@sjcrh/proteinpaint-client 2.213.0 → 2.214.0

package/dist/geneVariant-ZPINPLRP.js

@@ -1,289 +0,0 @@
-import {
-  excludeFilterByTag,
-  fillGroupsetGroups,
-  filterInit,
-  filterPromptInit,
-  getDtTermValues,
-  getNormalRoot,
-  getPillNameDefault,
-  make_radios,
-  renderTable,
-  vocabInit
-} from "./chunk-QI6X4V43.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-7HPICVA4.js";
-import "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-YU7CVG4B.js";
-import "./chunk-HH5JKOE6.js";
-import {
-  getDtsFromGroups
-} from "./chunk-RU2UHH7M.js";
-import {
-  getColors
-} from "./chunk-57Z4VYLM.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import {
-  rgb
-} from "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// termsetting/handlers/geneVariant.ts
-var colorScale = getColors(5);
-function getHandler(self) {
-  return {
-    getPillName(d) {
-      let name = d.name;
-      if (!name) {
-        if (d.genes) name = d.genes.map((g) => g.gene).join(", ");
-        else if (d.chr) name = `${d.chr}:${d.start}-${d.stop}`;
-        else name = d.id || "geneVariant";
-      }
-      return getPillNameDefault(self, { name });
-    },
-    getPillStatus() {
-      let text;
-      const q = self.q;
-      if (q.type == "predefined-groupset") {
-        const groupsetting = self.term.groupsetting;
-        if (!groupsetting?.lst?.length) throw "no predefined groupsets found";
-        const groupset = groupsetting.lst[q.predefined_groupset_idx];
-        text = groupset.name;
-      } else if (q.type == "custom-groupset") {
-        const n = q.customset.groups.length;
-        text = `Divided into ${n} groups`;
-      } else {
-        text = "any variant class";
-      }
-      if (self.term.sampleTypeLabel) {
-        text += ` (${self.term.sampleTypeLabel})`;
-      }
-      return { text };
-    },
-    async showEditMenu(div) {
-      await makeEditMenu(self, div);
-    }
-  };
-}
-async function makeEditMenu(self, _div) {
-  delete self.groups;
-  const div = _div.append("div").style("margin", "10px");
-  div.append("div").style("font-size", "1.2rem").text(self.term.name);
-  const optsDiv = div.append("div").style("margin-top", "10px").style("margin-bottom", "1px");
-  const groupsDiv = div.append("div").style("display", "none").style("margin", "10px").style("vertical-align", "top");
-  optsDiv.append("div").style("font-weight", "bold").text("Group samples");
-  const q = self.q;
-  const isGroupset = q.type == "predefined-groupset" || q.type == "custom-groupset";
-  make_radios({
-    holder: optsDiv,
-    options: [
-      { label: "No sample grouping", value: "noGroup", checked: !isGroupset },
-      { label: "Assign samples to groups", value: "group", checked: isGroupset }
-    ],
-    callback: async (v) => {
-      if (v == "group") {
-        if (q.type == "values") Object.assign(q, { type: "custom-groupset", customset: { groups: [] } });
-        await makeGroupUI(self, groupsDiv);
-      } else {
-        clearGroupset(self);
-        groupsDiv.style("display", "none");
-      }
-    }
-  });
-  if (isGroupset) await makeGroupUI(self, groupsDiv);
-  if (self.usecase?.detail && ["term", "term0", "term2"].includes(self.usecase.detail) || self.opts.geneVariantEditMenuOnlyGrp) {
-    optsDiv.style("display", "none");
-    groupsDiv.style("margin", "0px");
-  }
-  div.append("div").style("margin-top", "25px").append("button").attr("data-testid", "sjpp-ts-gv-editui-applyBtn").text("Apply").on("click", () => {
-    const q2 = self.q;
-    if (q2.type == "predefined-groupset" || q2.type == "custom-groupset") {
-      if (!self.groups?.length) {
-        window.alert("Samples must be assigned to at least one group.");
-        return;
-      } else {
-        const dtLst = getDtsFromGroups(self.groups);
-        Object.assign(q2, { type: "custom-groupset", customset: { groups: self.groups }, dtLst });
-        self.vocabApi.rememberGvQ?.(self.term, q2);
-      }
-    } else {
-      if (q2.type != "values") throw `q.type must be 'values'`;
-    }
-    self.api.runCallback();
-  });
-}
-async function makeGroupUI(self, div) {
-  div.style("display", "block");
-  div.selectAll("*").remove();
-  div.append("div").style("margin", "15px 0px").text(
-    "Group samples by mutation status. Samples are assigned to first possible group. Only tested samples are considered."
-  );
-  const filterTableDiv = div.append("div");
-  const addNewGroupBtnHolder = div.append("div");
-  const q = self.q;
-  if (q.type != "predefined-groupset" && q.type != "custom-groupset") throw "unexpected q.type";
-  if (!self.groups) {
-    let groupset;
-    if (q.type == "predefined-groupset") {
-      const groupsetting = self.term.groupsetting;
-      if (!groupsetting.lst?.length) throw "no predefined groupsets found";
-      await fillGroupsetGroups(self.term, q.predefined_groupset_idx, self.vocabApi);
-      groupset = groupsetting.lst[q.predefined_groupset_idx];
-    } else {
-      groupset = q.customset;
-    }
-    if (!groupset) throw "groupset is missing";
-    if (!Array.isArray(groupset.groups)) throw "groupset.groups is not array";
-    self.groups = structuredClone(groupset.groups);
-  }
-  const dtTerms = structuredClone(self.term.childTerms);
-  for (const dtTerm of dtTerms) {
-    await getDtTermValues(dtTerm, self.filter, self.vocabApi, { withMnames: true });
-  }
-  const vocabApi = vocabInit({ vocab: { terms: dtTerms } });
-  vocabApi.termdbConfig = { queries: self.vocabApi.termdbConfig.queries };
-  vocabApi.vocab.genome = self.vocabApi.vocab?.genome;
-  const filterPrompt = await filterPromptInit({
-    holder: addNewGroupBtnHolder,
-    vocabApi,
-    emptyLabel: "Add group",
-    header_mode: "hide_search",
-    callback: (f) => {
-      const filter2 = getNormalRoot(f);
-      addNewGroup(filter2, self.groups);
-      makeGroupUI(self, div);
-    },
-    debug: self.opts.debug
-  });
-  const filter = structuredClone(self.filter);
-  filterPrompt.main(excludeFilterByTag(filter, "cohortFilter"));
-  if (!self.groups.length) {
-    filterTableDiv.style("display", "none");
-    return;
-  }
-  filterTableDiv.style("display", "").selectAll("*").remove();
-  const tableArg = {
-    div: filterTableDiv,
-    columns: [
-      {},
-      // blank column to add delete buttons
-      {
-        label: "NAME",
-        editCallback: async (i, cell) => {
-          const newName = cell.value;
-          const index = self.groups.findIndex((group) => group.name == newName);
-          if (index != -1) {
-            alert(`Group named ${newName} already exists`);
-            makeGroupUI(self, div);
-          } else {
-            self.groups[i].name = newName;
-            makeGroupUI(self, div);
-          }
-        }
-      },
-      {
-        label: "COLOR",
-        editCallback: async (i, cell) => {
-          self.groups[i].color = cell.color;
-          makeGroupUI(self, div);
-        }
-      },
-      //{ label: '#SAMPLE' }, // will re-enable when filtered sample count can be supported for gdc
-      { label: "FILTER" }
-    ],
-    rows: [],
-    striped: false,
-    // no alternating row bg color so delete button appears more visible
-    showLines: false
-  };
-  for (const g of self.groups) {
-    tableArg.rows.push([
-      {},
-      // blank cell to add delete button
-      { value: g.name },
-      // to allow click to show <input>
-      { color: g.color },
-      // { value: 'n=' + (await self.vocabApi.getFilteredSampleCount(g.filter)) }, // will re-enable when filtered sample count can be supported for gdc
-      {}
-      // blank cell to show filter ui
-    ]);
-  }
-  renderTable(tableArg);
-  for (const [i, row] of tableArg.rows.entries()) {
-    row[0].__td.append("div").attr("class", "sja_menuoption").style("padding", "1px 6px").html("&times;").on("click", () => {
-      self.groups.splice(i, 1);
-      makeGroupUI(self, div);
-    });
-    const group = self.groups[i];
-    filterInit({
-      holder: row[3].__td,
-      vocabApi,
-      header_mode: "hide_search",
-      callback: (f) => {
-        if (!f || f.lst.length == 0) {
-          const i2 = self.groups.findIndex((g) => g.name == group.name);
-          self.groups.splice(i2, 1);
-        } else {
-          excludeGeneNameFromFilter(f);
-          group.filter = f;
-        }
-        makeGroupUI(self, div);
-      }
-    }).main(group.filter);
-  }
-}
-function addNewGroup(filter, groups, name) {
-  if (!groups) throw "groups is missing";
-  if (!name) {
-    const base = "New group";
-    name = base;
-    for (let i = 0; ; i++) {
-      name = base + (i === 0 ? "" : " " + i);
-      if (!groups.find((g) => g.name === name)) break;
-    }
-  }
-  excludeGeneNameFromFilter(filter);
-  const newGroup = {
-    name,
-    type: "filter",
-    filter,
-    color: rgb(colorScale(groups.length)).formatHex()
-  };
-  groups.push(newGroup);
-}
-function excludeGeneNameFromFilter(filter) {
-  for (const item of filter.lst) {
-    if (item.type == "tvslst") {
-      excludeGeneNameFromFilter(item);
-    } else if (item.type == "tvs") {
-      item.tvs.excludeGeneName = true;
-    } else {
-      throw "unexpected item.type";
-    }
-  }
-}
-function clearGroupset(self) {
-  self.q.type = "values";
-  delete self.q.predefined_groupset_idx;
-  delete self.q.customset;
-  delete self.q.dtLst;
-  self.q.hiddenValues = {};
-}
-export {
-  getHandler
-};
-//# sourceMappingURL=geneVariant-ZPINPLRP.js.map