@sjcrh/proteinpaint-client 2.226.0 → 2.227.1

package/dist/oncomatrix.spec-LDWTZ7LO.js

@@ -0,0 +1,439 @@
+import {
+  getRunPp
+} from "./chunk-V7CB5D7A.js";
+import {
+  detectOne
+} from "./chunk-WA3C3A2M.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import {
+  runproteinpaint
+} from "./chunk-QV6VZLS5.js";
+import "./chunk-O7346S3P.js";
+import "./chunk-IT7EE7LY.js";
+import "./chunk-VBUDRJJG.js";
+import "./chunk-O6T4SDC7.js";
+import "./chunk-3R6VYZYB.js";
+import "./chunk-MKAF2BHB.js";
+import "./chunk-4FTH4L3A.js";
+import "./chunk-6UHSGC6G.js";
+import "./chunk-NB4C446B.js";
+import "./chunk-CXCAQOFB.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-ILAYJZBC.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-VVWZ4BOI.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-2IAELUCN.js";
+import "./chunk-CFYWQJ7F.js";
+import "./chunk-2N345NXD.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import {
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// plots/matrix/test/oncomatrix.spec.js
+var import_tape = __toESM(require_tape(), 1);
+var runpp = getRunPp("mass", {
+  state: {
+    dslabel: "GDC",
+    genome: "hg38"
+  },
+  debug: 1
+});
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- plots/matrix.gdc (aka OncoMatrix) -***-");
+  test.end();
+});
+var termlst = [
+  { term: { name: "IDH1", type: "geneVariant" } },
+  { term: { name: "EGFR", type: "geneVariant" } },
+  { id: "case.disease_type" },
+  { id: "case.diagnoses.age_at_diagnosis" }
+];
+(0, import_tape.default)("2 geneVariant, 2 dict terms", function(test) {
+  test.timeoutAfter(2e4);
+  test.plan(10);
+  runpp({
+    state: {
+      nav: { header_mode: "hidden" },
+      // must set to hidden for gdc, since it lacks termdb method to get cohort size..
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            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
+            }
+          },
+          termgroups: [{ lst: termlst }]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    await testMatrixrendering(matrix);
+    await testLegendRendering(matrix);
+    await testBtnRendering(matrix);
+    await testZoom(matrix);
+    await testCaseLabelCharLimit(matrix);
+    await testRowLabelCharLimit(matrix);
+    await testGroupBy(matrix);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+  async function testMatrixrendering(matrix) {
+    await detectOne({ elem: matrix.Inner.dom.seriesesG.node(), selector: "image" });
+    test.equal(matrix.Inner.dom.seriesesG.selectAll("image").size(), 1, `should render 1 <image> element`);
+    test.equal(
+      matrix.Inner.dom.svg.selectAll(".sjpp-matrix-term-label-g").node().querySelectorAll("text").length,
+      termlst.length,
+      `should render ${termlst.length} <series> elements`
+    );
+  }
+  async function testLegendRendering(matrix) {
+    test.true(matrix.Inner.dom.legendG.nodes().length > 0, `should render legend`);
+    test.true(matrix.Inner.dom.legendG.selectAll("rect").size() > 0, `should render legend rects`);
+    test.true(matrix.Inner.dom.legendG.selectAll("text").size() > 0, `should render legend text`);
+  }
+  async function testBtnRendering(matrix) {
+    test.equal(matrix.Inner.dom.controls.node().querySelectorAll("button").length, 10, `should render buttons`);
+  }
+  async function testZoom(matrix) {
+    await matrix.Inner.app.dispatch({
+      type: "plot_edit",
+      id: matrix.Inner.id,
+      config: {
+        settings: {
+          matrix: {
+            zoomLevel: 10
+          }
+        }
+      }
+    });
+    test.equal(matrix.Inner.config.settings.matrix.zoomLevel, 10, `should zoom in`);
+  }
+  async function testCaseLabelCharLimit(matrix) {
+    await matrix.Inner.app.dispatch({
+      type: "plot_edit",
+      id: matrix.Inner.id,
+      config: {
+        settings: {
+          matrix: {
+            collabelmaxchars: 10
+          }
+        }
+      }
+    });
+    test.equal(
+      matrix.Inner.config.settings.matrix.collabelmaxchars,
+      10,
+      `should limit case label characters to ${matrix.Inner.config.settings.matrix.collabelmaxchars}`
+    );
+  }
+  async function testRowLabelCharLimit(matrix) {
+    await matrix.Inner.app.dispatch({
+      type: "plot_edit",
+      id: matrix.Inner.id,
+      config: {
+        settings: {
+          matrix: {
+            rowlabelmaxchars: 10
+          }
+        }
+      }
+    });
+    test.equal(
+      matrix.Inner.config.settings.matrix.rowlabelmaxchars,
+      10,
+      `should limit row label characters to ${matrix.Inner.config.settings.matrix.rowlabelmaxchars}`
+    );
+  }
+  async function testGroupBy(matrix) {
+    await matrix.Inner.app.dispatch({
+      type: "plot_edit",
+      id: matrix.Inner.id,
+      config: {
+        divideBy: {
+          id: "case.primary_site",
+          q: {
+            type: "values"
+          },
+          term: {
+            id: "case.primary_site",
+            name: "Primary Site",
+            type: "categorical"
+          }
+        }
+      }
+    });
+    test.equal(
+      matrix.Inner.config.divideBy.id,
+      "case.primary_site",
+      `should group by ${matrix.Inner.config.divideBy.id}`
+    );
+  }
+});
+(0, import_tape.default)("2 geneVariant, 2 dict terms, divideBy", function(test) {
+  test.timeoutAfter(2e4);
+  test.plan(5);
+  runpp({
+    state: {
+      nav: { header_mode: "hidden" },
+      // must set to hidden for gdc, since it lacks termdb method to get cohort size..
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            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
+            }
+          },
+          divideBy: {
+            id: "case.disease_type"
+          },
+          termgroups: [{ lst: termlst }]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    await testSortingFunctionalities(matrix);
+    await testMaxCases(matrix);
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+  async function testMaxCases(matrix) {
+    test.equal(matrix.Inner.config.settings.matrix.maxSample, 2e3, `should limit max cases to 2000`);
+    await matrix.Inner.app.dispatch({
+      type: "plot_edit",
+      id: matrix.Inner.id,
+      config: {
+        settings: {
+          matrix: {
+            maxSample: 1e3
+          }
+        }
+      }
+    });
+    test.equal(matrix.Inner.config.settings.matrix.maxSample, 1e3, `should limit max cases to 1000`);
+  }
+  async function testSortingFunctionalities(matrix) {
+    await matrix.Inner.app.dispatch({
+      type: "plot_edit",
+      id: matrix.Inner.id,
+      config: {
+        settings: {
+          matrix: {
+            groupSamplesBy: "disease_type"
+          }
+        }
+      }
+    });
+    test.equal(
+      matrix.Inner.config.settings.matrix.groupSamplesBy,
+      "disease_type",
+      `should group samples by ${matrix.Inner.config.settings.matrix.groupSamplesBy}`
+    );
+    await matrix.Inner.app.dispatch({
+      type: "plot_edit",
+      id: matrix.Inner.id,
+      config: {
+        settings: {
+          matrix: {
+            sortSampleGrpsBy: "hits"
+          }
+        }
+      }
+    });
+    test.equal(
+      matrix.Inner.config.settings.matrix.sortSampleGrpsBy,
+      "hits",
+      `should sort sample groups by ${matrix.Inner.config.settings.matrix.sortSampleGrpsBy}`
+    );
+    await matrix.Inner.app.dispatch({
+      type: "plot_edit",
+      id: matrix.Inner.id,
+      config: {
+        settings: {
+          matrix: {
+            sortSamplesBy: "name"
+          }
+        }
+      }
+    });
+    test.equal(
+      matrix.Inner.config.settings.matrix.sortSamplesBy,
+      "name",
+      `should sort cases by ${matrix.Inner.config.settings.matrix.sortSamplesBy}`
+    );
+  }
+});
+(0, import_tape.default)("2 geneVariant, 2 dict terms, 1 gene exp, 1 survival", function(test) {
+  test.timeoutAfter(2e4);
+  test.plan(1);
+  const termlst2 = [...termlst, { term: { name: "MYC", type: "geneExpression" } }, { id: "Overall Survival" }];
+  runpp({
+    state: {
+      nav: { header_mode: "hidden" },
+      // must set to hidden for gdc, since it lacks termdb method to get cohort size..
+      plots: [
+        {
+          chartType: "matrix",
+          settings: {
+            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
+            }
+          },
+          termgroups: [{ lst: termlst2 }]
+        }
+      ]
+    },
+    matrix: {
+      callbacks: {
+        "postRender.test": runTests
+      }
+    }
+  });
+  async function runTests(matrix) {
+    matrix.on("postRender.test", null);
+    const numSeries = termlst2.length;
+    test.equal(
+      matrix.Inner.dom.svg.selectAll(".sjpp-matrix-term-label-g .sjpp-matrix-label").size(),
+      numSeries,
+      `should render ${numSeries} <series> elements`
+    );
+    if (test._ok) matrix.Inner.app.destroy();
+    test.end();
+  }
+});
+(0, import_tape.default)("launch matrix with gdc launcher and top mutated genes, gliomas", function(test) {
+  test.timeoutAfter(1e5);
+  test.plan(2);
+  const holder = select_default("body").append("div").node();
+  const topGeneNum = 10;
+  runproteinpaint({
+    holder,
+    noheader: 1,
+    launchGdcMatrix: true,
+    filter0: {
+      op: "and",
+      content: [{ op: "in", content: { field: "cases.disease_type", value: ["Gliomas"] } }]
+    },
+    settings: {
+      matrix: {
+        maxGenes: topGeneNum,
+        // asks to load this number of top mutated genes. will be shown in a separate group from termlst
+        maxSample: 1e4
+      }
+    },
+    termgroups: [{ lst: termlst }],
+    opts: {
+      matrix: {
+        callbacks: {
+          "postRender.test": runTests
+        }
+      }
+    }
+  });
+  function runTests(matrix) {
+    test.true(
+      holder.querySelectorAll("svg text").length > 200,
+      "should have the expected number of rendered svg text elements"
+    );
+    const rowcount = topGeneNum + termlst.length;
+    test.equal(
+      select_default(holder).selectAll(".sjpp-matrix-term-label-g").node().querySelectorAll("text").length,
+      rowcount,
+      `should render ${rowcount} <series> elements`
+    );
+    if (test._ok) setTimeout(matrix.destroy, 1e3);
+    test.end();
+  }
+});
+(0, import_tape.default)("top mutated genes from APOLLO-LUAD, CNV only", function(test) {
+  test.timeoutAfter(1e5);
+  test.plan(2);
+  const holder = select_default("body").append("div").node();
+  const topGeneNum = 10;
+  runproteinpaint({
+    holder,
+    noheader: 1,
+    debugmode: true,
+    launchGdcMatrix: true,
+    filter0: { op: "in", content: { field: "cases.project.project_id", value: ["APOLLO-LUAD"] } },
+    settings: {
+      matrix: {
+        maxGenes: topGeneNum,
+        maxSample: 1e4
+      }
+    },
+    opts: {
+      matrix: {
+        debug: 1,
+        callbacks: {
+          "postRender.test": runTests
+        }
+      }
+    }
+  });
+  async function runTests(matrix) {
+    await matrix.Inner.app.dispatch({
+      type: "plot_edit",
+      id: matrix.id,
+      config: {
+        legendGrpFilter: {
+          isAtomic: true,
+          type: "tvslst",
+          in: true,
+          join: "and",
+          lst: []
+        }
+      }
+    });
+    test.true(
+      holder.querySelectorAll("svg text").length > 90,
+      "should have the expected number of rendered svg text elements"
+    );
+    test.equal(
+      select_default(holder).selectAll(".sjpp-matrix-term-label-g").node().querySelectorAll("text").length,
+      topGeneNum,
+      `should render ${topGeneNum} <series> elements`
+    );
+    if (test._ok) setTimeout(matrix.destroy, 1e3);
+    test.end();
+  }
+});
+//# sourceMappingURL=oncomatrix.spec-LDWTZ7LO.js.map