@sjcrh/proteinpaint-client 2.220.0 → 2.221.0

package/dist/databrowser.ui-A6ZSIUG4.js

@@ -1,421 +0,0 @@
-import {
-  isURL,
-  makeBtn,
-  makeFileUpload,
-  makePrompt,
-  makeResetBtn,
-  makeTextAreaInput,
-  makeTextInput
-} from "./chunk-5EBRF6Z7.js";
-import {
-  appInit
-} from "./chunk-U3CWWOHL.js";
-import "./chunk-6DESNDD5.js";
-import "./chunk-C7KUMZQM.js";
-import "./chunk-B5IJAQG4.js";
-import "./chunk-DZBPF5QI.js";
-import "./chunk-FZYVPRVQ.js";
-import "./chunk-4E2F26CC.js";
-import "./chunk-FE5TCBIT.js";
-import "./chunk-K2ARLT2A.js";
-import "./chunk-O6T4SDC7.js";
-import {
-  Tabs,
-  appear,
-  sayerror
-} from "./chunk-PEKCVKJK.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-YR6EXI2K.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/databrowser/dictionary.parse.js
-function parseDictionary(input) {
-  const terms = {};
-  const lines = input.trim().split(/\r?\n/);
-  const header = lines[0].split("	");
-  const term_idIndex = header.findIndex((l) => l.toLowerCase().includes("term_id"));
-  const variableIndex = header.findIndex((l) => l.toLowerCase().includes("variable"));
-  if (term_idIndex != -1) parseDataDictionary(lines, header);
-  if (variableIndex != -1) parsePhenotree(lines, header);
-  if (variableIndex == -1 && term_idIndex == -1) {
-    throw `Unrecognized file format. Please check the header names.`;
-  }
-  function parseDataDictionary(lines2, header2) {
-    const parIdIndex = header2.findIndex((l) => l.toLowerCase().includes("parent_id"));
-    if (parIdIndex == -1) {
-      throw `Missing required 'parent_id' header`;
-    }
-    const nameIndex = header2.findIndex((l) => l.toLowerCase().includes("name"));
-    if (nameIndex == -1) {
-      throw `Missing required 'Name' header`;
-    }
-    const typeIndex = header2.findIndex((l) => {
-      const v = l.trim().toLowerCase();
-      return v === "type";
-    });
-    if (typeIndex == -1) {
-      throw `Missing required 'Type' header`;
-    }
-    const valuesIndex = header2.findIndex((l) => l.toLowerCase().includes("values"));
-    if (valuesIndex == -1) {
-      throw `Missing required 'Values' header`;
-    }
-    if (parIdIndex == -1 || nameIndex == -1 || typeIndex == -1 || valuesIndex == -1) {
-      throw `Missing required header(s)`;
-    }
-    const parentIds = /* @__PURE__ */ new Set();
-    for (const [i, line] of lines2.entries()) {
-      if (i === 0) continue;
-      const lineNum = i + 1;
-      try {
-        const cols = line.split("	");
-        for (const [i2, c] of cols.entries()) {
-          const colNum = i2 + 1;
-          let foundProblem;
-          if (i2 == valuesIndex) continue;
-          if (c == "" || c == "-") {
-            foundProblem = true;
-            throw `Blank or '-' entered for line ${lineNum}, column ${colNum}`;
-          }
-          if (foundProblem == true) throw `Invalid entry for line ${lineNum}, column ${colNum}`;
-        }
-        const termId = cols[term_idIndex];
-        const type = cols[typeIndex];
-        terms[termId] = {
-          id: termId,
-          name: cols[nameIndex].trim().replace(/"/g, ""),
-          parent_id: cols[parIdIndex] != "root" ? cols[parIdIndex] : null,
-          type: cols[typeIndex] != "non graphable" ? cols[typeIndex] : null
-        };
-        parentIds.add(terms[termId].parent_id);
-        if (type == "categorical") {
-          terms[termId].values = {};
-        }
-        const values = cols[valuesIndex].trim().replace(/"/g, "").split(";");
-        for (const x of values) {
-          const v = x.trim();
-          if (v == "") continue;
-          const segments = v.split("=");
-          const key = segments.shift();
-          const label = segments.join("=");
-          if (!label) throw `Values="${v}" in line ${lineNum} not in a key = value format.`;
-          if (!terms[termId].values) terms[termId].values = {};
-          terms[termId].values[key] = { label };
-        }
-        const numValues = Object.keys(terms[termId].values).length;
-        terms[termId].groupsetting = { disabled: numValues < 3 };
-        validateNumericTermCategories(terms[termId]);
-      } catch (e) {
-        throw `Line ${lineNum} error: ${e}`;
-      }
-    }
-    for (const t in terms) terms[t].isleaf = !parentIds.has(terms[t].id);
-  }
-  function parsePhenotree(lines2, header2) {
-    if (variableIndex == -1) {
-      throw `Missing required 'Variable' header`;
-    }
-    const typeIndex = header2.findIndex((l) => {
-      const v = l.trim().toLowerCase();
-      return v === "type";
-    });
-    if (typeIndex == -1) {
-      throw `Missing required 'Type' header`;
-    }
-    const categoriesIndex = header2.findIndex((l) => l.toLowerCase().includes("categories"));
-    const levelColIndexes = header2.map((c, i) => c.toLowerCase().includes("level_") ? i : -1).filter((i) => i != -1);
-    if (!levelColIndexes.length) levelColIndexes.push(variableIndex);
-    const unitIndex = header2.findIndex((l) => l.toLowerCase().includes("unit"));
-    const sampleTypeIndex = header2.findIndex((l) => {
-      const v = l.trim().toLowerCase();
-      return v === "sample_type";
-    });
-    const additionalAttrIndexes = header2.findIndex((l) => l.toLowerCase().includes("additional attributes"));
-    const termNameToId = {};
-    const parentTermNames = /* @__PURE__ */ new Set();
-    const parent2ChildOrder = /* @__PURE__ */ new Map();
-    parent2ChildOrder.set(null, []);
-    for (const [i, line] of lines2.entries()) {
-      if (i === 0) continue;
-      const lineNum = i + 1;
-      try {
-        const cols = line.split("	");
-        const levelNames = levelColIndexes.map((i2) => cols[i2].trim().replace(/"/g, "")).filter((c) => c != "-");
-        if (levelNames.length != new Set(levelNames).size) {
-          throw `Non-unique levels in line ${lineNum}: ${JSON.stringify(levelNames)}`;
-        }
-        for (const [i2, lvlName] of levelNames.entries()) {
-          if (i2 == 0) {
-            if (parent2ChildOrder.get(null).indexOf(lvlName) == -1) parent2ChildOrder.get(null).push(lvlName);
-          }
-          if (i2 != levelNames.length - 1) {
-            if (!parent2ChildOrder.has(lvlName)) parent2ChildOrder.set(lvlName, []);
-          }
-          for (const n of levelNames) {
-            if (i2 == levelNames.indexOf(n) - 1) {
-              if (parent2ChildOrder.get(lvlName).indexOf(n) == -1) parent2ChildOrder.get(lvlName).push(n);
-            }
-          }
-        }
-        const name = levelNames.pop();
-        const firstDashIndex = cols.indexOf("-");
-        if (firstDashIndex != -1 && firstDashIndex < cols.indexOf(name)) {
-          throw `Blank or '-' value detected between levels in line ${lineNum}`;
-        }
-        const term = parseCategories(cols[typeIndex], cols[categoriesIndex], lineNum, name);
-        const id = cols[variableIndex] || name;
-        if (id in terms) {
-          const orig = terms[id];
-          throw `Error: Multiple config rows for term.id='${id}': lines# ${orig.lineNum} and ${lineNum}`;
-        }
-        terms[id] = {
-          id,
-          name,
-          type: term.type,
-          values: term.values,
-          groupsetting: term.groupsetting,
-          // *** temporary attributes to be deleted later ***
-          ancestry: levelNames.slice(),
-          // to be deleted later, used to fill in missing terms
-          parent_name: levelNames.pop() || null,
-          // will change this later to parent_id
-          lineNum
-          // to be deleted later
-        };
-        if (cols[unitIndex] != null) terms[id].unit = cols[unitIndex];
-        if (cols[sampleTypeIndex] != null) terms[id].sample_type = cols[sampleTypeIndex];
-        if (cols[additionalAttrIndexes]) {
-          Object.assign(terms[id], JSON.parse(cols[additionalAttrIndexes]));
-        }
-        termNameToId[name] = id;
-        parentTermNames.add(terms[id].parent_name);
-      } catch (e) {
-        throw `Line ${lineNum} error: ${e}`;
-      }
-    }
-    trackMissingTerms(termNameToId, terms, parentTermNames, parent2ChildOrder);
-    for (const id in terms) {
-      const term = terms[id];
-      term.child_order = parent2ChildOrder.get(term.parent_name).indexOf(term.name) + 1;
-      term.isleaf = !parentTermNames.has(term.name);
-      term.parent_id = termNameToId[term.parent_name] || null;
-      delete term.parent_name;
-      delete term.lineNum;
-      delete term.ancestry;
-    }
-  }
-  return { terms: Object.values(terms) };
-}
-function parseCategories(type, catJSON, lineNum, varName) {
-  if (!type) throw `No type provided for variable: ${varName} on line ${lineNum}`;
-  const term = {
-    type,
-    values: catJSON == "" || catJSON == void 0 ? {} : JSON.parse(catJSON)
-  };
-  validateNumericTermCategories(term);
-  if (term.type == "categorical") {
-    const numValues = Object.keys(term.values).length;
-    term.groupsetting = { disabled: numValues < 3 };
-  }
-  return term;
-}
-function trackMissingTerms(termNameToId, terms, parentTermNames, parent2ChildOrder) {
-  for (const id in terms) {
-    const term = terms[id];
-    for (const [i, name] of term.ancestry.entries()) {
-      if (name in termNameToId) {
-        const id2 = termNameToId[name];
-        const ancestor = terms[id2];
-        if (i - 1 < 0 && ancestor.parent_name || ancestor.parent_name != term.ancestry[i - 1]) {
-          throw `Different parents for term=${name}, '${term.ancestry[i - 1]}' and '${ancestor.parent_name}'`;
-        }
-        continue;
-      }
-      terms[name] = {
-        id: name,
-        name,
-        isleaf: false,
-        ancestry: term.ancestry.slice(0, i)
-      };
-      terms[name].parent_name = terms[name].ancestry.slice(-1)[0] || null;
-      termNameToId[name] = name;
-      parentTermNames.add(name);
-    }
-  }
-}
-function validateNumericTermCategories(term) {
-  if (term.type != "integer" && term.type != "float") return;
-  if (!term.values) return;
-  if (typeof term.values != "object") throw "numeric .values{} is not object";
-  for (const key in term.values) {
-    if (key == "") throw "Cannot use empty string as an uncomputable category";
-    const tmp = Number(key);
-    if (Number.isNaN(tmp)) {
-      throw `Uncomputable category of a numeric term is required to be a number (here uses non-numeric value of ${key}).`;
-    }
-    term.values[key].uncomputable = true;
-  }
-}
-
-// src/databrowser/databrowser.ui.js
-function init_databrowserUI(holder, debugmode) {
-  const wrapper = holder.append("div").style("margin", "20px 20px 20px 40px").style(
-    "font-family",
-    "'Lucida Sans', 'Lucida Sans Regular', 'Lucida Grande', 'Lucida Sans Unicode', Geneva, Verdana, sans-serif"
-  ).style("place-items", "center left").style("overflow", "hidden").classed("sjpp-app-ui", true);
-  const obj = {};
-  infoSection(wrapper);
-  makeSectionHeader(wrapper, "Data Dictionary");
-  const tabs_div = wrapper.append("div").style("margin-left", "2vw");
-  makeDataDictionaryTabs(tabs_div, obj);
-  const controlBtns_div = wrapper.append("div").style("display", "flex").style("align-items", "center").style("margin", "40px 0px 40px 130px");
-  submitButton(controlBtns_div, obj, wrapper, holder);
-  makeResetBtn(controlBtns_div, obj, ".databrowser_input");
-  if (debugmode) window.doms = obj;
-  return obj;
-}
-function infoSection(div) {
-  div.append("div").style("margin", "10px").style("opacity", "0.65").html(`
-			<ul>
-                <li>
-                    Please see the <a href="https://github.com/stjude/proteinpaint/wiki/Data-Browser" target="_blank">documentation</a> for more information.
-                </li>
-				<li>
-					Download an example data dictionary <a href="https://proteinpaint.stjude.org/ppdemo/databrowser/dictionaryDemoData.tar.gz" target="_self" "download>here</a>.
-				</li>
-            </ul>`);
-}
-function makeSectionHeader(div, text) {
-  const header = makePrompt(div, text);
-  header.style("font-size", "1.5em").style("color", "#003366").style("margin", "20px 10px 40px 10px").classed("sjpp-databrowser-section-header", true);
-  const hr = div.append("hr");
-  hr.style("color", "ligthgrey").style("margin", "-30px 0px 15px 0px").style("width", "50vw").style("opacity", "0.4");
-}
-function makeDataDictionaryTabs(tabs_div, obj) {
-  const tabs = [
-    {
-      label: "Select File",
-      active: true,
-      width: 95,
-      callback: async (event, tab) => {
-        tab.contentHolder.style("border", "none").style("display", "block");
-        appear(tab.contentHolder);
-        tab.contentHolder.append("div").html(`<p style="margin-left: 10px; opacity: 0.65;">Select a file from your computer.</p>`);
-        makeFileUpload2(tab.contentHolder, obj);
-        delete tab.callback;
-      }
-    },
-    {
-      label: "Paste Data",
-      active: false,
-      width: 95,
-      callback: async (event, tab) => {
-        tab.contentHolder.style("border", "none").style("display", "block");
-        appear(tab.contentHolder);
-        tab.contentHolder.append("div").html(
-          `<p style="margin-left: 10px; opacity: 0.65;">Paste data dictionary or phenotree in a tab delimited format.</p>`
-        );
-        makeCopyPasteInput(tab.contentHolder, obj);
-        delete tab.callback;
-      }
-    },
-    {
-      label: "File Path",
-      active: false,
-      width: 95,
-      callback: async (event, tab) => {
-        tab.contentHolder.style("border", "none").style("display", "block");
-        appear(tab.contentHolder);
-        tab.contentHolder.append("div").html(`<p style="margin-left: 10px; opacity: 0.65;">Provide a URL file path.</p>`);
-        makePrompt(tab.contentHolder, "URL");
-        makeTextEntryFilePathInput(tab.contentHolder, obj);
-        delete tab.callback;
-      }
-    }
-  ];
-  new Tabs({ holder: tabs_div, tabs }).main();
-}
-function makeTextEntryFilePathInput(div, obj) {
-  const filepath_div = div.append("div").style("display", "inline-block");
-  const filepath = makeTextInput(filepath_div).style("border", "1px solid rgb(138, 177, 212)").classed("databrowser_input", true).on("keyup", async () => {
-    const data = filepath.property("value").trim();
-    if (isURL(data)) {
-      const txt = await fetch(data).then((req) => req.text()).then((txt2) => {
-        obj.data = parseDictionary(txt2);
-      });
-    } else {
-    }
-  });
-}
-function makeFileUpload2(div, obj) {
-  const upload_div = div.append("div").style("display", "inline-block");
-  const upload = makeFileUpload(upload_div).classed("databrowser_input", true);
-  upload.on("change", (event) => {
-    const file = event.target.files[0];
-    const reader = new FileReader();
-    reader.onload = (event2) => {
-      obj.data = parseDictionary(event2.target.result);
-    };
-    reader.readAsText(file, "utf8");
-  });
-}
-function makeCopyPasteInput(div, obj) {
-  const paste_div = div.append("div").style("display", "block");
-  const paste = makeTextAreaInput({ div: paste_div, rows: 10 }).style("border", "1px solid rgb(138, 177, 212)").style("margin", "0px 0px 0px 20px").classed("databrowser_input", true).on("keyup", async () => {
-    obj.data = parseDictionary(paste.property("value").trim());
-  });
-}
-function submitButton(div, obj, wrapper, holder) {
-  const submit = makeBtn({
-    div,
-    text: "Create Data Browser",
-    color: "white",
-    backgroundColor: "#001aff",
-    border: "2px solid #001aff"
-  });
-  const errorMessage_div = div.append("div");
-  submit.style("margin-right", "10px").style("font-size", "16px").classed("sjpp-ui-submitBtn", true).attr("type", "submit").on("click", () => {
-    if (!obj.data || obj.data == void 0) {
-      const sayerrorDiv = errorMessage_div.append("div").style("display", "inline-block").style("max-width", "20vw");
-      sayerror(sayerrorDiv, "Please provide data");
-      setTimeout(() => sayerrorDiv.remove(), 3e3);
-    } else {
-      wrapper.remove();
-      appInit({
-        holder,
-        state: {
-          vocab: {
-            terms: obj.data.terms
-          },
-          plots: [
-            {
-              chartType: "dictionary"
-            }
-          ]
-        }
-      });
-    }
-  });
-}
-export {
-  init_databrowserUI
-};
-//# sourceMappingURL=databrowser.ui-A6ZSIUG4.js.map

package/dist/dictionary-TQUVCHIN.js

@@ -1,109 +0,0 @@
-import {
-  appInit
-} from "./chunk-PEKCVKJK.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-YR6EXI2K.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import "./chunk-WJLRU5OF.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/dictionary.js
-var MassDict = class _MassDict {
-  static type = "tree";
-  constructor(opts) {
-    this.type = _MassDict.type;
-    this.dom = {
-      holder: opts.holder.style("padding", "20px"),
-      header: opts.header
-    };
-  }
-  async init(appState) {
-    const config = appState.plots.find((p) => p.id === this.id) || {};
-    const opts = {
-      vocabApi: this.app.vocabApi,
-      holder: this.dom.holder,
-      state: this.getState(appState),
-      tree: {
-        click_term: (_term) => {
-          const term = _term.term || _term;
-          const _config = Object.assign({}, config?.spawnConfig, {
-            chartType: term.type == "survival" ? "survival" : "summary",
-            term: _term.term ? _term : { term }
-          });
-          this.app.dispatch({
-            type: "plot_create",
-            config: _config
-          });
-          this.app.dispatch({
-            type: "plot_delete",
-            id: this.id
-          });
-        }
-      }
-    };
-    if (config?.tree?.usecase) {
-      opts.tree.usecase = config.tree.usecase;
-    }
-    this.dom.holder.style("position", "relative");
-    const loadingDiv = this.dom.holder.append("div").attr("class", "sjpp-loading-overlay").style("display", "");
-    loadingDiv.append("div").attr("class", "sjpp-spinner");
-    try {
-      this.tree = await appInit(opts);
-    } finally {
-      loadingDiv.remove();
-    }
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id) || {};
-    const tree = { usecase: { target: "dictionary" } };
-    if (config?.tree?.usecase?.specialCase) {
-      tree.usecase.specialCase = config.tree.usecase.specialCase;
-    }
-    return {
-      tree,
-      vocab: appState.vocab,
-      activeCohort: appState.activeCohort,
-      termfilter: appState.termfilter,
-      selectdTerms: appState.selectedTerms,
-      customTerms: appState.customTerms
-    };
-  }
-  main() {
-    if (this.dom.header) this.dom.header.text("Data Variables");
-    this.tree.dispatch({
-      type: "app_refresh",
-      state: this.state
-    });
-  }
-};
-var dictInit = getCompInit(MassDict);
-var componentInit = dictInit;
-function getPlotConfig(opts, app) {
-  const config = { hidePlotFilter: true };
-  return copyMerge(config, opts);
-}
-export {
-  componentInit,
-  dictInit,
-  getPlotConfig
-};
-//# sourceMappingURL=dictionary-TQUVCHIN.js.map

package/dist/dnaMethylation-ZMJYY3ML.js

@@ -1,29 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-YDIIKD7O.js";
-import "./chunk-PEKCVKJK.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-YR6EXI2K.js";
-import "./chunk-CNFTQSNE.js";
-import "./chunk-RIHO7ZD5.js";
-import "./chunk-TVJOSRCH.js";
-import "./chunk-3CIL7KH7.js";
-import "./chunk-T4XPCSLP.js";
-import "./chunk-4TJO2DGU.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-MHWYRNGA.js";
-import "./chunk-JHLF2ZC2.js";
-import "./chunk-WJLRU5OF.js";
-import "./chunk-HBNB5TRH.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-6XKAOSQE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  SearchHandler
-};
-//# sourceMappingURL=dnaMethylation-ZMJYY3ML.js.map