id0 = levels[0].k\n\t\t\t\tn.v0 = m[levels[0].k]\n\t\t\t\tif (i == 1) {\n\t\t\t\t\tn.id1 = levels[1].k\n\t\t\t\t\tn.v1 = m[levels[1].k]\n\t\t\t\t}\n\t\t\t\tif (i == 2) {\n\t\t\t\t\tn.id2 = levels[2].k\n\t\t\t\t\tn.v1 = m[levels[2].k]\n\t\t\t\t}\n\n\t\t\t\tnodes[thisv] = n\n\t\t\t}\n\t\t\tnodes[thisv].lst.push(m)\n\t\t\tif (i == levels.length - 1) {\n\t\t\t\tsize[thisv] += 1\n\t\t\t}\n\t\t}\n\t}\n\n\tconst nlst = [{ id: hardcode_root, name: hardcode_root }]\n\n\tfor (const chid in lp) {\n\t\tconst paid = lp[chid]\n\t\tconst n = nodes[chid]\n\t\tconst fields = chid.split(hierarchy_spacer)\n\t\tnlst.push({\n\t\t\tid: chid,\n\t\t\tparentId: paid,\n\t\t\tlst: n.lst,\n\t\t\tvalue: size[chid],\n\t\t\tname: fields[fields.length - 1], // show this instead of chid\n\t\t\tfull: n.full,\n\t\t\tid0: n.id0,\n\t\t\tv0: n.v0,\n\t\t\tid1: n.id1,\n\t\t\tv1: n.v1,\n\t\t\tid2: n.id2,\n\t\t\tv2: n.v2\n\t\t})\n\t}\n\treturn nlst\n}\n\nfunction getkey(m, i, levels) {\n\t// if i is 0, return 'root'\n\tconst klst = [hardcode_root]\n\tfor (let j = 0; j < i; j++) {\n\t\tklst.push(m[levels[j].k])\n\t}\n\tif (i >= 0) {\n\t\tklst.push(m[levels[i].k])\n\t}\n\treturn klst.join(hierarchy_spacer)\n}\n"],
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+  "names": []
+}

package/dist/chunk-JLSN2WF5.js

@@ -0,0 +1,95 @@
+import {
+  keyupEnter
+} from "./chunk-2LCTMDCS.js";
+import {
+  dofetch,
+  dofetch3
+} from "./chunk-RCYTUKAJ.js";
+import {
+  require_debounce
+} from "./chunk-LSEFWW72.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// src/gene.js
+var import_debounce = __toESM(require_debounce(), 1);
+var tip;
+function gene_searchbox(p) {
+  if (!tip) {
+    tip = new Menu({ padding: "" });
+    tip.d.style("z-index", 1e3);
+  }
+  const input = p.div.append("input").attr("placeholder", "Search gene").style("width", p.width || "100px");
+  const printdiv = p.resultdiv || (p.tip ? p.tip.d : tip.d);
+  function fold() {
+    if (p.resultdiv) {
+      p.resultdiv.selectAll("*").remove();
+    } else if (p.tip) {
+      p.tip.hide();
+    } else {
+      tip.hide();
+    }
+  }
+  input.on("keyup", (event) => {
+    const str = event.target.value;
+    if (str.length <= 1) {
+      fold();
+      return;
+    }
+    if (keyupEnter(event)) {
+      const hitgene = printdiv.select(".sja_menuoption");
+      if (hitgene.size() > 0) {
+        p.callback(hitgene.text());
+        fold();
+      }
+      return;
+    }
+    debouncer();
+  });
+  input.node().focus();
+  function genesearch() {
+    dofetch("genelookup", { genome: p.genome, input: input.property("value") }).then((data) => {
+      if (data.error) throw data.error;
+      if (!data.hits) throw ".hits[] missing";
+      if (p.resultdiv) {
+        p.resultdiv.selectAll("*").remove();
+      } else if (p.tip) {
+        p.tip.clear().showunder(input.node());
+      } else {
+        tip.clear().showunder(input.node());
+      }
+      for (const name of data.hits) {
+        printdiv.append("div").attr("class", "sja_menuoption").text(name).on("click", () => {
+          p.callback(name);
+          fold();
+        });
+      }
+    }).catch((err) => {
+      printdiv.append("div").text(err.message || err);
+      if (err.stack) console.log(err.stack);
+    });
+  }
+  const debouncer = (0, import_debounce.debounce)(genesearch, 300);
+}
+function findgenemodel_bysymbol(genome, str) {
+  return dofetch3("genelookup", {
+    body: {
+      deep: 1,
+      input: str,
+      genome
+    }
+  }).then((data) => {
+    if (data.error) throw data.error;
+    if (!data.gmlst || data.gmlst.length == 0) return null;
+    return data.gmlst;
+  }).catch((e) => {
+    throw e;
+  });
+}
+
+export {
+  gene_searchbox,
+  findgenemodel_bysymbol
+};
+//# sourceMappingURL=chunk-JLSN2WF5.js.map