@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/notify-CJGEVJGO.js

@@ -1,234 +0,0 @@
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import "./chunk-HFNDKYVF.js";
-
-// src/notify.ts
-var sseMessageStorageKey = "sjpp-sse-message";
-var notifyDiv = setNotifyDiv();
-var notifyElem = notifyDiv.node();
-var refresh = notifyElem.__ppRefresh;
-var sse;
-function notify(_data, now) {
-  const data = _data.filter((d) => d.status != "ok" || !d.time || now - d.time < 5e3 || refresh.lastCall < d.time);
-  const divs = notifyDiv.selectAll(`.sjpp-sse-message`).data(data, (d) => d.key);
-  divs.exit().filter((d) => !d.duration).remove();
-  divs.style("color", getColor).style("border", getBorder).html(getHtml).each(function(d) {
-    if (d.duration) {
-      setTimeout(
-        () => select_default(this).transition().duration(d.duration || 0).style("opacity", 0).remove(),
-        d.duration
-      );
-    }
-  });
-  divs.enter().append("div").attr("class", "sjpp-sse-message").style("margin", "5px").style("padding", "5px").style("border", getBorder).style("color", getColor).html(getHtml).each(function(d) {
-    if (d.duration) {
-      setTimeout(
-        () => select_default(this).transition().duration(d.duration).style("opacity", 0).remove(),
-        d.duration
-      );
-    }
-  });
-  return data;
-}
-function setNotifyDiv() {
-  const divId = `#sjpp-notify-div-sse-refresh`;
-  const notifyElem2 = document.body.querySelector(divId);
-  let notifyDiv2;
-  if (notifyElem2) notifyDiv2 = select_default(notifyElem2);
-  else {
-    notifyDiv2 = select_default("body").append("div").attr("id", divId.slice(1)).style("position", "fixed").style("top", `16px`).style("right", "10px").style("font-size", "1.2em").style("background-color", "rgba(250, 250, 250, 0.75)").style("z-index", 1e4);
-    notifyDiv2.node().__ppRefresh = setRefresh(notifyDiv2);
-  }
-  return notifyDiv2;
-}
-function getHtml(d) {
-  return `${d.key}: ${d.message}`;
-}
-function getColor(d) {
-  return d.color || (d.status == "ok" ? "green" : "red");
-}
-function getBorder(d) {
-  return `1px solid ${d.color || "#000"}`;
-}
-function setRefresh(notifyDiv2) {
-  const refresh2 = {
-    // used in both sessionStorage and serverconfig.features
-    key: "sseRefreshMode",
-    // default starting mode, may be replaced by:
-    // - using the rendered dom.select dropdown (tab-specific behavior)
-    // - setting sessionStorage.setItem(/*refresh.key*/, ) manually (tab-specific)
-    // - setting serverconfig.features[/*refresh.key*/] (applies across tabs)
-    mode: "full_except_on_unhide",
-    // available mode options
-    modeOptions: {
-      appOnly: "call runproteinpaint() on the same DOM element, with the original argument + any HMR state",
-      appOnly_except_on_unhide: "same as reload, except when a hidden browser tab is made visible",
-      full: "call window.reload() to refresh from URL params and/or runpp() arguments, this may have less memory leaks than the default approach",
-      full_except_on_unhide: "same as full reload, except when a hidden browser tab is made visible",
-      none: "do not refresh the app view"
-    },
-    // the callback to call when a notification includes `reload: true`,
-    // will be overriden by setRefreshCallback()
-    callback: () => window.location.reload(),
-    // the Unix timestamp when callback() was last called
-    lastCall: Date.now(),
-    mostRecentMsg: 0,
-    dom: {},
-    // sse = the connection to /sse route
-    sse: void 0,
-    update(mode) {
-      if (!refresh2.modeOptions[mode]) {
-        console.log(`invalid refresh.mode='${mode}'`);
-        return;
-      }
-      refresh2.mode = mode;
-      refresh2.dom.select.property("value", mode);
-      if (sessionStorage.getItem(refresh2.key) != mode) {
-        sessionStorage.setItem(refresh2.key, mode);
-      }
-    },
-    destroy() {
-      disconnect(refresh2.sse);
-      for (const k of Object.keys(refresh2.dom)) {
-        if (typeof refresh2.dom[k] == "function") refresh2.dom[k].remove();
-        delete refresh2.dom[k];
-      }
-    }
-  };
-  const features = JSON.parse(sessionStorage.getItem("optionalFeatures") || "{}");
-  refresh2.mode = sessionStorage.getItem(refresh2.key) || features[refresh2.key] || refresh2.mode;
-  sessionStorage.setItem(refresh2.key, refresh2.mode);
-  const handleCls = ".sja-sse-refresh-opts-div";
-  notifyDiv2.selectAll(handleCls).remove();
-  const elem = notifyDiv2.insert("div", "div").attr("class", handleCls.slice(1)).style("text-align", "right");
-  const s = {
-    w: "32px",
-    h: "24px",
-    o: 0.5,
-    bg: "#ececec"
-  };
-  const handle = elem.append("div").style("display", "inline-block").style("width", s.w).style("height", s.h).style("overflow", "hidden").style("background-color", s.bg).on("mouseover", function() {
-    handle.style("width", "").style("height", "").style("opacity", "").style("background-color", "");
-  }).on("mouseout", function() {
-    handle.style("width", s.w).style("height", s.h).style("opacity", s.o).style("background-color", s.bg);
-  });
-  const dom = {
-    elem,
-    label: handle.append("label")
-  };
-  dom.label.append("span").style("font-family", "consola arial").style("font-size", "1rem").attr("title", "Click on the select input and hover over an option for details").html(`SSE refresh mode (tab-specific) <br/>`);
-  dom.select = dom.label.append("select").on("change", () => {
-    refresh2.mode = refresh2.dom.select.property("value");
-    sessionStorage.setItem(refresh2.key, refresh2.mode);
-  });
-  dom.select.selectAll("option").data(Object.keys(refresh2.modeOptions)).enter().append("option").attr("value", (key) => key).attr("title", (key) => refresh2.modeOptions[key]).property("selected", (key) => key == refresh2.mode).html((key) => key);
-  refresh2.dom = dom;
-  return refresh2;
-}
-function setRefreshCallback(callback) {
-  refresh.callback = callback;
-}
-var host = sessionStorage.getItem("hostURL") || window.testHost || "";
-var sseUrl = host.endsWith("/") ? `${host}sse` : `${host}/sse`;
-if (!document.hidden) setSse();
-function setSse() {
-  if (sse && sse == refresh.sse && sse.readyState != 2) return;
-  if (refresh.sse) disconnect(refresh.sse);
-  sse = new EventSource(sseUrl);
-  refresh.sse = sse;
-  sse.onmessage = (event) => {
-    if (sse != refresh.sse) {
-      disconnect(sse);
-      return;
-    }
-    const data = JSON.parse(event.data);
-    if (!data.length) return;
-    handleMessageData(data, { save: true });
-  };
-  sse.onerror = (_) => {
-    if (sse != refresh.sse) sse.close();
-  };
-}
-function handleMessageData(_data, opts = {}) {
-  if (!_data.length) return;
-  const now = Date.now();
-  const data = [..._data];
-  if (data.length && (refresh.mode == "none" || opts.unhidden)) {
-    data.unshift({
-      key: "skipped refresh",
-      message: "no auto-refresh",
-      status: "ok",
-      color: "black",
-      duration: 2500,
-      reload: false,
-      time: Date.now()
-    });
-  }
-  const renderedData = notify(data, now);
-  if (data[0]?.key == "skipped refresh") return;
-  const mostRecentMsg = Math.max(0, ...renderedData.map((d) => d.time));
-  if (opts.save) localStorage.setItem(sseMessageStorageKey, JSON.stringify(data));
-  if (mostRecentMsg && mostRecentMsg - refresh.lastCall > 100) {
-    refresh.lastCall = refresh.mostRecentMsg ? mostRecentMsg : Math.max(mostRecentMsg, now);
-    refresh.mostRecentMsg = mostRecentMsg;
-    if (refresh.mode == "none") {
-    } else if (refresh.mode == "appOnly") {
-      console.clear();
-      if (refresh.pendingCall) clearTimeout(refresh.pendingCall);
-      refresh.pendingCall = setTimeout(refresh.callback, 500);
-    } else if (refresh.mode == "full") {
-      if (refresh.pendingCall) clearTimeout(refresh.pendingCall);
-      refresh.pendingCall = setTimeout(() => window.location.reload(), 500);
-    } else if (!refresh.modeOptions[refresh.mode]) {
-      console.warn(`invalid value ${refresh.key}='${refresh.mode}', triggering refresh instead`);
-      console.clear();
-      if (refresh.pendingCall) clearTimeout(refresh.pendingCall);
-      refresh.pendingCall = setTimeout(refresh.callback, 500);
-    }
-  }
-}
-function disconnect(sse2) {
-  if (!sse2) return;
-  if (sse2.readyState != 2) sse2.close();
-  if (sse2 == refresh.sse) delete refresh.sse;
-  delete sse2.onmessage;
-}
-document.onvisibilitychange = () => {
-  if (document.hidden) {
-    disconnect(refresh.sse);
-  } else {
-    const msg = localStorage.getItem(sseMessageStorageKey);
-    const data = JSON.parse(msg || "[]");
-    const opts = { unhidden: refresh.mode.endsWith("except_on_unhide") };
-    if (!refresh.lastUnhide) refresh.lastUnhide = 0;
-    handleMessageData(
-      data.filter((m) => !m.key.includes("skipped") && m.time > refresh.lastUnhide),
-      opts
-    );
-    if (!refresh.sse || refresh.sse.readyState === 2) {
-      setSse();
-    } else {
-      console.warn("will reuse sse connection");
-    }
-  }
-};
-window.onstorage = (event) => {
-  if (refresh.sse || document.hidden) return;
-  switch (event.key) {
-    case refresh.key:
-      refresh.update(event.newValue);
-      break;
-    case sseMessageStorageKey:
-      {
-        const msg = localStorage.getItem(sseMessageStorageKey);
-        const data = JSON.parse(msg || "[]");
-        handleMessageData(data);
-      }
-      break;
-  }
-};
-export {
-  setRefreshCallback
-};
-//# sourceMappingURL=notify-CJGEVJGO.js.map

package/dist/oncomatrix-RRJWFDVF.js

@@ -1,293 +0,0 @@
-import {
-  appInit
-} from "./chunk-KLV7RCJM.js";
-import "./chunk-762BT2DY.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-HZETQJGD.js";
-import {
-  fillTermWrapper,
-  vocabInit
-} from "./chunk-KBYRXJ6Y.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-Y7S3EY6T.js";
-import {
-  dofetch3
-} from "./chunk-RCYTUKAJ.js";
-import "./chunk-A6TQGNDQ.js";
-import "./chunk-HYZG6OPC.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-B2F23ESD.js";
-import "./chunk-IQIXGTQV.js";
-import "./chunk-UCLS2SVB.js";
-import {
-  copyMerge
-} from "./chunk-MVTCBVSX.js";
-import "./chunk-F6V4AYWP.js";
-import "./chunk-5OHXYXLD.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-JOT4WDJE.js";
-import "./chunk-OTCYJP7G.js";
-import "./chunk-GXINX3WK.js";
-import "./chunk-SOED2SLH.js";
-import "./chunk-XRVBHNCW.js";
-import "./chunk-BEWDIM6H.js";
-import "./chunk-IH7ILDJS.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-SEEYV6P2.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// gdc/oncomatrix.js
-var gdcGenome = "hg38";
-var gdcDslabel = "GDC";
-async function init(arg, holder, genomes) {
-  const toolGenome = arg.genome || gdcGenome;
-  const toolDslabel = arg.dslabel || gdcDslabel;
-  const genome = genomes[toolGenome];
-  try {
-    if (!genome) throw toolGenome + " missing";
-    const settings = arg.settings || {};
-    if (typeof settings != "object") throw "arg.settings{} not object";
-    if (!settings.matrix) settings.matrix = {};
-    if (typeof settings.matrix != "object") throw "arg.settings.matrix{} not object";
-    if (!settings.matrix.geneFilter) settings.matrix.geneFilter = "CGC";
-    if (!Number.isInteger(settings.matrix.maxGenes)) settings.matrix.maxGenes = 50;
-    if (arg.filter0 && typeof arg.filter0 != "object") throw "arg.filter0 not object";
-    const vocabApi = await vocabInit({
-      state: { vocab: { genome: toolGenome, dslabel: toolDslabel } }
-    });
-    vocabApi.getTermdbConfig();
-    const plotAppApi = await appInit({
-      holder: select_default(arg.holder).select(".sja_root_holder"),
-      genome,
-      state: copyMerge(
-        {
-          genome: toolGenome,
-          dslabel: toolDslabel,
-          termfilter: { filter0: arg.filter0 },
-          plots: [
-            // initialize with a geneset component, in case the genes lst is empty.
-            // This will be replaced with the actual matrix/hierCluster app once
-            // a valid geneset is selected.
-            {
-              chartType: "geneset",
-              toolName: "OncoMatrix",
-              settings: {
-                maxGenes: settings.matrix.maxGenes,
-                geneFilter: settings.matrix.geneFilter
-              }
-            }
-          ]
-        },
-        arg.state || {}
-      ),
-      app: arg.opts?.app || {},
-      geneset: {
-        mode: "geneVariant",
-        // consistent mode value as GeneSetEdit
-        genome,
-        genes: arg.genes,
-        reactsTo(action) {
-          if (action.type.startsWith("plot_")) return action.id === this.id;
-          if (action.type.startsWith("filter")) return true;
-          if (action.type == "app_refresh") return true;
-        },
-        showWaitMessage(div) {
-          div.style("margin", "20px");
-          div.append("div").text("Loading the top mutated genes in the current cohort...");
-        },
-        async callback(_genesetCompApi, twlst) {
-          if (!_genesetCompApi) return;
-          genesetCompApi = _genesetCompApi;
-          if (!matrixApi) {
-            const plotConfig = plotAppApi.getState().plots.find((p) => p.chartType == "matrix");
-            if (plotConfig) matrixApi = plotAppApi.getComponents(`plots.${plotConfig.id}`);
-          }
-          const termgroups = [
-            ...arg.termgroups || [],
-            {
-              //name: 'Gene Expression',
-              lst: twlst
-            }
-          ];
-          if (matrixApi) {
-            plotAppApi.dispatch({
-              type: "plot_edit",
-              id: matrixApi.id,
-              config: { termgroups }
-            });
-          } else {
-            plotAppApi.dispatch({
-              type: "plot_create",
-              config: {
-                chartType: "matrix",
-                // avoid making a dictionary request when there is no gene data;
-                // if there is gene data, then the arg.termgroups can be submitted and rehydrated on app/store.init()
-                termgroups,
-                divideBy: arg.divideBy || void 0,
-                // moved default settings to gdc.hg38.js termdb[chartType].settings
-                // but can still override in the runpp() argument
-                settings
-              }
-            });
-          }
-        }
-      },
-      recover: {
-        undoHtml: "Undo",
-        redoHtml: "Redo",
-        resetHtml: "Restore",
-        hide(state) {
-          return state.plots[0]?.chartType != "matrix";
-        },
-        adjustTrackedState: (state) => {
-          const s = structuredClone(state);
-          delete s.termfilter.filter0;
-          if (s.plots) {
-            for (const plot of s.plots) {
-              if (!plot.termgroups) continue;
-              for (const grp of plot.termgroups) {
-                if (!grp.lst) continue;
-                for (const tw of grp.lst) {
-                  if (!tw?.term) continue;
-                  delete tw.term.category2samplecount;
-                  delete tw.term.values;
-                }
-              }
-            }
-          }
-          return s;
-        }
-      },
-      matrix: copyMerge(
-        {
-          reactsTo(action) {
-            if (action.type.startsWith("plot_")) return action.id === this.id;
-            if (action.type.startsWith("filter")) return true;
-            if (action.type == "app_refresh") return true;
-          },
-          // these will display the inputs together in the Genes menu,
-          // instead of being rendered outside of the matrix holder
-          customInputs: {
-            genes: [
-              {
-                label: `Maximum # Genes`,
-                title: "Limit the number of displayed genes",
-                type: "number",
-                chartType: "matrix",
-                settingsKey: "maxGenes",
-                callback: async (value) => {
-                  for (const key in arg.opts?.app?.callbacks) {
-                    if (key.startsWith("preDispatch")) {
-                      arg.opts?.app?.callbacks[key]();
-                      break;
-                    }
-                  }
-                  const genes = await getGenes(
-                    arg,
-                    { maxGenes: value, geneFilter: settings.matrix.geneFilter },
-                    vocabApi
-                  );
-                  api.update({
-                    termgroups: [{ lst: genes }],
-                    settings: {
-                      matrix: { maxGenes: value }
-                    }
-                  });
-                }
-              }
-            ]
-          },
-          callbacks: {
-            "firstRender.gdcMatrix": async (matrixApi2) => {
-              matrixApi2.on("firstRender.gdcMatrix", null);
-              if (!genesetCompApi) return;
-              plotAppApi.dispatch({
-                type: "plot_delete",
-                id: genesetCompApi.id
-              });
-              genesetCompApi = void 0;
-            }
-          }
-        },
-        arg.opts?.matrix || {}
-      )
-    });
-    let matrixApi, genesetCompApi;
-    const api = {
-      getState: () => plotAppApi.getState(),
-      destroy: () => plotAppApi.destroy(),
-      update: async (arg2) => {
-        if (!matrixApi) {
-          const plotConfig = plotAppApi.getState().plots.find((p) => p.chartType == "matrix");
-          if (plotConfig) matrixApi = plotAppApi.getComponents(`plots.${plotConfig.id}`);
-        }
-        if (arg2.genes) {
-          plotAppApi.dispatch({
-            type: "plot_edit",
-            id: matrixApi.id,
-            config: {
-              termgroups: [
-                {
-                  lst: await Promise.all(
-                    arg2.genes.map(async (g) => {
-                      return await fillTermWrapper(
-                        {
-                          term: { gene: g.gene, type: "geneVariant", name: g.gene }
-                        },
-                        vocabApi
-                      );
-                    })
-                  )
-                }
-              ]
-            }
-          });
-        } else if ("filter0" in arg2) {
-          plotAppApi.dispatch({
-            type: "filter_replace",
-            filter0: arg2.filter0
-          });
-        } else if (matrixApi) {
-          plotAppApi.dispatch({
-            type: "plot_edit",
-            id: matrixApi.id,
-            config: arg2
-          });
-        }
-      },
-      triggerAbort: (_) => plotAppApi.triggerAbort(_)
-    };
-    return api;
-  } catch (e) {
-    throw e;
-  }
-}
-async function getGenes(arg, settings, vocabApi) {
-  const body = {
-    genome: gdcGenome,
-    dslabel: arg.dslabel || gdcDslabel,
-    maxGenes: settings.maxGenes,
-    geneFilter: settings.geneFilter
-  };
-  if (arg.filter0) body.filter0 = arg.filter0;
-  const data = await dofetch3("termdb/topMutatedGenes", { body });
-  if (data.error) throw data.error;
-  if (!data.genes) return;
-  return await Promise.all(
-    // do tempfix of "data.genes.slice(0,3).map" for faster testing
-    data.genes.map(async (i) => {
-      return fillTermWrapper({ term: { gene: i.gene, type: "geneVariant" } }, vocabApi);
-    })
-  );
-}
-export {
-  init
-};
-//# sourceMappingURL=oncomatrix-RRJWFDVF.js.map