@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/geneORA-VJMYI4BT.js

@@ -1,276 +0,0 @@
-import {
-  controlsInit,
-  downloadTable,
-  newSandboxDiv,
-  renderTable,
-  table2col
-} from "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import {
-  dofetch3
-} from "./chunk-6ZCHECOT.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import {
-  roundValueAuto
-} from "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/geneORA.js
-var tip = new Menu();
-var geneORA = class _geneORA {
-  static type = "geneORA";
-  constructor() {
-    this.type = _geneORA.type;
-  }
-  async init(opts) {
-    if (!this.opts.holder || !this.opts.header) {
-      const sandBox = newSandboxDiv(select_default(this.opts.holder.node().parentNode));
-      this.opts.header = sandBox.header;
-      this.opts.holder = sandBox.body;
-    }
-    const controlsDiv = this.opts.holder.append("div").style("display", "inline-block");
-    const mainDiv = this.opts.holder.append("div").style("display", "inline-block").style("margin-left", "50px");
-    const holder = mainDiv.append("div").style("display", "inline-block");
-    const detailsDiv = mainDiv.append("div").style("display", "inline-block").style("vertical-align", "top").style("margin-top", "50px");
-    const tableDiv = this.opts.holder.append("div").style("margin-left", "50px");
-    this.dom = {
-      holder,
-      header: this.opts.header,
-      controlsDiv,
-      detailsDiv,
-      tableDiv
-    };
-  }
-  async setControls() {
-    this.dom.controlsDiv.selectAll("*").remove();
-    const inputs = [
-      {
-        label: "P-value Filter Cutoff (Linear Scale)",
-        type: "number",
-        chartType: "geneORA",
-        settingsKey: "pvalue",
-        title: "P-value significance",
-        min: 0,
-        max: 1
-      },
-      {
-        label: "P-value Filter Type",
-        type: "radio",
-        chartType: "geneORA",
-        settingsKey: "adjusted_original_pvalue",
-        title: "Toggle between original and adjusted pvalues for volcano plot",
-        options: [
-          { label: "Adjusted", value: "adjusted" },
-          { label: "Original", value: "original" }
-        ]
-      },
-      {
-        label: "Gene Set Size Filter Cutoff",
-        type: "number",
-        chartType: "geneORA",
-        settingsKey: "gene_set_size_cutoff",
-        title: "Gene set size cutoff. Helps in filtering out large gene sets",
-        min: 0,
-        max: 2e4
-      },
-      {
-        label: "Filter Non-coding Genes",
-        type: "checkbox",
-        chartType: "geneORA",
-        settingsKey: "filter_non_coding_genes",
-        title: "Filter non-coding genes",
-        boxLabel: ""
-      }
-    ];
-    const geneSet = {
-      label: "Gene Set Group",
-      type: "dropdown",
-      chartType: "geneORA",
-      settingsKey: "pathway",
-      title: "Display table showing original and adjusted pvalues corresponding to each significant pathway",
-      boxLabel: ""
-    };
-    geneSet.options = this.app.opts.genome.termdbs.msigdb.analysisGenesetGroups;
-    if (!this.settings.pathway) {
-      this.settings.pathway = "-";
-    }
-    inputs.push(geneSet);
-    this.components = {
-      controls: await controlsInit({
-        app: this.app,
-        id: this.id,
-        holder: this.dom.controlsDiv,
-        inputs
-      })
-    };
-    this.components.controls.on("downloadClick.geneORA", () => {
-      downloadTable(this.gene_ora_table_rows, this.gene_ora_table_cols);
-    });
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) throw `No plot with id='${this.id}' found`;
-    return {
-      config
-    };
-  }
-  async main() {
-    this.config = JSON.parse(JSON.stringify(this.state.config));
-    this.settings = this.config.settings.geneORA;
-    await this.setControls();
-    this.dom.header.html(
-      this.config.geneORAparams.sample_genes.split(",").length + ' genes <span style="font-size:.8em;opacity:.7">GENE SET OVERREPRESENTATION ANALYSIS</span>'
-    );
-    render_geneORA(this);
-  }
-};
-async function render_geneORA(self) {
-  if (self.settings.pathway != "-") {
-    self.dom.detailsDiv.selectAll("*").remove();
-    self.dom.tableDiv.selectAll("*").remove();
-    self.config.geneORAparams.geneSetGroup = self.settings.pathway;
-    self.config.geneORAparams.filter_non_coding_genes = self.settings.filter_non_coding_genes;
-    const wait = self.dom.detailsDiv.append("div").text("Loading...");
-    let output;
-    try {
-      output = await rungeneORA(self.config.geneORAparams);
-      wait.remove();
-      if (output.error) {
-        throw output.error;
-      }
-    } catch (e) {
-      alert("Error: " + e);
-      return;
-    }
-    const table_stats = table2col({ holder: self.dom.detailsDiv });
-    const [t1, t2] = table_stats.addRow();
-    t2.style("text-align", "center").style("font-size", "0.8em").style("opacity", "0.8").text("COUNT");
-    const addStats = [
-      //{
-      //	label: 'Sample genes',
-      //	values: self.config.geneORAparams.sample_genes.split(',').length
-      //},
-      {
-        label: "Gene sets analyzed",
-        values: output.num_pathways
-      }
-    ];
-    if (self.config.geneORAparams.background_genes) {
-      addStats.push({
-        label: "Background genes",
-        values: self.config.geneORAparams.background_genes.split(",").length
-      });
-    }
-    for (const dataRow of addStats) {
-      const [td1, td2] = table_stats.addRow();
-      td1.text(dataRow.label);
-      td2.style("text-align", "end").text(dataRow.values);
-    }
-    self.gene_ora_table_cols = [
-      { label: "Gene set group" },
-      { label: "Original p-value (linear scale)" },
-      { label: "Adjusted p-value (linear scale)" },
-      { label: "Gene set size" },
-      { label: "Gene set hits" }
-    ];
-    self.gene_ora_table_rows = [];
-    for (const pathway of output.pathways) {
-      if (self.settings.adjusted_original_pvalue == "adjusted" && self.settings.pvalue >= pathway.p_value_adjusted && self.settings.gene_set_size_cutoff > pathway.gene_set_size) {
-        self.gene_ora_table_rows.push([
-          { value: pathway.pathway_name },
-          { value: roundValueAuto(pathway.p_value_original) },
-          { value: roundValueAuto(pathway.p_value_adjusted) },
-          { value: pathway.gene_set_size },
-          { value: pathway.gene_set_hits }
-        ]);
-      } else if (self.settings.adjusted_original_pvalue == "original" && self.settings.pvalue >= pathway.p_value_original && self.settings.gene_set_size_cutoff > pathway.gene_set_size) {
-        self.gene_ora_table_rows.push([
-          { value: pathway.pathway_name },
-          { value: roundValueAuto(pathway.p_value_original) },
-          { value: roundValueAuto(pathway.p_value_adjusted) },
-          { value: pathway.gene_set_size },
-          { value: pathway.gene_set_hits }
-        ]);
-      }
-    }
-    const d_ora = self.dom.tableDiv.append("div");
-    renderTable({
-      columns: self.gene_ora_table_cols,
-      rows: self.gene_ora_table_rows,
-      div: d_ora,
-      showLines: true,
-      maxHeight: "30vh",
-      resize: true
-    });
-  }
-}
-async function getPlotConfig(opts, app) {
-  try {
-    const config = {
-      //idea for fixing nav button
-      //samplelst: { groups: app.opts.state.groups}
-      settings: {
-        geneORA: {
-          pvalue: 0.05,
-          adjusted_original_pvalue: "adjusted",
-          pathway: void 0,
-          gene_set_size_cutoff: 2e3,
-          filter_non_coding_genes: true
-        },
-        controls: { isOpen: true }
-      }
-    };
-    return copyMerge(config, opts);
-  } catch (e) {
-    throw `${e} [geneORA getPlotConfig()]`;
-  }
-}
-var geneORAInit = getCompInit(geneORA);
-var componentInit = geneORAInit;
-function makeChartBtnMenu(holder, chartsInstance) {
-  chartsInstance.prepPlot({
-    config: {
-      chartType: "geneORA"
-    }
-  });
-}
-async function rungeneORA(body) {
-  return await dofetch3("genesetOverrepresentation", { body });
-}
-export {
-  componentInit,
-  geneORAInit,
-  getPlotConfig,
-  makeChartBtnMenu
-};
-//# sourceMappingURL=geneORA-VJMYI4BT.js.map

package/dist/geneVariant-LFM5SO2P.js

@@ -1,37 +0,0 @@
-import {
-  getDtsFromGroups,
-  getHandler
-} from "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  getDtsFromGroups,
-  getHandler
-};
-//# sourceMappingURL=geneVariant-LFM5SO2P.js.map

package/dist/geneVariant-OIKEV4JM.js

@@ -1,39 +0,0 @@
-import {
-  SearchHandler,
-  addParentTerm,
-  getChildTerms
-} from "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  SearchHandler,
-  addParentTerm,
-  getChildTerms
-};
-//# sourceMappingURL=geneVariant-OIKEV4JM.js.map

package/dist/geneVariant.integration.spec-T6BINPIN.js

@@ -1,196 +0,0 @@
-import {
-  hg38
-} from "./chunk-7VB2BKXW.js";
-import {
-  sleep
-} from "./chunk-SSPDNHDW.js";
-import {
-  require_tape
-} from "./chunk-QWOE5YTB.js";
-import {
-  SearchHandler,
-  vocabInit
-} from "./chunk-YWUVCXFS.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-3QBZ2Y77.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-KWM6B3NL.js";
-import "./chunk-UCLS2SVB.js";
-import "./chunk-6ZCHECOT.js";
-import "./chunk-MVTCBVSX.js";
-import "./chunk-2K5DSRBJ.js";
-import "./chunk-X4NI4JLQ.js";
-import "./chunk-L4QG7XZE.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-UWYCEYML.js";
-import "./chunk-7UHUOC6F.js";
-import "./chunk-ZYY54HBU.js";
-import "./chunk-EGWVYY7K.js";
-import "./chunk-AMYSEKPF.js";
-import "./chunk-TV74I3Y5.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// termdb/handlers/test/geneVariant.integration.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-async function getVocabApi() {
-  const vocabApi2 = vocabInit({ state: { vocab: { genome: "hg38-test", dslabel: "TermdbTest" } } });
-  if (!vocabApi2) throw "vocabApi is missing";
-  await vocabApi2.getTermdbConfig();
-  return vocabApi2;
-}
-var vocabApi = await getVocabApi();
-var handler = new SearchHandler();
-function getHolder() {
-  const holder = select_default("body").append("div");
-  return holder;
-}
-async function initializeSearchHandler(opts) {
-  const callback = opts.callback || (() => {
-  });
-  await handler.init({
-    holder: opts.holder,
-    app: { vocabApi },
-    genomeObj: hg38,
-    callback
-  });
-}
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- geneVariant search handler -***-");
-  test.end();
-});
-(0, import_tape.default)("Search handler layout", async (test) => {
-  const holder = getHolder();
-  await initializeSearchHandler({ holder });
-  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
-  test.ok(
-    mutationTypeRadiosDiv.selectAll('input[type="radio"]').size() > 0,
-    "Mutation type radio buttons should be present"
-  );
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  test.equal(
-    inputTypeRadiosDiv.selectAll('input[type="radio"]').size(),
-    2,
-    "Input type radio buttons should be present"
-  );
-  const searchDiv = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]');
-  test.equal(searchDiv.selectAll('input[type="search"]').size(), 1, "Gene search input should be present");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Single gene input", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(tw.term.type, "geneVariant", "term.type should be geneVariant");
-  test.equal(tw.q.type, "predefined-groupset", "q.type should be predefined-groupset");
-  test.equal(tw.q.predefined_groupset_idx, 0, "q.predefined_groupset_idx should be 0");
-  test.equal(tw.term.genes.length, 1, "term.genes[] should have length of 1");
-  test.deepEqual(
-    tw.term.genes[0],
-    { kind: "gene", id: "TP53", gene: "TP53", name: "TP53", type: "geneVariant" },
-    "term.genes[0] should have expected structure"
-  );
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Change mutation type", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const mutationTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-mutationTypeRadios"]');
-  const mutationTypeRadios = mutationTypeRadiosDiv.selectAll('input[type="radio"]');
-  const thirdRadio = mutationTypeRadios.nodes()[2];
-  thirdRadio.click();
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  const geneSetDiv = inputTypeRadiosDiv.selectAll("div").filter((d) => d.value == "geneset");
-  test.equal(geneSetDiv.style("display"), "none", "Gene set option should be hidden for CNV");
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(tw.q.predefined_groupset_idx, 2, "q.predefined_groupset_idx should be 2 upon selecting third radio button");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Gene set input", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
-  const secondRadio = inputTypeRadios.nodes()[1];
-  secondRadio.click();
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  geneSearchInput.value = "KRAS";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
-  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
-  await sleep(100);
-  submitButton.click();
-  await sleep(100);
-  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
-  test.equal(tw.term.name, "TP53, KRAS", "term.name should concatenate gene names");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Gene set input - custom name", async (test) => {
-  let tw;
-  const callback = (_tw) => {
-    tw = _tw;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const inputTypeRadiosDiv = holder.select('[data-testid="sjpp-genevariant-genesetTypeRadios"]');
-  const inputTypeRadios = inputTypeRadiosDiv.selectAll('input[type="radio"]');
-  const secondRadio = inputTypeRadios.nodes()[1];
-  secondRadio.click();
-  const geneSearchInput = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').select('input[type="search"]').node();
-  geneSearchInput.value = "TP53";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  geneSearchInput.value = "KRAS";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  const nameInput = holder.select('[data-testid="sja_genesetinput_name"]').node();
-  nameInput.value = "Test gene set";
-  const buttons = holder.select('[data-testid="sjpp-genevariant-geneSearchDiv"]').selectAll("button").nodes();
-  const submitButton = buttons.find((btn) => btn.textContent.trim() === "Submit");
-  await sleep(100);
-  submitButton.click();
-  await sleep(100);
-  test.equal(tw.term.genes.length, 2, "term.genes[] should have length of 2");
-  test.equal(tw.term.name, "Test gene set", "term.name should be custom name");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-//# sourceMappingURL=geneVariant.integration.spec-T6BINPIN.js.map