@sjcrh/proteinpaint-client 2.191.4 → 2.192.0

package/dist/hierCluster.integration.spec-SSDN7LSH.js

@@ -1,395 +0,0 @@
-import {
-  appInit
-} from "./chunk-N2SKTCDK.js";
-import "./chunk-HKSNADSX.js";
-import "./chunk-SKMFMGCD.js";
-import {
-  detectOne,
-  sleep
-} from "./chunk-DJQTUDJM.js";
-import "./chunk-W55XSG6K.js";
-import {
-  require_tape
-} from "./chunk-QWOE5YTB.js";
-import "./chunk-4KY4XKJV.js";
-import "./chunk-74ZU4BT6.js";
-import "./chunk-IW57W7EQ.js";
-import "./chunk-ZTYNN6G5.js";
-import "./chunk-DKVUOBIE.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-LTOBEUM2.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-WKNI3HRQ.js";
-import "./chunk-VGYTAYFK.js";
-import "./chunk-67DBIM6H.js";
-import {
-  fillTermWrapper
-} 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 {
-  NUMERIC_DICTIONARY_TERM,
-  TermTypes
-} from "./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";
-
-// plots/matrix/test/hierCluster.integration.spec.js
-var import_tape = __toESM(require_tape(), 1);
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- plots/hierCluster.js -***-");
-  test.end();
-});
-(0, import_tape.default)("basic render", async (test) => {
-  test.timeoutAfter(4e3);
-  const { app, hc } = await getHierClusterApp({ terms: getGenes() });
-  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 4, "should render 4 gene rows");
-  test.equal(hc.dom.sampleLabelG.selectAll(".sjpp-matrix-label").size(), 60, "should render 60 sample columns");
-  if (test._ok) app.destroy();
-  test.end();
-});
-(0, import_tape.default)("filter", async (test) => {
-  test.timeoutAfter(4e3);
-  const { app, hc } = await getHierClusterApp({
-    terms: getGenes(),
-    filter: {
-      type: "tvslst",
-      join: "",
-      in: true,
-      lst: [{ type: "tvs", tvs: { term: { id: "diaggrp" }, values: [{ key: "Acute lymphoblastic leukemia" }] } }]
-    }
-  });
-  test.equal(hc.dom.sampleLabelG.selectAll(".sjpp-matrix-label").size(), 36, "should render 36 sample columns");
-  if (test._ok) app.destroy();
-  test.end();
-});
-(0, import_tape.default)("avoid race condition - specified gene list", async (test) => {
-  test.timeoutAfter(4e3);
-  test.plan(4);
-  const { app, hc } = await getHierClusterApp({ terms: getGenes() });
-  const termgroups = structuredClone(hc.config.termgroups);
-  const lst = await Promise.all([
-    fillTermWrapper({ term: { gene: "KRAS", name: "KRAS", type: "geneExpression" } }, app.vocabApi),
-    fillTermWrapper({ term: { gene: "AKT1", name: "AKT1", type: "geneExpression" } }, app.vocabApi),
-    fillTermWrapper({ term: { gene: "TP53", name: "TP53", type: "geneExpression" } }, app.vocabApi),
-    fillTermWrapper({ term: { gene: "BCR", name: "BCR", type: "geneExpression" } }, app.vocabApi)
-  ]);
-  termgroups[0].lst = lst;
-  const responseDelay = 250;
-  hc.origRequestData = hc.requestData;
-  hc.requestData = async () => {
-    const lst2 = hc.config.termgroups[0].lst;
-    const data = await hc.origRequestData({});
-    if (lst2.length === 3) return data;
-    await sleep(250);
-    return data;
-  };
-  const prom = {};
-  const postRenderTest = new Promise((resolve) => {
-    prom.resolve = resolve;
-  });
-  app.on("postRender.test1", () => {
-    app.on("postRender.test1", null);
-    prom.resolve();
-  });
-  await Promise.all([
-    app.dispatch({
-      type: "plot_edit",
-      id: hc.id,
-      config: { termgroups }
-    }),
-    (async () => {
-      await sleep(0);
-      const termgroups2 = structuredClone(hc.config.termgroups);
-      termgroups2[0].lst = lst.slice(0, 3);
-      await app.dispatch({
-        type: "plot_edit",
-        id: hc.id,
-        config: { termgroups: termgroups2 }
-      });
-    })()
-  ]);
-  await postRenderTest;
-  await sleep(responseDelay + 500);
-  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 3, "should render 3 gene rows");
-  const rects = hc.dom.seriesesG.selectAll(".sjpp-mass-series-g rect");
-  const hits = rects.filter((d) => d.key !== "BCR" && d.value.class != "WT" && d.value.class != "Blank");
-  test.equal(
-    rects.size(),
-    180,
-    "should have the expected total number of matrix cell rects, inlcuding WT and not tested"
-  );
-  test.equal(hits.size(), 180, "should have the expected number of matrix cell rects with hits");
-  test.equal(
-    app.Inner.dom.holder.selectAll(".sja_errorbar").filter(function() {
-      return this.style.display != "none";
-    }).size(),
-    0,
-    "should not display errors"
-  );
-  if (test._ok) app.destroy();
-});
-(0, import_tape.default)("avoid race condition - reused fetch response cache", async (test) => {
-  test.timeoutAfter(4e3);
-  test.plan(4);
-  const { app, hc } = await getHierClusterApp({ terms: getGenes() });
-  const termgroups = structuredClone(hc.config.termgroups);
-  const responseDelay = 250;
-  hc.origRequestData = hc.requestData;
-  hc.requestData = async () => {
-    const lst = hc.config.termgroups[0].lst;
-    const data = await hc.origRequestData({});
-    if (lst.length === 3) return data;
-    return data;
-    await sleep(responseDelay);
-    return data;
-  };
-  const prom = {};
-  const postRenderTest = new Promise((resolve) => {
-    prom.resolve = resolve;
-  });
-  app.on("postRender.test1", () => {
-    app.on("postRender.test1", null);
-    prom.resolve();
-  });
-  await Promise.all([
-    app.dispatch({
-      type: "plot_edit",
-      id: hc.id,
-      config: { termgroups }
-    }),
-    (async () => {
-      await sleep(0);
-      const _termgroups = structuredClone(termgroups);
-      _termgroups[0].lst = _termgroups[0].lst.slice(0, 3);
-      await app.dispatch({
-        type: "plot_edit",
-        id: hc.id,
-        config: { termgroups: _termgroups }
-      });
-    })()
-  ]);
-  await postRenderTest;
-  await sleep(responseDelay + 500);
-  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 3, "should render 3 gene rows");
-  const rects = hc.dom.seriesesG.selectAll(".sjpp-mass-series-g rect");
-  const hits = rects.filter((d) => d.key !== "BCR" && d.value.class != "WT" && d.value.class != "Blank");
-  test.equal(
-    rects.size(),
-    180,
-    "should have the expected total number of matrix cell rects, inlcuding WT and not tested"
-  );
-  test.equal(hits.size(), 180, "should have the expected number of matrix cell rects with hits");
-  test.equal(
-    app.Inner.dom.holder.selectAll(".sja_errorbar").filter(function() {
-      return this.style.display != "none";
-    }).size(),
-    0,
-    "should not display errors"
-  );
-  if (test._ok) app.destroy();
-});
-(0, import_tape.default)("dendrogram click", async function(test) {
-  test.timeoutAfter(5e3);
-  test.plan(3);
-  let numRenders = 0;
-  const { app, hc } = await getHierClusterApp({ terms: getGenes() });
-  const img = await detectOne({ elem: hc.dom.topDendrogram.node(), selector: "image" });
-  const svgBox = hc.dom.svg.node().getBoundingClientRect();
-  const imgBox = img.getBBox();
-  img.dispatchEvent(
-    new MouseEvent("click", {
-      //'view': window,
-      bubbles: true,
-      cancelable: true,
-      clientX: svgBox.x + hc.dimensions.xOffset + imgBox.x + imgBox.width / 2,
-      clientY: svgBox.y + imgBox.y + imgBox.height / 2
-    })
-  );
-  test.deepEqual(
-    hc.clickedClusterIds,
-    [
-      46,
-      54,
-      37,
-      28,
-      27,
-      51,
-      53,
-      44,
-      49,
-      25,
-      34,
-      11,
-      20,
-      41,
-      45,
-      29,
-      33,
-      17,
-      15,
-      2,
-      38,
-      42,
-      30,
-      36,
-      22,
-      9,
-      14,
-      3,
-      4,
-      31,
-      13,
-      26,
-      1,
-      16,
-      8,
-      10,
-      5,
-      6,
-      7,
-      23,
-      47,
-      48,
-      35,
-      43,
-      21,
-      32,
-      18,
-      24,
-      56
-    ],
-    `should give the expected clickedClusterIds`
-  );
-  test.deepEqual(
-    ["Zoom in", "List 50 samples"],
-    [...hc.dom.dendroClickMenu.d.node().querySelectorAll(".sja_menuoption")].map((elem) => elem.__data__.label),
-    "should show the expected menu options on dendrogram click"
-  );
-  hc.dom.dendroClickMenu.d.node().querySelector(".sja_menuoption").parentNode.lastChild.click();
-  await sleep(5);
-  test.equal(
-    hc.dom.dendroClickMenu.d.node().querySelectorAll(".sjpp_row_wrapper").length,
-    50,
-    "should list the expected number of samples"
-  );
-  if (test._ok) {
-    hc.dom.dendroClickMenu.clear().hide();
-    app.destroy();
-  }
-});
-(0, import_tape.default)("numericDictTerm", async function(test) {
-  const terms = [
-    {
-      id: "aaclassic_5",
-      // tw.id must be provided
-      term: { id: "aaclassic_5", name: "a1", type: "float" },
-      // requires {id,name,type}; term.name doesn't need to be real, unique name works
-      q: { mode: "continuous" }
-      // set to continuous to avoid validating tw.term.bins
-    },
-    { id: "hrtavg", term: { id: "hrtavg", name: "a2", type: "float" }, q: { mode: "continuous" } },
-    { id: "agedx", term: { id: "agedx", name: "a3", type: "float" }, q: { mode: "continuous" } }
-  ];
-  const { app, hc } = await getHierClusterApp({ terms, dataType: NUMERIC_DICTIONARY_TERM });
-  test.equal(hc.dom.termLabelG.selectAll(".sjpp-matrix-label").size(), 3, "should render 3 rows");
-  if (test._ok) app.destroy();
-  test.end();
-});
-async function getHierClusterApp(_opts = {}) {
-  const holder = select_default("body").append("div");
-  const defaults = {
-    debug: true,
-    holder,
-    genome: "hg38-test",
-    state: {
-      genome: "hg38-test",
-      dslabel: "TermdbTest",
-      termfilter: { filter0: _opts.filter0 },
-      plots: [
-        {
-          chartType: "hierCluster",
-          dataType: _opts.dataType || TermTypes.GENE_EXPRESSION,
-          settings: {
-            hierCluster: {
-              termGroupName: "Gene Expression (CGC genes only)"
-            },
-            matrix: {
-              // the matrix autocomputes the colw based on available screen width,
-              // need to set an exact screen width for consistent tests using getBBox()
-              availContentWidth: 1200
-            }
-          },
-          // force empty termgroups, genes since the instance requestData() will not have expression data,
-          // and will cause a non-trival error if using the actual requestData(), which will be mocked below
-          termgroups: [],
-          // _opts.termgroups || [],
-          // !!! there will be an initial load error since this is an empty geneset,
-          // !!! but will be ignored since it's not relevant to this test
-          terms: _opts.terms || [],
-          filter: _opts.filter
-        }
-      ]
-    },
-    app: {
-      features: ["recover"],
-      callbacks: _opts?.app?.callbacks || {}
-    },
-    recover: {
-      undoHtml: "Undo",
-      redoHtml: "Redo",
-      resetHtml: "Restore",
-      adjustTrackedState(state) {
-        const s = structuredClone(state);
-        delete s.termfilter.filter0;
-        return s;
-      }
-    },
-    hierCluster: _opts?.hierCluster || {}
-  };
-  const opts = Object.assign(defaults, _opts);
-  const app = await appInit(opts);
-  holder.select(".sja_errorbar").node()?.lastChild?.click();
-  const hc = Object.values(app.Inner.components.plots).find(
-    (p) => p.type == "hierCluster" || p.chartType == "hierCluster"
-  ).Inner;
-  return { app, hc };
-}
-function getGenes() {
-  return [
-    { gene: "AKT1", type: "geneExpression" },
-    { gene: "TP53", type: "geneExpression" },
-    { gene: "BCR", type: "geneExpression" },
-    { gene: "KRAS", type: "geneExpression" }
-  ];
-}
-//# sourceMappingURL=hierCluster.integration.spec-SSDN7LSH.js.map

package/dist/hierCluster.interactivity-DKBSJ644.js

@@ -1,54 +0,0 @@
-import {
-  addSelectedRowsOptions,
-  addSelectedSamplesOptions,
-  getAllChildrenClusterIds,
-  getClusterFromLeftDendrogram,
-  getClusterFromTopDendrogram,
-  setClusteringBtn,
-  showTable4selectedRows,
-  showTable4selectedSamples,
-  triggerZoomBranch
-} from "./chunk-NSXZPWRP.js";
-import "./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 "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  addSelectedRowsOptions,
-  addSelectedSamplesOptions,
-  getAllChildrenClusterIds,
-  getClusterFromLeftDendrogram,
-  getClusterFromTopDendrogram,
-  setClusteringBtn,
-  showTable4selectedRows,
-  showTable4selectedSamples,
-  triggerZoomBranch
-};
-//# sourceMappingURL=hierCluster.interactivity-DKBSJ644.js.map

package/dist/hierCluster.renderers-OG6LZAT7.js

@@ -1,21 +0,0 @@
-import {
-  maySetSandboxHeader,
-  plotDendrogramHclust,
-  renderImage
-} from "./chunk-SHWLROJG.js";
-import "./chunk-NOEAT6CX.js";
-import "./chunk-4UWS5Y3N.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 {
-  maySetSandboxHeader,
-  plotDendrogramHclust,
-  renderImage
-};
-//# sourceMappingURL=hierCluster.renderers-OG6LZAT7.js.map

package/dist/imagePlot-M5JSHEY4.js

@@ -1,163 +0,0 @@
-import {
-  PlotBase,
-  controlsInit
-} 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 {
-  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 "./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 "./chunk-I6Y4O3RR.js";
-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-
-// plots/imagePlot.ts
-var ImagePlot = class _ImagePlot extends PlotBase {
-  static {
-    this.type = "imagePlot";
-  }
-  constructor(opts, api) {
-    super(opts, api);
-    this.opts = opts;
-    this.api = api;
-    this.type = _ImagePlot.type;
-    if (this.opts?.header) {
-      if (this.opts?.headerText)
-        this.opts.header.append("span").style("padding-right", "5px").text(this.opts.headerText);
-      this.opts.header.append("span").text("IMAGE PLOT").style("font-size", "0.7em").style("opacity", 0.6);
-    }
-  }
-  getState(appState) {
-    const config = appState.plots.find((p) => p.id === this.id);
-    if (!config) {
-      throw `No plot with id='${this.id}' found. Did you set this.id before this.api = getComponentApi(this)?`;
-    }
-    return {
-      config,
-      termfilter: appState.termfilter,
-      vocab: appState.vocab
-    };
-  }
-  async init(appState) {
-    const config = this.getState(appState).config;
-    const holder = this.opts.holder.append("div").attr("data-testid", "sjpp-imagePlot-holder");
-    this.dom = {
-      holder,
-      controlsHolder: holder.append("div").attr("data-testid", "sjpp-imagePlot-controlsDiv").style("display", "inline-block"),
-      imageHolder: holder.append("div").attr("data-testid", "sjpp-imagePlot-imagesDiv").style("display", "inline-block")
-    };
-    const sampleId = config.sample?.sampleId || config.sample?.sID;
-    let images;
-    if (config?.imgDir) {
-      const img = await dofetch3(
-        `img?file=${config.imgDir.folder}${config.imgDir.folder.endsWith("/") ? "" : "/"}${sampleId}/${config.imgDir.fileName}`
-      );
-      if (!img || img?.error) throw new Error(img?.error || "Error fetching image");
-      images = [img];
-    } else {
-      const result = await this.app.vocabApi.getSampleImages(sampleId);
-      if (result.error) throw new Error(result.error);
-      images = result.images;
-    }
-    for (const img of images) {
-      this.dom.imageHolder.append("img").style("padding", "10px").attr("src", img.src).attr("width", config.settings.imagePlot.width).attr("height", config.settings.imagePlot.height);
-    }
-  }
-  async setControls() {
-    this.components = {
-      controls: await controlsInit({
-        app: this.app,
-        id: this.id,
-        holder: this.dom.controlsHolder,
-        inputs: [
-          {
-            label: "Image width",
-            type: "number",
-            chartType: this.type,
-            settingsKey: "width"
-          },
-          {
-            label: "Image height",
-            type: "number",
-            chartType: this.type,
-            settingsKey: "height"
-          }
-        ]
-      })
-    };
-  }
-  async main() {
-  }
-};
-async function getPlotConfig(opts) {
-  const settings = getDefaultImagePlotSettings();
-  if (opts.settings) copyMerge(settings, opts.settings);
-  const config = {
-    settings: {
-      controls: {
-        isOpen: false
-      },
-      imagePlot: settings
-    }
-  };
-  return copyMerge(config, opts);
-}
-function getDefaultImagePlotSettings() {
-  return {
-    width: 500,
-    height: 500
-  };
-}
-var imagePlotInit = getCompInit(ImagePlot);
-var componentInit = imagePlotInit;
-async function renderImagePlot(state, holder, sample) {
-  const opts = {
-    holder,
-    state: {
-      vocab: state.vocab,
-      plots: [
-        {
-          chartType: "imagePlot",
-          sample
-        }
-      ]
-    }
-  };
-  const plot = await import("./plot.app-NRUARQCN.js");
-  await plot.appInit(opts);
-}
-export {
-  componentInit,
-  getDefaultImagePlotSettings,
-  getPlotConfig,
-  imagePlotInit,
-  renderImagePlot
-};
-//# sourceMappingURL=imagePlot-M5JSHEY4.js.map

package/dist/importPlot-YH7ZY6RJ.js

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package/dist/isoformExpression-EV27MKYZ.js

@@ -1,40 +0,0 @@
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-import "./chunk-OMR2DT66.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HFNDKYVF.js";
-export {
-  SearchHandler,
-  filterIsoforms
-};
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