@sjcrh/proteinpaint-client 2.207.0 → 2.207.1

package/dist/expclust.gdc.spec-TFJEXEAA.js

@@ -1,302 +0,0 @@
-import {
-  getRunPp
-} from "./chunk-6KCG2NFA.js";
-import {
-  detectOne
-} from "./chunk-FYXIK6Y6.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import {
-  runproteinpaint
-} from "./chunk-XZXGNMNK.js";
-import "./chunk-26VFFI2G.js";
-import "./chunk-Y34GYPF6.js";
-import "./chunk-LWOWC4PF.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-XERHX42E.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-B2XYBFGT.js";
-import "./chunk-4FTH4L3A.js";
-import "./chunk-IGJOH5LV.js";
-import "./chunk-NQDF3U2C.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-CCYVGZGI.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-N7DVQTPC.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-GRVO7RW4.js";
-import "./chunk-7CJKL3LK.js";
-import "./chunk-HZ3TCGBK.js";
-import "./chunk-IZUYLFOX.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/test/expclust.gdc.spec.js
-var import_tape = __toESM(require_tape(), 1);
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- plots/hierCluster.gdc -***-");
-  test.end();
-});
-(0, import_tape.default)("TME genes and dictionary variables, survival", function(test) {
-  test.timeoutAfter(6e4);
-  runpp({
-    state: {
-      nav: { header_mode: "hidden" },
-      // must set to hidden for gdc, since it lacks termdb method to get cohort size..
-      plots: [
-        {
-          chartType: "hierCluster",
-          dataType: "geneExpression",
-          /* not needed, reenable to add other customizations
-          settings: {
-          	hierCluster: {
-          		termGroupName: 'Gene Expression (CGC genes only)'
-          	}
-          },
-          */
-          terms: TMEgenes,
-          termgroups: [{ name: "Variables", lst: dictTerms }]
-        }
-      ]
-    },
-    hierCluster: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(hierCluster) {
-    hierCluster.on("postRender.test", null);
-    await testhierClusterrendering(hierCluster);
-    await testLegendRendering(hierCluster);
-    await testBtnRendering(hierCluster);
-    await testZoom(hierCluster);
-    await testCaseLabelCharLimit(hierCluster);
-    await testClusteringMethod(hierCluster);
-    await testRowColumnDendrograms(hierCluster);
-    await testzScoreCap(hierCluster);
-    if (test._ok) hierCluster.Inner.app.destroy();
-    test.end();
-  }
-  async function testhierClusterrendering(hierCluster) {
-    await detectOne({ elem: hierCluster.Inner.dom.seriesesG.node(), selector: "image" });
-    test.equal(hierCluster.Inner.dom.seriesesG.selectAll("image").size(), 1, `should render 1 <image> element`);
-    test.equal(
-      hierCluster.Inner.dom.svg.selectAll(".sjpp-matrix-term-label-g").node().querySelectorAll("text").length,
-      TMEgenes.length + dictTerms.length,
-      `should render ${TMEgenes.length + dictTerms.length} <series> elements`
-    );
-    test.pass("hierCluster rendered");
-  }
-  async function testLegendRendering(hierCluster) {
-    test.true(hierCluster.Inner.dom.legendG.nodes().length > 0, `should render legend`);
-    test.true(hierCluster.Inner.dom.legendG.selectAll("rect").size() > 0, `should render legend rects`);
-    test.true(hierCluster.Inner.dom.legendG.selectAll("text").size() > 0, `should render legend text`);
-  }
-  async function testBtnRendering(hierCluster) {
-    test.equal(hierCluster.Inner.dom.controls.node().querySelectorAll("button").length, 9, `should render buttons`);
-  }
-  async function testZoom(hierCluster) {
-    await hierCluster.Inner.app.dispatch({
-      type: "plot_edit",
-      id: hierCluster.Inner.id,
-      config: {
-        settings: {
-          hierCluster: {
-            zoomLevel: 10
-          },
-          //note zoom works via matrix settings, not hierCluster
-          matrix: {
-            zoomLevel: 10
-          }
-        }
-      }
-    });
-    test.equal(
-      hierCluster.Inner.config.settings.hierCluster.zoomLevel,
-      10,
-      `config.settings.hiercluster.zoomlevel does not allow zoom in on the UI`
-    );
-    test.equal(
-      hierCluster.Inner.config.settings.matrix.zoomLevel,
-      10,
-      `config.settings.matrix.zoomlevel allows zoom in on the UI`
-    );
-  }
-  async function testCaseLabelCharLimit(hierCluster) {
-    await hierCluster.Inner.app.dispatch({
-      type: "plot_edit",
-      id: hierCluster.Inner.id,
-      config: {
-        settings: {
-          matrix: {
-            collabelmaxchars: 10
-          }
-        }
-      }
-    });
-    test.equal(
-      hierCluster.Inner.config.settings.matrix.collabelmaxchars,
-      10,
-      `should limit case label characters to ${hierCluster.Inner.config.settings.matrix.collabelmaxchars}`
-    );
-  }
-  async function testClusteringMethod(hierCluster) {
-    await hierCluster.Inner.app.dispatch({
-      type: "plot_edit",
-      id: hierCluster.Inner.id,
-      config: {
-        settings: {
-          hierCluster: {
-            clusterMethod: "complete",
-            distanceMethod: "euclidean"
-          }
-        }
-      }
-    });
-    test.equal(
-      hierCluster.Inner.config.settings.hierCluster.clusterMethod,
-      "complete",
-      `should change clustering method to ${hierCluster.Inner.config.settings.hierCluster.clusterMethod}`
-    );
-    test.equal(
-      hierCluster.Inner.config.settings.hierCluster.distanceMethod,
-      "euclidean",
-      `should change clustering method to ${hierCluster.Inner.config.settings.hierCluster.distanceMethod}`
-    );
-  }
-  async function testRowColumnDendrograms(hierCluster) {
-    await hierCluster.Inner.app.dispatch({
-      type: "plot_edit",
-      id: hierCluster.Inner.id,
-      config: {
-        settings: {
-          hierCluster: {
-            colDendrogramHeight: 100,
-            rowDendrogramWidth: 200
-          }
-        }
-      }
-    });
-    test.equal(
-      hierCluster.Inner.config.settings.hierCluster.colDendrogramHeight,
-      100,
-      `should change column dendrogram height to ${hierCluster.Inner.config.settings.hierCluster.colDendrogramHeight}`
-    );
-    test.equal(
-      hierCluster.Inner.config.settings.hierCluster.rowDendrogramWidth,
-      200,
-      `should change row dendrogram width to ${hierCluster.Inner.config.settings.hierCluster.rowDendrogramWidth}`
-    );
-  }
-  async function testzScoreCap(hierCluster) {
-    await hierCluster.Inner.app.dispatch({
-      type: "plot_edit",
-      id: hierCluster.Inner.id,
-      config: {
-        settings: {
-          hierCluster: {
-            zScoreCap: 10
-          }
-        }
-      }
-    });
-    test.equal(
-      hierCluster.Inner.config.settings.hierCluster.zScoreCap,
-      10,
-      `should cap zscore at ${hierCluster.Inner.config.settings.hierCluster.zScoreCap}`
-    );
-  }
-});
-(0, import_tape.default)("gdc laucher with top variably expressed genes, for gliomas", function(test) {
-  const maxGeneCount = 5;
-  runproteinpaint({
-    debug: true,
-    holder: select_default("body").append("div").node(),
-    noheader: 1,
-    launchGdcHierCluster: true,
-    filter0: {
-      op: "and",
-      content: [{ op: "in", content: { field: "cases.disease_type", value: ["Gliomas"] } }]
-    },
-    settings: {
-      hierCluster: {
-        maxGenes: maxGeneCount
-      }
-    },
-    termgroups: [
-      {
-        name: "Variables",
-        lst: dictTerms
-      }
-    ],
-    opts: {
-      hierCluster: {
-        callbacks: {
-          "postRender.test": runTests
-        }
-      }
-    }
-  });
-  async function runTests(hierCluster) {
-    hierCluster.on("postRender.test", null);
-    await detectOne({ elem: hierCluster.Inner.dom.seriesesG.node(), selector: "image" });
-    test.equal(hierCluster.Inner.dom.seriesesG.selectAll("image").size(), 1, `should render 1 <image> element`);
-    test.equal(
-      hierCluster.Inner.dom.svg.selectAll(".sjpp-matrix-term-label-g").node().querySelectorAll("text").length,
-      maxGeneCount + dictTerms.length,
-      `should render ${maxGeneCount + dictTerms.length} <series> elements`
-    );
-    if (test._ok) hierCluster.Inner.app.destroy();
-    test.end();
-  }
-});
-var runpp = getRunPp("mass", {
-  state: {
-    dslabel: "GDC",
-    genome: "hg38"
-  },
-  debug: 1
-});
-var TMEgenes = [
-  { gene: "KIF11" },
-  { gene: "BUB1B" },
-  { gene: "BUB1" },
-  { gene: "CDK1" },
-  { gene: "CDC20" },
-  { gene: "AURKB" },
-  { gene: "TPX2" },
-  { gene: "CCNB2" },
-  { gene: "CCNA2" },
-  { gene: "TOP2A" },
-  { gene: "AURKA" },
-  { gene: "KIF20A" },
-  { gene: "KIF2C" },
-  { gene: "CDCA8" }
-];
-var dictTerms = [
-  { id: "case.disease_type" },
-  { id: "case.primary_site" },
-  { id: "case.demographic.gender" },
-  { id: "Overall Survival" }
-];
-//# sourceMappingURL=expclust.gdc.spec-TFJEXEAA.js.map