@sjcrh/proteinpaint-client 2.195.1-0 → 2.196.0

package/dist/dictionary-6R4YTXTP.js

@@ -1,118 +0,0 @@
-import {
-  appInit
-} from "./chunk-BY2G7JFL.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IT47WJE7.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-LQJMCE7G.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-BCJGSAEG.js";
-import "./chunk-MXIZBTDI.js";
-import "./chunk-WVVJO7V3.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import "./chunk-7O3STTMH.js";
-import "./chunk-7KRS7L4U.js";
-import "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-TJYRBEBK.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-SOTB4FRE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.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-6R4YTXTP.js.map

package/dist/dnaMethylation-4GIMBCIN.js

@@ -1,38 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-DQ3COI44.js";
-import "./chunk-BY2G7JFL.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IT47WJE7.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-LQJMCE7G.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-BCJGSAEG.js";
-import "./chunk-MXIZBTDI.js";
-import "./chunk-WVVJO7V3.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import "./chunk-7O3STTMH.js";
-import "./chunk-7KRS7L4U.js";
-import "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-TJYRBEBK.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-SOTB4FRE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  SearchHandler
-};
-//# sourceMappingURL=dnaMethylation-4GIMBCIN.js.map

package/dist/dnaMethylation.integration.spec-CVMXGCAW.js

@@ -1,203 +0,0 @@
-import {
-  hg38
-} from "./chunk-7VB2BKXW.js";
-import {
-  SearchHandler
-} from "./chunk-DQ3COI44.js";
-import {
-  sleep
-} from "./chunk-DJQTUDJM.js";
-import {
-  require_tape
-} from "./chunk-TUMA63WX.js";
-import {
-  vocabInit
-} from "./chunk-BY2G7JFL.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-IT47WJE7.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-LQJMCE7G.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-BCJGSAEG.js";
-import "./chunk-MXIZBTDI.js";
-import "./chunk-WVVJO7V3.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import {
-  TermTypes
-} from "./chunk-7O3STTMH.js";
-import "./chunk-7KRS7L4U.js";
-import "./chunk-BKPDYW5T.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-TJYRBEBK.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-SOTB4FRE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HFNDKYVF.js";
-
-// termdb/handlers/test/dnaMethylation.integration.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-var vocabApi = await getVocabApi();
-var handler = new SearchHandler();
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- dnaMethylation search handler -***-");
-  test.end();
-});
-(0, import_tape.default)("Search handler layout", async (test) => {
-  const holder = getHolder();
-  await initializeSearchHandler({ holder });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  test.ok(geneSearchInput, "should display gene search input");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Coordinate search", async (test) => {
-  let term;
-  const callback = (_term) => {
-    term = _term;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  const chr = "chr17";
-  const start = 7661778;
-  const stop = 7687537;
-  const coord = `${chr}:${start}-${stop}`;
-  geneSearchInput.value = coord;
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(term.chr, chr, "term.chr should equal input chr");
-  test.equal(term.start, start, "term.start should equal input start");
-  test.equal(term.stop, stop, "term.stop should equal input stop");
-  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Single position search (chr:pos format)", async (test) => {
-  let term;
-  const callback = (_term) => {
-    term = _term;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  geneSearchInput.value = "chr17:7669073";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(term.chr, "chr17", "term.chr should equal input chr");
-  test.equal(term.start, 7669073, "term.start should be exact position, not 400bp-expanded");
-  test.equal(term.stop, 7669074, "term.stop should be start+1 for a single CpG site");
-  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Single position search (chr:pos-pos format)", async (test) => {
-  let term;
-  const callback = (_term) => {
-    term = _term;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  geneSearchInput.value = "chr17:7669073-7669073";
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  test.equal(term.chr, "chr17", "term.chr should equal input chr");
-  test.equal(term.start, 7669073, "term.start should be exact position, not 400bp-expanded");
-  test.equal(term.stop, 7669074, "term.stop should be start+1 for a single CpG site");
-  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Gene search", async (test) => {
-  let term;
-  const callback = (_term) => {
-    term = _term;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  const geneSymbol = "TP53";
-  geneSearchInput.value = geneSymbol;
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(100);
-  const blockSvg = holder.select('[data-testid="sjpp_block_svg"]').node();
-  test.ok(blockSvg, "should render block svg");
-  const submitBtn = holder.select('[data-testid="sjpp-dnaMethylation-submitDiv"]').select("button").node();
-  submitBtn.click();
-  await sleep(100);
-  test.equal(term.chr, "chr17", "term.chr should be TP53 chr");
-  test.equal(term.start, 7661778, "term.start should be TP53 start");
-  test.equal(term.stop, 7687537, "term.stop should be TP53 stop");
-  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-(0, import_tape.default)("Gene search with navigation", async (test) => {
-  let term;
-  const callback = (_term) => {
-    term = _term;
-  };
-  const holder = getHolder();
-  await initializeSearchHandler({ holder, callback });
-  const geneSearchInput = holder.select(".sja_genesearchinput").node();
-  const geneSymbol = "TP53";
-  geneSearchInput.value = geneSymbol;
-  geneSearchInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(1e3);
-  const blockCoordInput = holder.select(".sja_Block_div").select("input").node();
-  const chr = "chr17";
-  const start = 7682350;
-  const stop = 7684350;
-  const coord = `${chr}:${start}-${stop}`;
-  blockCoordInput.value = coord;
-  blockCoordInput.dispatchEvent(new KeyboardEvent("keyup", { key: "Enter", code: "Enter", bubbles: true }));
-  await sleep(1e3);
-  const submitBtn = holder.select('[data-testid="sjpp-dnaMethylation-submitDiv"]').select("button").node();
-  submitBtn.click();
-  await sleep(100);
-  test.equal(term.chr, chr, "term.chr should equal input chr");
-  test.equal(term.start, 7682349, "term.start should equal input start");
-  test.equal(term.stop, 7684349, "term.stop should equal input stop");
-  test.equal(term.type, TermTypes.DNA_METHYLATION, "term.type should be dnaMethylation");
-  if (test["_ok"]) holder.remove();
-  test.end();
-});
-async function getVocabApi() {
-  const vocabApi2 = vocabInit({ state: { vocab: { genome: "hg38-test", dslabel: "TermdbTest" } } });
-  if (!vocabApi2) throw "vocabApi is missing";
-  await vocabApi2.getTermdbConfig();
-  return vocabApi2;
-}
-function getHolder() {
-  const holder = select_default("body").append("div");
-  return holder;
-}
-async function initializeSearchHandler(opts) {
-  const callback = opts.callback || (() => {
-  });
-  const hg38_copy = structuredClone(hg38);
-  hg38_copy.hasSNP = false;
-  await handler.init({
-    holder: opts.holder,
-    app: { vocabApi },
-    genomeObj: hg38_copy,
-    callback
-  });
-}
-//# sourceMappingURL=dnaMethylation.integration.spec-CVMXGCAW.js.map

package/dist/dofetch-4Z4ZYQ4K.js

@@ -1,51 +0,0 @@
-import {
-  clearServerDataCache,
-  dofetch,
-  dofetch2,
-  dofetch3,
-  getRequiredAuth,
-  getSavedToken,
-  includeEmbedder,
-  isInSession,
-  mayAddJwtToRequest,
-  mayShowAuthUi,
-  namedFetch,
-  processFormData,
-  setAuth,
-  setDsAuthOk,
-  setTokenByDsRoute
-} from "./chunk-WVVJO7V3.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-I73KUUYG.js";
-import "./chunk-7O3STTMH.js";
-import "./chunk-7KRS7L4U.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-TJYRBEBK.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-SOTB4FRE.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-KYBIQBXE.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  clearServerDataCache,
-  dofetch,
-  dofetch2,
-  dofetch3,
-  getRequiredAuth,
-  getSavedToken,
-  includeEmbedder,
-  isInSession,
-  mayAddJwtToRequest,
-  mayShowAuthUi,
-  namedFetch,
-  processFormData,
-  setAuth,
-  setDsAuthOk,
-  setTokenByDsRoute
-};
-//# sourceMappingURL=dofetch-4Z4ZYQ4K.js.map