@sjcrh/proteinpaint-client 2.191.4 → 2.193.0

package/dist/NumericHandler.unit.spec-NKLYDVTG.js

@@ -1,219 +0,0 @@
-import {
-  agedx
-} from "./chunk-32AI7I4C.js";
-import {
-  NumericHandler
-} from "./chunk-ZXTHADSC.js";
-import "./chunk-WHI6466S.js";
-import {
-  termjson
-} from "./chunk-DHPLHIVP.js";
-import {
-  sleep
-} from "./chunk-DJQTUDJM.js";
-import {
-  require_tape
-} from "./chunk-QWOE5YTB.js";
-import {
-  TwRouter
-} from "./chunk-SA7APTJR.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-SKREEF3H.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-UI7OCM2A.js";
-import "./chunk-YZK37YCC.js";
-import "./chunk-7EMWHCVW.js";
-import "./chunk-7IYJZZQI.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-QH6W3NVF.js";
-import "./chunk-NOEAT6CX.js";
-import "./chunk-4UWS5Y3N.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.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";
-
-// termsetting/handlers/test/NumericHandler.unit.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-async function getNumericHandler(_opts = {}) {
-  const term = JSON.parse(JSON.stringify(termjson.agedx));
-  if (term.bins.default.type == "regular-bin") term.bins.default.bin_size = 500;
-  const rawTw = {
-    term,
-    q: {
-      mode: "discrete",
-      //type: 'regular-bin',
-      ...term.bins.default
-    }
-  };
-  const tw = await TwRouter.initRaw(rawTw);
-  const handler = new NumericHandler({
-    termsetting: {
-      tw,
-      term: rawTw.term,
-      q: rawTw.q,
-      opts: {
-        numericEditMenuVersion: ["continuous", "discrete", "binary", "spline"],
-        // _opts will any matching override previous opts key-values
-        ..._opts
-      },
-      api: {
-        async runCallback() {
-          const self = handler.termsetting;
-          const q = handler.editHandler.q;
-          self.tw = await TwRouter.initRaw({ term: self.term, q }, self.opts);
-        }
-      },
-      dom: {
-        tip: {
-          hide() {
-          }
-        }
-      },
-      vocabApi: {
-        getViolinBox() {
-          return agedx;
-        },
-        getPercentile() {
-          return {
-            values: [0.03537315665, 3.13072460515, 8.164619357749999, 17.8726813385]
-          };
-        }
-      }
-    }
-  });
-  const holder = select_default("body").append("div").style("width", "fit-content").style("margin", "20px").style("padding", "5px").style("border", "1px solid #000");
-  return {
-    rawTw,
-    tw,
-    handler,
-    holder,
-    destroy: () => {
-      if (handler.editHandler && "destroy" in handler.editHandler) handler.editHandler.destroy();
-      if (typeof handler.destroy == "function") handler.destroy();
-      holder.remove();
-    }
-  };
-}
-(0, import_tape.default)("\n", (test) => {
-  test.comment("-***- NumericHandler.unit.spec -***-");
-  test.end();
-});
-(0, import_tape.default)("tabs data and pill status", async (test) => {
-  const { handler, destroy } = await getNumericHandler();
-  test.deepEqual(
-    handler.tabs.map((t) => t.label),
-    ["Continuous", "Discrete", "Cubic spline", "Binary"],
-    "sets the expected tab data"
-  );
-  test.deepEqual(handler.getPillStatus(), { text: "bin size=500" }, `should give the expected pill status`);
-  if (test._ok) destroy();
-  test.end();
-});
-(0, import_tape.default)("editHandler", async (test) => {
-  const { handler, destroy } = await getNumericHandler();
-  handler.density_data = { min: 0, max: 100 };
-  await handler.setEditHandler(handler.tabs[0]);
-  test.equal(
-    handler.editHandler.constructor.name,
-    "NumContEditor",
-    `sets the expected editHandler for mode='continuous'`
-  );
-  await handler.setEditHandler(handler.tabs[1]);
-  test.equal(
-    handler.editHandler.constructor.name,
-    "NumDiscreteEditor",
-    `sets the expected editHandler for mode='discrete'`
-  );
-  await handler.setEditHandler(handler.tabs[2]);
-  test.equal(handler.editHandler.constructor.name, "NumSplineEditor", `sets the expected editHandler for mode='binary'`);
-  await handler.setEditHandler(handler.tabs[3]);
-  test.equal(handler.editHandler.constructor.name, "NumBinaryEditor", `sets the expected editHandler for mode='spline'`);
-  if (test._ok) destroy();
-  test.end();
-});
-(0, import_tape.default)("showEditMenu, multiple modes", async (test) => {
-  const { handler, holder, destroy } = await getNumericHandler();
-  await handler.showEditMenu(holder);
-  await sleep(0);
-  test.equal(handler.editHandler.dom.density_div.selectAll("svg").size(), 1, `should render a density plot svg`);
-  test.equal(
-    handler.dom.topBar?.selectAll(".sj-toggle-button").size(),
-    4,
-    `should render 4 tabs, one toggle button for each mode`
-  );
-  test.equal(handler.dom.btnDiv?.selectAll("button").size(), 2, `should render an apply and reset button`);
-  test.deepEqual(handler.getPillStatus(), { text: "bin size=500" }, "should have the expected initial pill status");
-  const tabBtns = handler.dom.topBar.node().querySelectorAll("button");
-  tabBtns[2].click();
-  await sleep(10);
-  handler.dom.btnDiv.select("button").node().click();
-  await sleep(10);
-  test.deepEqual(
-    handler.getPillStatus(),
-    { text: "cubic spline" },
-    "should have a different pill status after switching q.modes"
-  );
-  if (test._ok) destroy();
-  test.end();
-});
-(0, import_tape.default)("showEditMenu, single mode", async (test) => {
-  const { handler, holder, destroy } = await getNumericHandler({ numericEditMenuVersion: ["binary"] });
-  await handler.showEditMenu(holder);
-  await sleep(0);
-  test.equal(handler.editHandler.dom.density_div.selectAll("svg").size(), 1, `should render a density plot svg`);
-  test.equal(
-    handler.dom.topBar?.selectAll(".sj-toggle-button").size(),
-    void 0,
-    `should not render mode toggle buttons`
-  );
-  test.equal(handler.dom.btnDiv?.selectAll("button").size(), 2, `should render an apply and reset button`);
-  if (test._ok) destroy();
-  test.end();
-});
-(0, import_tape.default)("apply and reset", async (test) => {
-  test.timeoutAfter(50);
-  test.plan(2);
-  const { handler, holder, destroy } = await getNumericHandler();
-  handler.editHandler = {
-    getEditedQ() {
-      test.pass("should trigger editHandler.getEditedQ() from applyEdits()");
-      return { mode: "discrete", type: "regular-bin" };
-    },
-    undoEdits() {
-      test.pass("should trigger editHandler.undoEdits() from undoEdits()");
-    }
-  };
-  try {
-    await handler.renderButtons(holder);
-    const btns = holder.node()?.querySelectorAll("button");
-    if (btns?.length) {
-      btns[0].click();
-      btns[1].click();
-    }
-    if (test._ok) destroy();
-    test.end();
-  } catch (e) {
-    test.fail("should trigger editHandler.getEditedQ and .undoEdits(): " + e);
-  }
-});
-//# sourceMappingURL=NumericHandler.unit.spec-NKLYDVTG.js.map

package/dist/ProteomeInput-5KMNE3PZ.js

@@ -1,396 +0,0 @@
-import {
-  getDefaultGseaSettings
-} from "./chunk-VHOEJBFP.js";
-import "./chunk-UOVALHAJ.js";
-import {
-  PlotBase,
-  getDefaultVolcanoSettings,
-  sayerror,
-  table2col
-} from "./chunk-SA7APTJR.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-SKREEF3H.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  Tabs
-} from "./chunk-HBW42TDT.js";
-import "./chunk-G6O3URDN.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-UI7OCM2A.js";
-import "./chunk-YZK37YCC.js";
-import {
-  dofetch3
-} from "./chunk-7EMWHCVW.js";
-import "./chunk-7IYJZZQI.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-QH6W3NVF.js";
-import {
-  NumericModes,
-  PROTEOME_DAP
-} from "./chunk-NOEAT6CX.js";
-import {
-  TermTypeGroups
-} from "./chunk-4UWS5Y3N.js";
-import "./chunk-DD4R5P6W.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-KSGA62R2.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-TOU7EVFQ.js";
-import "./chunk-OAWQ6LOO.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/ProteomeInput.ts
-var ProteomeInput = class _ProteomeInput extends PlotBase {
-  static {
-    this.type = "ProteomeInput";
-  }
-  constructor(opts, api) {
-    super(opts, api);
-    this.type = _ProteomeInput.type;
-    this.opts = opts;
-    this.components = {};
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      config,
-      activeCohort: appState.activeCohort,
-      termdbConfig: appState.termdbConfig
-    };
-  }
-  async init(appState) {
-    const state = this.getState(appState);
-    const proteomeDetails = state.config.proteomeDetails;
-    const { organism, assay, cohort } = proteomeDetails;
-    const organisms = state.termdbConfig?.queries?.proteome?.organisms || {};
-    const cohortConfig = organisms[organism]?.assays?.[assay]?.cohorts?.[cohort];
-    this.dom = this.initDom(proteomeDetails);
-    this.tabs = [
-      {
-        label: "Single protein",
-        isVisible: () => true,
-        callback: async (_event, tab) => {
-          await this.renderSingleProtein(tab, proteomeDetails, state.activeCohort);
-          delete tab.callback;
-        }
-      },
-      {
-        label: "Two proteins",
-        isVisible: () => true,
-        callback: async (_event, tab) => {
-          await this.renderTwoProteinSelect(tab, proteomeDetails, state.activeCohort);
-          delete tab.callback;
-        }
-      },
-      {
-        label: "Hierarchical clustering",
-        isVisible: () => true,
-        callback: async (_event, tab) => {
-          await this.renderMultiProteinSelect(tab, proteomeDetails, state.activeCohort);
-          delete tab.callback;
-        }
-      },
-      {
-        label: "DAP Volcano",
-        isVisible: () => !!cohortConfig?.DAPfile,
-        callback: async (_event, tab) => {
-          await this.renderDapVolcano(tab, proteomeDetails);
-          delete tab.callback;
-        }
-      }
-    ];
-    const chartTabs = new Tabs({
-      holder: this.dom.tabs,
-      tabs: this.tabs,
-      tabsPosition: "vertical"
-    });
-    await chartTabs.main();
-  }
-  initDom(proteomeDetails) {
-    const { organism, assay, cohort } = proteomeDetails;
-    this.opts.header.append("span").style("padding-right", "5px").text(`${organism} ${assay}: ${cohort}`);
-    this.opts.header.append("span").text("PROTEOME").style("font-size", "0.7em").style("opacity", "0.6");
-    return {
-      tabs: this.opts.holder.append("div").style("margin", "10px").attr("data-testid", "sjpp-proteome-input-tabs-wrapper")
-    };
-  }
-  getUsecase(proteomeDetails) {
-    const { organism, assay, cohort } = proteomeDetails;
-    return {
-      target: "proteomeAbundance",
-      detail: "term",
-      proteomeDetails: { organism, assay, cohort },
-      label: `Organism: ${organism}; Assay: ${assay}; Sample set: ${cohort}`
-    };
-  }
-  async renderSingleProtein(tab, proteomeDetails, activeCohort) {
-    const { organism, assay, cohort } = proteomeDetails;
-    const row = tab.contentHolder.style("padding", "15px");
-    row.append("div").style("padding", "5px").style("margin-bottom", "5px").text("Select a protein:");
-    const treeHolder = row.append("div");
-    const termdb = await import("./app-AIIN4WDE.js");
-    termdb.appInit({
-      vocabApi: this.app.vocabApi,
-      holder: treeHolder,
-      state: {
-        activeCohort,
-        nav: { header_mode: "search_only" },
-        tree: { usecase: this.getUsecase(proteomeDetails) }
-      },
-      tree: {
-        click_term: (term) => {
-          const t = structuredClone(term.term || term);
-          t.dataTypeDetails = { organism, assay, cohort };
-          const config = {
-            chartType: "summary",
-            term: { term: t, q: { mode: NumericModes.continuous } },
-            assayCohortTitle: `${organism} ${assay}: ${cohort}`,
-            proteomeDetails: { organism, assay, cohort }
-          };
-          const overlayTerm = this.getState(this.app.getState()).termdbConfig?.queries?.proteome?.organisms?.[organism]?.overlayTerm;
-          if (overlayTerm) config.term2 = { term: structuredClone(overlayTerm), q: {} };
-          this.dispatchEdits(config);
-        }
-      }
-    });
-  }
-  addProteinSearchbox(row, proteomeDetails, onSelect) {
-    const usecase = this.getUsecase(proteomeDetails);
-    const tip = new Menu({ padding: "0px" });
-    const searchbox = row.append("input").attr("type", "search").attr("placeholder", "Protein").attr("class", "sja_genesearchinput").style("width", "200px");
-    const mark = row.append("span").style("margin-left", "5px");
-    const word = row.append("span").style("margin-left", "5px").style("font-size", ".8em").style("opacity", 0.6);
-    let debounceTimer;
-    const doSearch = async () => {
-      const v = searchbox.property("value").trim();
-      if (v.length < 2) {
-        tip.hide();
-        return;
-      }
-      try {
-        const data = await this.app.vocabApi.findTerm(v, "", usecase, TermTypeGroups.PROTEOME_ABUNDANCE);
-        if (!data.lst?.length) {
-          mark.style("color", "red").html("&cross;");
-          word.text("No match");
-          tip.hide();
-        } else {
-          tip.clear().showunder(searchbox.node());
-          for (const term of data.lst) {
-            tip.d.append("div").attr("class", "sja_menuoption").style("border-radius", "0px").text(term.name).on("click", () => {
-              tip.hide();
-              searchbox.property("value", term.name);
-              mark.style("color", "green").html("&check;");
-              word.text(term.name);
-              onSelect(term);
-            });
-          }
-        }
-      } catch (e) {
-        mark.style("color", "red").html("&cross;");
-        word.text(e.message || "Error");
-      }
-    };
-    searchbox.on("keyup", async (event) => {
-      if (event.key === "Escape") {
-        tip.hide();
-        return;
-      }
-      clearTimeout(debounceTimer);
-      mark.html("");
-      word.text("");
-      debounceTimer = setTimeout(doSearch, 300);
-    });
-    return { searchbox, mark, word };
-  }
-  async renderTwoProteinSelect(tab, proteomeDetails, _activeCohort) {
-    const { organism, assay, cohort } = proteomeDetails;
-    const holder = tab.contentHolder.style("padding", "10px");
-    let selectedTerm1 = null;
-    let selectedTerm2 = null;
-    const gene1row = holder.append("div").style("padding", "5px");
-    const gene2row = holder.append("div").style("padding", "5px").style("display", "none");
-    const submitBtn = holder.append("button").attr("type", "button").attr("disabled", true);
-    gene1row.append("span").text("Select the first protein:");
-    this.addProteinSearchbox(gene1row, proteomeDetails, (term) => {
-      selectedTerm1 = term;
-      gene2row.style("display", "block");
-    });
-    gene2row.append("span").text("Select the second protein:");
-    this.addProteinSearchbox(gene2row, proteomeDetails, (term) => {
-      selectedTerm2 = term;
-      submitBtn.attr("disabled", null);
-    });
-    submitBtn.text("Submit").style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").style("margin-top", "10px").on("click", async () => {
-      if (!selectedTerm1 || !selectedTerm2) {
-        sayerror(holder, "Please select two proteins.");
-        return;
-      }
-      const t1 = structuredClone(selectedTerm1);
-      const t2 = structuredClone(selectedTerm2);
-      t1.dataTypeDetails = { organism, assay, cohort };
-      t2.dataTypeDetails = { organism, assay, cohort };
-      await this.dispatchEdits({
-        chartType: "summary",
-        term: { term: t1, q: { mode: NumericModes.continuous } },
-        term2: { term: t2, q: { mode: NumericModes.continuous } },
-        assayCohortTitle: `${organism} ${assay}: ${cohort}`,
-        proteomeDetails: { organism, assay, cohort }
-      });
-    });
-  }
-  async renderMultiProteinSelect(tab, proteomeDetails, activeCohort) {
-    const { organism, assay, cohort } = proteomeDetails;
-    const holder = tab.contentHolder.style("padding", "10px");
-    const usecase = this.getUsecase(proteomeDetails);
-    const termdb = await import("./app-AIIN4WDE.js");
-    const treeHolder = holder.append("div");
-    termdb.appInit({
-      vocabApi: this.app.vocabApi,
-      holder: treeHolder,
-      state: {
-        activeCohort,
-        nav: { header_mode: "search_only" },
-        tree: { usecase }
-      },
-      tree: {
-        submit_lst: (termlst) => {
-          const twlst = termlst.map((term) => {
-            const t = structuredClone(term);
-            t.dataTypeDetails = { organism, assay, cohort };
-            return { term: t, q: { mode: NumericModes.continuous } };
-          });
-          if (twlst.length < 3) {
-            alert("At least three proteins are required for hierarchical clustering. Please select more proteins.");
-            return;
-          }
-          this.dispatchEdits({
-            chartType: "hierCluster",
-            dataType: "proteomeAbundance",
-            termgroups: [{ name: "Protein Abundance Cluster", lst: twlst, type: "hierCluster" }],
-            assayCohortTitle: `${organism} ${assay}: ${cohort}`,
-            proteomeDetails: { organism, assay, cohort }
-          });
-        }
-      }
-    });
-    const enforceMinAndLayout = () => {
-      const submitBtn = treeHolder.select("button").node();
-      if (submitBtn) {
-        const selectedCount = treeHolder.selectAll('.sja_menuoption[aria-label="Click to delete"]').size();
-        submitBtn.disabled = selectedCount < 3;
-      }
-      const node = treeHolder.node();
-      const divs = node.querySelectorAll("div");
-      for (const div of divs) {
-        if (div.style.flexWrap === "wrap" && div.style.display === "inline-block") {
-          div.style.display = "flex";
-        }
-      }
-    };
-    const observer = new MutationObserver(enforceMinAndLayout);
-    observer.observe(treeHolder.node(), {
-      childList: true,
-      subtree: true,
-      attributes: true,
-      attributeFilter: ["style"]
-    });
-  }
-  async renderDapVolcano(tab, proteomeDetails) {
-    const { organism, assay, cohort } = proteomeDetails;
-    const holder = tab.contentHolder.style("padding", "15px");
-    const countsDiv = holder.append("div");
-    countsDiv.append("span").text("Loading sample counts...");
-    try {
-      const result = await dofetch3("termdb/dapVolcano", {
-        body: {
-          genome: this.app.vocabApi.vocab.genome,
-          dslabel: this.app.vocabApi.vocab.dslabel,
-          organism,
-          assay,
-          cohort,
-          countsOnly: true
-        }
-      });
-      countsDiv.selectAll("*").remove();
-      if (result.error) throw result.error;
-      const table = table2col({ holder: countsDiv });
-      table.table.style("margin-left", "5px").style("padding", "5px 10px");
-      {
-        const [c1, c2] = table.addRow();
-        c1.html(`<span style="font-size:.8em;font-weight:bold">CONTROL</span>`);
-        c2.html(`${result.sample_size1} samples`);
-      }
-      {
-        const [c1, c2] = table.addRow();
-        c1.html(`<span style="font-size:.8em;font-weight:bold">CASE</span>`);
-        c2.html(`${result.sample_size2} samples`);
-      }
-    } catch (e) {
-      countsDiv.selectAll("*").remove();
-      countsDiv.append("span").style("color", "#999").text("Sample counts unavailable");
-      console.error(e.stack);
-    }
-    holder.append("button").attr("class", "sjpp_apply_btn sja_filter_tag_btn sja_sharp_border").text("Launch Volcano").on("click", async () => {
-      await this.dispatchEdits({
-        chartType: "differentialAnalysis",
-        childType: "volcano",
-        termType: PROTEOME_DAP,
-        headerText: `${organism} ${assay}: ${cohort}`,
-        proteomeDetails: { organism, assay, cohort },
-        settings: {
-          volcano: {
-            ...getDefaultVolcanoSettings({}, { termType: PROTEOME_DAP }),
-            pValueType: "original"
-          },
-          gsea: getDefaultGseaSettings({})
-        },
-        highlightedData: [],
-        hidePlotFilter: true
-      });
-    });
-  }
-  async dispatchEdits(config) {
-    await this.app.dispatch({
-      type: "app_refresh",
-      subactions: [
-        { type: "plot_create", config },
-        { type: "plot_delete", id: this.id }
-      ]
-    });
-  }
-  async main() {
-  }
-};
-var proteomeInputInit = getCompInit(ProteomeInput);
-var componentInit = proteomeInputInit;
-function getPlotConfig(opts) {
-  const config = {
-    chartType: "ProteomeInput",
-    hidePlotFilter: true
-  };
-  return copyMerge(config, opts);
-}
-export {
-  ProteomeInput,
-  componentInit,
-  getPlotConfig,
-  proteomeInputInit
-};
-//# sourceMappingURL=ProteomeInput-5KMNE3PZ.js.map