@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/oncomatrix.spec-BME6CQWF.js

@@ -1,448 +0,0 @@
-import {
-  detectOne
-} from "./chunk-ECIBJXFT.js";
-import {
-  getRunPp
-} from "./chunk-FACITNG5.js";
-import {
-  require_tape
-} from "./chunk-TUMA63WX.js";
-import {
-  runproteinpaint
-} from "./chunk-BNAO6N5X.js";
-import "./chunk-5QMBB4SK.js";
-import "./chunk-H3N4KYKL.js";
-import "./chunk-W7OS7BNM.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-5DMVORBB.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-WXPFMVU6.js";
-import "./chunk-WKNI3HRQ.js";
-import "./chunk-NODQZTWK.js";
-import "./chunk-TKW5TW4Z.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-LSEFWW72.js";
-import "./chunk-3SHZTAGF.js";
-import "./chunk-HYOEWQ5P.js";
-import "./chunk-6QCYT6G2.js";
-import "./chunk-FN5XPUPH.js";
-import "./chunk-IIT367QZ.js";
-import "./chunk-RZGEKL77.js";
-import "./chunk-OTTMHVYH.js";
-import "./chunk-GNS6CQMA.js";
-import "./chunk-JVPWIVDT.js";
-import "./chunk-4WF3XDQP.js";
-import "./chunk-7JRDJNLR.js";
-import "./chunk-M3J4MINX.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-MPSLUEI4.js";
-import "./chunk-6PNPHACF.js";
-import "./chunk-WPHUM5S5.js";
-import "./chunk-JNITUVXP.js";
-import "./chunk-2KXLYFAO.js";
-import "./chunk-LOZEKOES.js";
-import "./chunk-VQZ2Z5YU.js";
-import "./chunk-UJELJXJG.js";
-import "./chunk-BZTWTH4Y.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-HFNDKYVF.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-BME6CQWF.js.map