@sjcrh/proteinpaint-client 2.225.0 → 2.227.0

package/dist/condition-PYFOEVX5.js

@@ -0,0 +1,323 @@
+import {
+  getPillNameDefault,
+  make_radios,
+  sayerror,
+  set_hiddenvalues,
+  throwMsgWithFilePathAndFnName
+} from "./chunk-YBXQBSFY.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-QKVKQD6S.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-VVWZ4BOI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-2IAELUCN.js";
+import "./chunk-CFYWQJ7F.js";
+import "./chunk-2N345NXD.js";
+import {
+  copyMerge
+} from "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// termsetting/handlers/condition.ts
+var cutoffGrades = [1, 2, 3, 4, 5];
+function getHandler(self) {
+  return {
+    getPillName(d) {
+      return getPillNameDefault(self, d);
+    },
+    getPillStatus() {
+      return getPillStatus(self);
+    },
+    showEditMenu(div) {
+      if (self.q.mode == "discrete") {
+        return showMenu_discrete(self, div);
+      }
+      if (self.q.mode == "binary" || self.q.mode == "cuminc" || self.q.mode == "cox") {
+        return showMenu_cutoff(self, div);
+      }
+      console.error("invalid q.mode:", self.q.mode);
+      throw "invalid q.mode";
+    }
+    // async postMain() {
+    // 	const body = self.opts.getBodyParams?.() || {} //make sure term1_q is added
+    // 	const data = await self.vocabApi.getCategories(self.term, self.filter!, body)
+    // 	//not really sure this is necessary but it's consistent across other handlers
+    // 	self.category2samplecount = []
+    // 	for (const d of data.lst) {
+    // 		self.category2samplecount.push({
+    // 			key: d.key,
+    // 			label: d.label,
+    // 			count: d.samplecount
+    // 		})
+    // 		// }
+    // 	}
+    // }
+  };
+}
+function getPillStatus(self) {
+  const text = self.q?.name;
+  if (text) return { text };
+  if (self.q.mode == "discrete") {
+    if (self.q.breaks?.length) {
+      return { text: self.q.breaks.length + 1 + " groups" };
+    } else {
+      if (self.q.bar_by_grade) {
+        if (self.q.value_by_max_grade) return { text: "Max. Grade" };
+        if (self.q.value_by_most_recent) return { text: "Most Recent Grade" };
+        if (self.q.value_by_computable_grade) return { text: "Any Grade" };
+        return { text: "Error: unknown grade setting", bgcolor: "red" };
+      }
+      if (self.q.bar_by_children) return { text: "Sub-condition" };
+    }
+  }
+  if (self.q.mode == "binary") {
+    return {
+      text: self.usecase?.target == "regression" ? self.data.q.groups.find((x) => x.name != self.data.refGrp).name : "binary"
+    };
+  }
+  if (self.q.mode == "cuminc" || self.q.mode == "cox") {
+    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
+    return { text: `Grades ${self.q.breaks[0]}-5` };
+  }
+  return {};
+}
+async function showMenu_discrete(self, div) {
+  const value_type_div = div.append("div").style("margin", "10px 0px 10px 5px").style("border-left", "solid 1px #ededed");
+  value_type_div.append("div").style("display", "inline-block").style("margin", "0px 0px 5px 5px").style("color", "rgb(136, 136, 136)").text("Grade type:");
+  const value_type_select = value_type_div.append("select").style("display", "inline").style("margin", "0px 10px").on("change", () => {
+    const i = value_type_select.property("selectedIndex");
+    self.q.bar_by_grade = i != 3;
+    self.q.bar_by_children = i == 3;
+    self.q.value_by_max_grade = i == 0;
+    self.q.value_by_most_recent = i == 1;
+    self.q.value_by_computable_grade = i == 2 || i == 3;
+    self.dom.tip.hide();
+    self.api.runCallback();
+  });
+  value_type_select.append("option").text("Max grade per patient");
+  value_type_select.append("option").text("Most recent grade per patient");
+  value_type_select.append("option").text("Any grade per patient");
+  if (self.term.subconditions) {
+    value_type_select.append("option").text("Sub-conditions");
+  }
+  value_type_select.property(
+    "selectedIndex",
+    self.q.bar_by_children ? 3 : self.q.value_by_computable_grade ? 2 : self.q.value_by_most_recent ? 1 : 0
+  );
+  if (self.q.bar_by_children) {
+    return;
+  }
+  const breaksSelectorDiv = div.append("div").style("margin", "20px 0px 10px 5px").style("border-left", "solid 1px #ededed");
+  breaksSelectorDiv.append("div").text("Divide grades into groups (optional):").style("margin", "0px 0px 10px 5px").style("color", "rgb(136, 136, 136)");
+  const holder = breaksSelectorDiv.append("div").style("display", "flex").style("align-items", "start").style("margin-left", "10px").style("width", "100%");
+  const gradeValuesDiv = holder.append("div").style("margin-right", "20px");
+  const rangeNameDiv = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center").style("margin-right", "5px");
+  gradeValuesDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Cutoff grades");
+  const textarea = gradeValuesDiv.append("textarea").style("width", "100px").style("height", "70px").on("keyup", textarea2gradeUI);
+  gradeValuesDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
+  if (self.q.breaks?.length) {
+    textarea.property("value", self.q.breaks.join("\n"));
+  }
+  textarea2gradeUI();
+  function textarea2gradeUI() {
+    rangeNameDiv.selectAll("*").remove();
+    const breaks = textarea2breaks();
+    if (!breaks.length) {
+      delete self.q.breaks;
+      delete self.q.groups;
+      return;
+    }
+    if (!self.term.values) throwMsgWithFilePathAndFnName(`Missing term values`);
+    const grades = Object.keys(self.term.values).filter((g) => !self.term.values?.[g].uncomputable).map(Number).sort((a, b) => a - b);
+    const groups = getGroups(grades, breaks);
+    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
+    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Label");
+    for (const [i, g] of groups.entries()) {
+      rangeNameDiv.append("div").text(g.name.replace(/Grades* /, ""));
+      rangeNameDiv.append("div").append("input").attr("type", "text").property("value", g.name).style("margin", "2px 0px").on("change", function() {
+        groups[i].name = this.value;
+      });
+    }
+    self.q.breaks = breaks;
+    self.q.groups = groups;
+  }
+  function textarea2breaks() {
+    const str = textarea.property("value").trim();
+    if (!str) return [];
+    const lst = [...new Set(str.split("\n"))];
+    const breaks = [];
+    for (const x of lst) {
+      const b = Number(x);
+      if (!Number.isInteger(b)) {
+        sayerror(div, "cutoff grade must be an integer value");
+        return [];
+      }
+      if (b < 1 || b > 5) {
+        sayerror(div, `cutoff grade must be within grades 1-5`);
+        return [];
+      }
+      breaks.push(b);
+    }
+    if (!breaks.length) return [];
+    return breaks.sort((i, j) => i - j);
+  }
+  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
+    event.target.disabled = true;
+    event.target.innerHTML = "Loading...";
+    self.api.runCallback();
+  });
+}
+function showMenu_cutoff(self, div) {
+  const holder = div.append("div").style("margin", "10px").style("display", "grid").style("grid-template-columns", "auto auto").style("gap", "20px");
+  holder.append("div").text("Grade cutoff").style("opacity", 0.4);
+  const sd = holder.append("div");
+  const gradeSelect = sd.append("select").on("change", changeGradeSelect);
+  for (const i of cutoffGrades) {
+    gradeSelect.append("option").text(self.term.values?.[i].label);
+  }
+  gradeSelect.property("selectedIndex", self.q.breaks[0] - 1);
+  holder.append("div").text(self.q.mode == "binary" ? "Group 1" : "Censored").style("opacity", 0.4);
+  const g1n = holder.append("div").style("opacity", 0.4);
+  holder.append("div").text(self.q.mode == "binary" ? "Group 2" : "Event").style("opacity", 0.4);
+  const g2n = holder.append("div").style("opacity", 0.4);
+  changeGradeSelect();
+  function changeGradeSelect() {
+    const grade = gradeSelect.property("selectedIndex") + 1;
+    g1n.selectAll("*").remove();
+    g2n.selectAll("*").remove();
+    const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
+    for (const i of grades) {
+      if (i < grade) {
+        g1n.append("div").text(self.term.values?.[i].label);
+      } else {
+        g2n.append("div").text(self.term.values?.[i].label);
+      }
+    }
+  }
+  const timeUnit = self.vocabApi.termdbConfig.timeUnit;
+  let timeScaleChoice;
+  if (self.q.mode == "cox") {
+    timeScaleChoice = self.q.timeScale;
+    holder.append("div").text("Time axis").style("opacity", 0.4);
+    const options = [
+      {
+        label: timeUnit.charAt(0).toUpperCase() + timeUnit.slice(1),
+        value: "time"
+      },
+      { label: "Age", value: "age" }
+    ];
+    if (self.q.timeScale == "age") {
+      options[1].checked = true;
+    } else {
+      options[0].checked = true;
+    }
+    make_radios({
+      holder: holder.append("div"),
+      options,
+      styles: { padding: "" },
+      callback: (v) => timeScaleChoice = v
+    });
+  }
+  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
+    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
+    const grade = gradeSelect.property("selectedIndex") + 1;
+    self.q.breaks[0] = grade;
+    if (self.q.mode == "binary") {
+      const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
+      self.q.groups = getGroups(grades, self.q.breaks);
+      self.refGrp = self.q.groups[0].name;
+    }
+    if (self.q.mode == "cox") self.q.timeScale = timeScaleChoice;
+    event.target.disabled = true;
+    event.target.innerHTML = "Loading...";
+    self.api.runCallback();
+  });
+}
+function getGroups(grades, breaks) {
+  grades.sort((a, b2) => a - b2);
+  const groups = [];
+  let group = { values: [] };
+  let b;
+  for (const g of grades) {
+    if (breaks.includes(g)) {
+      b = g;
+      const max = Math.max(...group.values);
+      if (!groups.length) {
+        if (group.values.length == 1) {
+          if (group.values[0] !== 0) throw "unexpected group value";
+          group.name = "Grade 0";
+        } else {
+          if (group.values.length == 2 && group.values.includes(-1) && group.values.includes(0)) {
+            group.name = "Not tested/Grade 0";
+          } else {
+            group.name = group.values.includes(-1) ? `Not tested/Grade 0 - Grade ${max}` : `Grades 0-${max}`;
+          }
+        }
+      } else {
+        group.name = group.values.length == 1 ? `Grade ${group.values[0]}` : `${group.name}-${max}`;
+      }
+      groups.push(group);
+      group = {
+        name: `Grade ${b}`,
+        values: [g]
+      };
+    } else {
+      group.values.push(g);
+    }
+  }
+  group.name = `Grades ${b}-5`;
+  groups.push(group);
+  return groups;
+}
+function fillTW(tw, vocabApi, defaultQ) {
+  set_hiddenvalues(tw.q, tw.term);
+  if (defaultQ) {
+    copyMerge(tw.q, defaultQ);
+  }
+  if (!Object.keys(tw.q).includes("mode")) tw.q.mode = "discrete";
+  if (!tw.q.valueFor) {
+    const q = tw.q;
+    if (!q.bar_by_grade && !q.bar_by_children) q.bar_by_grade = true;
+    tw.q.valueFor = tw.q.bar_by_children ? "children" : "grade";
+  }
+  if (tw.q.valueFor == "grade") {
+    if (tw.q.value_by_max_grade || tw.q.value_by_most_recent || tw.q.value_by_computable_grade) {
+    } else {
+      tw.q.value_by_max_grade = true;
+    }
+  }
+  if (tw.q.mode == "binary" || tw.q.mode == "cox" || tw.q.mode == "cuminc") {
+    const defaultBreak = tw.q.mode == "binary" ? 1 : 3;
+    if (!tw.q.breaks?.length) tw.q.breaks = [defaultBreak];
+    if (tw.q.breaks.length != 1 || ![1, 2, 3, 4, 5].includes(tw.q.breaks[0])) throw "invalid tw.q.breaks";
+  }
+  if (tw.q.valueFor == "grade") {
+    if (tw.q.breaks?.length) {
+      if (!tw.term.values) throw "missing term.values";
+      if (tw.q.mode == "discrete" || tw.q.mode == "binary") {
+        const grades = Object.keys(tw.term.values).filter((g) => tw.q.mode == "discrete" ? !tw.term.values?.[g].uncomputable : g).map(Number).sort((a, b) => a - b);
+        tw.q.groups = getGroups(grades, tw.q.breaks);
+      }
+    }
+    if (tw.q.mode == "cox") {
+      if (!tw.q.timeScale) tw.q.timeScale = "time";
+      if (!["age", "time"].includes(tw.q.timeScale)) throw "invalid q.timeScale";
+    }
+  }
+}
+export {
+  fillTW,
+  getHandler
+};
+//# sourceMappingURL=condition-PYFOEVX5.js.map

package/dist/controls-RVNIN66W.js

@@ -0,0 +1,30 @@
+import {
+  controlsInit,
+  renderTerm1Label
+} from "./chunk-YBXQBSFY.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-QKVKQD6S.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-VVWZ4BOI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-2IAELUCN.js";
+import "./chunk-CFYWQJ7F.js";
+import "./chunk-2N345NXD.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  controlsInit,
+  renderTerm1Label
+};
+//# sourceMappingURL=controls-RVNIN66W.js.map

package/dist/controls.config-XVEYYBI4.js

@@ -0,0 +1,30 @@
+import {
+  configUiInit,
+  initByInput
+} from "./chunk-YBXQBSFY.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-QKVKQD6S.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-VVWZ4BOI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-2IAELUCN.js";
+import "./chunk-CFYWQJ7F.js";
+import "./chunk-2N345NXD.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  configUiInit,
+  initByInput
+};
+//# sourceMappingURL=controls.config-XVEYYBI4.js.map

package/dist/correlation-MNL4DGSW.js

@@ -0,0 +1,91 @@
+import {
+  appInit
+} from "./chunk-KTJUDDVQ.js";
+import "./chunk-IBUDYN5E.js";
+import "./chunk-OVXHMJJJ.js";
+import "./chunk-VPRP24DY.js";
+import "./chunk-GKA6USKV.js";
+import "./chunk-FA2B6PKK.js";
+import "./chunk-4E2F26CC.js";
+import "./chunk-7NVFEGCE.js";
+import "./chunk-2B3CYHUF.js";
+import "./chunk-O6T4SDC7.js";
+import "./chunk-YBXQBSFY.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-QKVKQD6S.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-VVWZ4BOI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-2IAELUCN.js";
+import "./chunk-CFYWQJ7F.js";
+import "./chunk-2N345NXD.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// gdc/correlation.ts
+async function init(arg, holder, genomes) {
+  const useGenome = arg.genome || "hg38";
+  const useDslabel = arg.dslabel || "GDC";
+  if (!genomes[useGenome]) throw useGenome + " missing";
+  const massApi = await appInit({
+    //debug: arg.debugmode, // is debug accepted?
+    genome: genomes[useGenome],
+    holder,
+    state: {
+      genome: useGenome,
+      dslabel: useDslabel,
+      termfilter: { filter0: arg.filter0 },
+      nav: { activeTab: 1, header_mode: window.location.pathname.includes("example.gdc") ? void 0 : "only_buttons" },
+      plots: arg.state?.plots || [
+        { chartType: "summaryInput" }
+        // default shows summaryInput ui, can change
+        //{ chartType: 'barchart', term: {id: 'case.demographic.gender'} }, // uncomment for quicker testing
+      ]
+    },
+    opts: Object.assign(
+      {
+        // todo additional customizations
+        // dictionary:{header:'Select a variable to build Correlation Plot'}
+        // some way to make gene exp violin/boxplot to use log scale by default, but numeric dict term should not
+      },
+      arg.opts || {}
+    ),
+    barchart: arg.opts?.barchart || {},
+    violin: arg.opts?.violin || {},
+    boxplot: arg.opts?.boxplot || {},
+    app: arg.opts?.app || {}
+  });
+  const api = {
+    update: async (updateArg) => {
+      if (!massApi) return;
+      if ("filter0" in updateArg) {
+        massApi.dispatch({
+          type: "app_refresh",
+          subactions: [
+            {
+              type: "filter_replace",
+              filter0: updateArg.filter0
+            }
+          ]
+        });
+      }
+    },
+    triggerAbort: (reason = "") => massApi.triggerAbort(reason)
+  };
+  return api;
+}
+export {
+  init
+};
+//# sourceMappingURL=correlation-MNL4DGSW.js.map