@sjcrh/proteinpaint-client 2.221.0 → 2.222.0

package/dist/chunk-XV3KWMG3.js

@@ -0,0 +1,103 @@
+import {
+  SearchHandler,
+  fillTermWrapper,
+  table2col,
+  termsettingInit
+} from "./chunk-4ASBDE27.js";
+
+// plots/summarizeMutationDiagnosis.ts
+async function makeChartBtnMenu(holder, chartsInstance) {
+  let dictTw;
+  {
+    const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.disease;
+    if (!t) throw "defaultTw4correlationPlot missing";
+    dictTw = structuredClone(t);
+    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
+  }
+  const table = table2col({
+    holder: holder.append("div"),
+    margin: "0px 10px 10px 10px",
+    cellPadding: "10px"
+  });
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Mutation Variable");
+    const searchDiv = td2.append("div");
+    const geneSearchInst = new SearchHandler();
+    geneSearchInst.init({
+      holder: searchDiv,
+      app: chartsInstance.app,
+      // required to supply "opts.app.vocabApi" for the search ui
+      genomeObj: chartsInstance.app.opts.genome,
+      msg: "Hit ENTER to launch plot.",
+      /* the geneTw below is used as it comes, so a grouping the user built for this gene
+      elsewhere can be offered here, see keepsQ in client/termdb/TermTypeSearch.ts */
+      keepsQ: true,
+      callback: async (geneTw) => {
+        await fillTermWrapper(geneTw, chartsInstance.app.vocabApi);
+        launchPlot({
+          tw1: dictTw,
+          tw2: geneTw,
+          chartsInstance,
+          holder
+        });
+      }
+    });
+    searchDiv.style("padding", "0px 0px 5px 0px");
+  }
+  {
+    const [td1, td2] = table.addRow();
+    td1.text("Compare Mutations Against");
+    const pillDiv = td2.append("div"), waitDiv = td2.append("div").style("font-size", ".7em").text("LOADING ...");
+    const pill = await termsettingInit({
+      menuOptions: "{edit,replace}",
+      /** presumably this usecase let it restrict to dictionary term ui, and hide genomic queries
+      target="filter" works for gdc since in gdc ds it is overriding filter to dict
+      but is not a general fix for non-gdc ds, which Replace menu will launch genomic+dict options
+      maybe this is okay for non-gdc ds as the default dictTw is meaningful
+      */
+      usecase: { target: "filter" },
+      vocabApi: chartsInstance.app.vocabApi,
+      holder: pillDiv,
+      callback: async (tw) => {
+        waitDiv.text("LOADING ...");
+        try {
+          await pill.main(tw);
+          dictTw = tw;
+          waitDiv.text("Click to edit/replace the variable before searching gene.");
+        } catch (e) {
+          waitDiv.text("Error: " + (e.message || e));
+        }
+      }
+    });
+    try {
+      await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
+      await pill.main(dictTw);
+      waitDiv.text("Click to edit/replace the variable before searching gene.");
+    } catch (e) {
+      waitDiv.text("Error: " + (e.message || e));
+    }
+  }
+}
+function launchPlot({ tw1, tw2, chartsInstance, holder }) {
+  const chart = {
+    config: {
+      chartType: tw1?.term?.type == "survival" ? "survival" : "summary",
+      // TODO define sandbox header with gene+term name
+      term: tw1,
+      term2: tw2
+    }
+  };
+  chartsInstance.plotCreate(chart);
+  holder.selectAll("*").remove();
+  holder.append("div").style("margin", "20px").text("LOADING CHART ...");
+  setTimeout(() => {
+    holder.style("display", "none");
+  }, 1e3);
+}
+
+export {
+  makeChartBtnMenu,
+  launchPlot
+};
+//# sourceMappingURL=chunk-XV3KWMG3.js.map

package/dist/chunk-YFFQ7JTJ.js

@@ -0,0 +1,123 @@
+import {
+  pickCollectionFraction,
+  renderTable
+} from "./chunk-4ASBDE27.js";
+
+// termdb/handlers/termCollection.ts
+var SearchHandler = class {
+  async init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    opts.holder.style("display", "");
+    const termlst = opts.details.termlst ?? [];
+    const memberType = opts.details.memberType || opts.details.type;
+    if (opts.termCollectionSelectionMode === "fraction" && memberType === "numeric") {
+      pickCollectionFraction({
+        holder: opts.holder,
+        term: makeTerm(opts.details, termlst, opts.usecase),
+        callback: (tw) => opts.callback(tw)
+      });
+      return;
+    }
+    const tableDiv = opts.holder.append("div");
+    renderTable({
+      columns: [{ label: "VARIABLES" }],
+      rows: termlst.map((t) => {
+        return [{ value: t.name }];
+      }),
+      div: tableDiv,
+      maxWidth: "30vw",
+      maxHeight: "40vh",
+      // the button is disabled while the selection cannot be submitted
+      noButtonCallback: () => updateSelectBtn(),
+      striped: false,
+      showHeader: true,
+      //false,
+      selectAll: true,
+      columnButtons: void 0,
+      //Leave until table.js is typed
+      buttons: void 0
+    });
+    let categoryTable;
+    let ckSource = [];
+    if (opts.details.categoryKeys) {
+      ckSource = opts.details.categoryKeys;
+      const categoryDiv = opts.holder.append("div").style("margin-top", "15px");
+      const values = opts.details.termlst[0].values || {};
+      categoryTable = categoryDiv.append("div");
+      renderTable({
+        columns: [{ label: "CATEGORIES" }],
+        rows: ckSource.map((ck) => {
+          return [{ value: values[ck.key]?.label ?? ck.key, checked: ck.shown }];
+        }),
+        div: categoryTable,
+        maxWidth: "30vw",
+        maxHeight: "40vh",
+        noButtonCallback: () => updateSelectBtn(),
+        striped: false,
+        showHeader: true,
+        //false,
+        selectAll: true,
+        columnButtons: void 0,
+        //Leave until table.js is typed
+        buttons: void 0
+      });
+    }
+    function getRowChecks(div) {
+      const trs = div.select("table").select("tbody").node().querySelectorAll("tr");
+      return [...trs].map((tr) => tr.querySelectorAll("td")[1]?.querySelector("input")?.checked === true);
+    }
+    function getSelectedTermlst() {
+      const checked = getRowChecks(tableDiv);
+      return termlst.filter((term, i) => checked[i]);
+    }
+    function getCategoryKeys() {
+      if (!categoryTable) return void 0;
+      const checked = getRowChecks(categoryTable);
+      return ckSource.map((ck, i) => ({ key: ck.key, shown: checked[i] }));
+    }
+    function getSelectionError() {
+      if (getSelectedTermlst().length < 2) return "Select at least two variables.";
+      if (getCategoryKeys()?.every((ck) => !ck.shown)) return "Select at least one category.";
+      return void 0;
+    }
+    function updateSelectBtn() {
+      if (!selectBtn) return;
+      const error = getSelectionError();
+      selectBtn.property("disabled", Boolean(error)).attr("title", error || null);
+    }
+    const selectBtn = opts.holder.append("div").style("float", "right").style("padding", "6px 20px").append("button").attr("data-testid", "sjpp-term-collection-select").text("Select").on("click", () => {
+      opts.callback({
+        // makeTerm() extracts propsByTermId (color, etc) for the selected terms
+        ...makeTerm(opts.details, getSelectedTermlst(), opts.usecase),
+        categoryKeys: getCategoryKeys()
+      });
+    });
+    updateSelectBtn();
+  }
+};
+function makeTerm(details, termlst, usecase) {
+  const propsByTermId = {};
+  if (details.propsByTermId) {
+    for (const term of termlst) {
+      if (details.propsByTermId[term.id]) propsByTermId[term.id] = details.propsByTermId[term.id];
+    }
+  }
+  return {
+    type: "termCollection",
+    termIds: termlst.map((term) => term.id),
+    termlst,
+    name: details.name,
+    valueTransform: details.valueTransformByPlots?.[usecase?.target],
+    // memberType = ds.cohort.termdb.termCollections[].type for client code
+    memberType: details.memberType || details.type,
+    categoryKeys: details.categoryKeys,
+    isleaf: true,
+    propsByTermId
+  };
+}
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-YFFQ7JTJ.js.map