@sjcrh/proteinpaint-client 2.208.0 → 2.210.0

package/dist/condition-ZUAQYF5C.js

@@ -1,327 +0,0 @@
-import {
-  getPillNameDefault,
-  make_radios,
-  sayerror,
-  set_hiddenvalues,
-  throwMsgWithFilePathAndFnName
-} from "./chunk-QJ3HYZH3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-DMWOK4DS.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-5IMFPVGT.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import "./chunk-GMRIEUBW.js";
-import "./chunk-4EZLVENZ.js";
-import {
-  copyMerge
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.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-ZUAQYF5C.js.map

package/dist/controls-ZPQ6SXD2.js

@@ -1,34 +0,0 @@
-import {
-  controlsInit,
-  renderTerm1Label
-} from "./chunk-QJ3HYZH3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-DMWOK4DS.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-5IMFPVGT.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import "./chunk-GMRIEUBW.js";
-import "./chunk-4EZLVENZ.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  controlsInit,
-  renderTerm1Label
-};
-//# sourceMappingURL=controls-ZPQ6SXD2.js.map

package/dist/controls.config-NELL5HY5.js

@@ -1,34 +0,0 @@
-import {
-  configUiInit,
-  initByInput
-} from "./chunk-QJ3HYZH3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-DMWOK4DS.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-5IMFPVGT.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import "./chunk-GMRIEUBW.js";
-import "./chunk-4EZLVENZ.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  configUiInit,
-  initByInput
-};
-//# sourceMappingURL=controls.config-NELL5HY5.js.map

package/dist/correlation-2X76UI3K.js

@@ -1,95 +0,0 @@
-import {
-  appInit
-} from "./chunk-XRMUUWLS.js";
-import "./chunk-TXIQ5PHR.js";
-import "./chunk-WXX2YD4Q.js";
-import "./chunk-72P6O537.js";
-import "./chunk-MSSPT5YM.js";
-import "./chunk-KAY2ODXX.js";
-import "./chunk-X46YA4CB.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-HKSRIEWJ.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-QJ3HYZH3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-DMWOK4DS.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-5IMFPVGT.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VMRO6DMC.js";
-import "./chunk-HKKTNIMX.js";
-import "./chunk-GMRIEUBW.js";
-import "./chunk-4EZLVENZ.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.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-2X76UI3K.js.map