@sjcrh/proteinpaint-client 2.207.1 → 2.208.0

package/dist/summary.integration.spec-4GTCG6HY.js

@@ -1,409 +0,0 @@
-import {
-  getRunPp
-} from "./chunk-ZENZ5H2Q.js";
-import {
-  detectOne,
-  detectStyle
-} from "./chunk-FYXIK6Y6.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-LGR6CJTW.js";
-import "./chunk-TMXW5HVE.js";
-import "./chunk-M5SYLBBC.js";
-import "./chunk-ONVIVITY.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-7HGZRJZZ.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-Y4PX2ECH.js";
-import "./chunk-4FTH4L3A.js";
-import "./chunk-EKQ7NYOU.js";
-import "./chunk-PC4MFDHP.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-HPAW7XDM.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-BZN2O76M.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-52QHIKH2.js";
-import "./chunk-A2ORIMUJ.js";
-import "./chunk-PPSWNLMG.js";
-import "./chunk-RUBZCKIX.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 "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import {
-  __toESM
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/test/summary.integration.spec.js
-var import_tape = __toESM(require_tape(), 1);
-var runpp = getRunPp("mass", {
-  state: {
-    nav: {
-      header_mode: "hide_search",
-      activeTab: 1
-    },
-    vocab: {
-      dslabel: "TermdbTest",
-      genome: "hg38-test"
-    }
-  },
-  debug: 1
-});
-var tabLabels2Find = ["Barchart", "Violin", "Boxplot"];
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- plots/summary -***-");
-  test.end();
-});
-(0, import_tape.default)('Render summary plot, term: "agedx"', (test) => {
-  test.timeoutAfter(6e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "summary",
-          childType: "barchart",
-          term: {
-            id: "agedx"
-          }
-        }
-      ]
-    },
-    summary: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(summary) {
-    summary.on("postRender.test", null);
-    testHeader(summary, summary.Inner.dom);
-    await testToggleButtons(summary, summary.Inner.dom);
-    await testOrientation(summary);
-    if (test._ok) summary.Inner.app.destroy();
-    test.end();
-  }
-  function testHeader(summary, dom) {
-    const headerText = dom.paneTitleDiv.select("div.sjpp-term-header").node();
-    const configTerm = summary.Inner.config.term.term.name;
-    test.equal(
-      headerText.innerHTML,
-      configTerm,
-      `Header text = ${headerText.innerHTML} should match term name = ${configTerm}`
-    );
-  }
-  async function testToggleButtons(summary, dom) {
-    const toggles = dom.chartToggles.selectAll("div > div> button").nodes().filter((d) => d.__data__.isVisible() == true);
-    let foundLabels = 0;
-    const notFoundLabels = [];
-    for (const toggle of toggles) {
-      if (tabLabels2Find.some((d) => d == toggle.__data__.label)) ++foundLabels;
-      else notFoundLabels.push(toggle.__data__.label);
-    }
-    if (notFoundLabels.length) test.fail(`Should not render tab(s) = ${notFoundLabels}`);
-    test.equal(tabLabels2Find.length, foundLabels, `Should render tabs: ${tabLabels2Find}`);
-    const foundTestPlot = await detectOne({
-      elem: summary.Inner.dom.holder.body.node(),
-      selector: ".sjpp-violin-plot",
-      trigger() {
-        toggles.find((d) => d.__data__.childType == "violin").click();
-      }
-    });
-    test.ok(foundTestPlot, `Should render violin after toggle`);
-    test.equal(summary.Inner.state.config.childType, "violin", `Should toggle to childType = violin`);
-    await detectStyle({
-      elem: summary.Inner.dom.plotDivs.barchart.node(),
-      matcher(mutations) {
-        for (const m of mutations) {
-          if (m.attributeName == "style" && m.target.style.display === "") return m;
-        }
-      },
-      trigger() {
-        toggles.find((d) => d.__data__.childType == "barchart").click();
-      }
-    });
-    test.equal(summary.Inner.state.config.childType, "barchart", `Should toggle back to childType = 'barchart'`);
-  }
-  async function testOrientation(summary) {
-    await summary.Inner.app.dispatch({
-      type: "plot_edit",
-      id: summary.Inner.id,
-      config: {
-        settings: { barchart: { orientation: "vertical" } }
-      }
-    });
-    test.notEqual(
-      summary.Inner.config.settings.barchart.orientation,
-      summary.Inner.config.settings.violin.orientation,
-      `Orientation change for barchart should not affect violin`
-    );
-  }
-});
-(0, import_tape.default)('Barchart tab only, term: "diaggrp"', (test) => {
-  test.timeoutAfter(3e3);
-  const message = `Should only show barchart tab in header`;
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "summary",
-          childType: "barchart",
-          term: {
-            id: "diaggrp"
-          }
-        }
-      ]
-    },
-    summary: {
-      callbacks: {
-        "postRender.test": runTest
-      }
-    }
-  });
-  async function runTest(summary) {
-    const toggles = summary.Inner.dom.chartToggles.selectAll("div > div> button").nodes().filter((d) => d.__data__.isVisible() == true);
-    test.ok(toggles.length == 1, `Should only render one tab`);
-    if (toggles[0].__data__.childType == "barchart") test.pass(message);
-    else test.fail(message);
-    if (test._ok) summary.Inner.app.destroy();
-    test.end();
-  }
-});
-(0, import_tape.default)('Barchart & violin toggles, term: "diaggrp", term2: "agedx"', (test) => {
-  test.timeoutAfter(3e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "summary",
-          childType: "barchart",
-          term: {
-            id: "diaggrp"
-          },
-          term2: {
-            id: "agedx"
-          }
-        }
-      ]
-    },
-    summary: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(summary) {
-    summary.on("postRender.test", null);
-    await detectOne({ elem: summary.Inner.dom.holder.body.node(), selector: ".pp-bars-svg" });
-    await testToggleButtons(summary, summary.Inner.dom);
-    if (test._ok) summary.Inner.app.destroy();
-    test.end();
-  }
-  async function testToggleButtons(summary, dom) {
-    const toggles = dom.chartToggles.selectAll("div > div> button").nodes().filter((d) => d.__data__.isVisible() == true);
-    toggles.find((d) => d.__data__.childType == "violin").click();
-    const foundTestPlot = await detectOne({
-      elem: dom.holder.body.node(),
-      selector: ".sjpp-violin-plot"
-    });
-    test.ok(foundTestPlot, `Should render violin after toggle`);
-    test.equal(summary.Inner.state.config.childType, "violin", `Should toggle to childType = violin`);
-    await detectStyle({
-      elem: dom.plotDivs.barchart.node(),
-      matcher(mutations) {
-        for (const m of mutations) {
-          if (m.attributeName == "style" && m.target.style.display === "") return m;
-        }
-      },
-      trigger() {
-        toggles.find((d) => d.__data__.childType == "barchart").click();
-      }
-    });
-    test.equal(summary.Inner.state.config.childType, "barchart", `Should toggle back to childType = 'barchart'`);
-  }
-});
-(0, import_tape.default)('Barchart & violin toggles, term: "agedx", term2: "diaggrp"', (test) => {
-  test.timeoutAfter(3e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "summary",
-          childType: "barchart",
-          term: {
-            id: "agedx"
-          },
-          term2: {
-            id: "diaggrp"
-          }
-        }
-      ]
-    },
-    summary: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(summary) {
-    summary.on("postRender.test", null);
-    const toggles = summary.Inner.dom.chartToggles.selectAll("div > div> button").nodes().filter((d) => d.__data__.isVisible() == true);
-    testToggleButtonRendering(toggles);
-    await testToggleButtons(summary, toggles);
-    if (test._ok) summary.Inner.app.destroy();
-    test.end();
-  }
-  function testToggleButtonRendering(toggles) {
-    let foundLabels = 0;
-    for (const toggle of toggles) {
-      if (tabLabels2Find.some((d) => d == toggle.__data__.label)) ++foundLabels;
-    }
-    test.equal(
-      tabLabels2Find.length,
-      toggles.length,
-      `Should render ${tabLabels2Find.length} tabs: ${tabLabels2Find} for <2 numeric terms`
-    );
-  }
-  async function testToggleButtons(summary, toggles) {
-    toggles.find((d) => d.__data__.childType == "violin").click();
-    const foundTestPlot = await detectOne({
-      elem: summary.Inner.dom.holder.body.node(),
-      selector: ".sjpp-violin-plot"
-    });
-    test.ok(foundTestPlot, `Should render violin after toggle`);
-    test.equal(summary.Inner.state.config.childType, "violin", `Should toggle to childType = violin`);
-    await detectStyle({
-      elem: summary.Inner.dom.plotDivs.barchart.node(),
-      matcher(mutations) {
-        for (const m of mutations) {
-          if (m.attributeName == "style" && m.target.style.display === "") return m;
-        }
-      },
-      trigger() {
-        toggles.find((d) => d.__data__.childType == "barchart").click();
-      }
-    });
-    test.equal(summary.Inner.state.config.childType, "barchart", `Should toggle back to childType = 'barchart'`);
-  }
-});
-(0, import_tape.default)('Barchart, violin, and scatter toggles, term: "agedx", term2: "hrtavg"', (test) => {
-  test.timeoutAfter(3e3);
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "summary",
-          childType: "barchart",
-          term: {
-            id: "agedx"
-          },
-          term2: {
-            id: "hrtavg"
-          }
-        }
-      ]
-    },
-    summary: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(summary) {
-    summary.on("postRender.test", null);
-    const sandboxDom = summary.Inner.dom;
-    const toggles = sandboxDom.chartToggles.selectAll("div > div> button").nodes().filter((d) => d.__data__.isVisible() == true);
-    testToggleButtonRendering(toggles);
-    await testToggling(summary, toggles);
-    if (test._ok) summary.Inner.app.destroy();
-    test.end();
-  }
-  function testToggleButtonRendering(toggles) {
-    const tabLabels2Find2 = [...tabLabels2Find];
-    tabLabels2Find2.push("Scatter");
-    let foundLabels = 0;
-    for (const toggle of toggles) {
-      if (tabLabels2Find2.some((d) => d == toggle.__data__.label)) ++foundLabels;
-    }
-    test.equal(
-      tabLabels2Find2.length,
-      toggles.length,
-      `Should render ${tabLabels2Find2.length} tabs: ${tabLabels2Find2} for 2 numeric terms`
-    );
-  }
-  async function testToggling(summary, toggles) {
-    toggles.find((d) => d.__data__.childType == "violin").click();
-    const foundTestPlot = await detectOne({
-      elem: summary.Inner.dom.holder.body.node(),
-      selector: ".sjpp-violin-plot"
-    });
-    test.ok(foundTestPlot, `Should render violin after toggle`);
-    test.equal(summary.Inner.state.config.childType, "violin", `Should toggle to childType = violin`);
-    await detectStyle({
-      elem: summary.Inner.dom.plotDivs.barchart.node(),
-      matcher(mutations) {
-        for (const m of mutations) {
-          if (m.attributeName == "style" && m.target.style.display === "") return m;
-        }
-      },
-      trigger() {
-        toggles.find((d) => d.__data__.childType == "barchart").click();
-      }
-    });
-    test.equal(summary.Inner.state.config.childType, "barchart", `Should toggle back to childType = 'barchart'`);
-  }
-});
-(0, import_tape.default)('Overlay continuity, term: "aaclassic_5", term2: "sex"', (test) => {
-  test.timeoutAfter(3e3);
-  const testTerm = "sex";
-  runpp({
-    state: {
-      plots: [
-        {
-          chartType: "summary",
-          childType: "barchart",
-          term: {
-            id: "aaclassic_5"
-          },
-          term2: {
-            id: testTerm
-          }
-        }
-      ]
-    },
-    summary: {
-      callbacks: {
-        "postRender.test": runTests
-      }
-    }
-  });
-  async function runTests(summary) {
-    summary.on("postRender.test", null);
-    await testOverlay(summary);
-    if (test._ok) summary.Inner.app.destroy();
-    test.end();
-  }
-  async function testOverlay(summary) {
-    const plots = summary.Inner.components.plots;
-    summary.Inner.dom.chartToggles.selectAll("div > div> button").nodes().find((d) => d.__data__.childType == "violin").click();
-    await detectOne({ elem: summary.Inner.dom.holder.body.node(), selector: ".sjpp-violin-plot" });
-    test.equal(
-      plots.violin.Inner.config.term2.term.id,
-      testTerm,
-      `Overlay term = ${testTerm} carried over to violin plot`
-    );
-  }
-});
-//# sourceMappingURL=summary.integration.spec-4GTCG6HY.js.map

package/dist/summaryInput-UK3TLC7M.js

@@ -1,242 +0,0 @@
-import {
-  PlotBase,
-  controlsInit,
-  defaultUiLabels,
-  fillTermWrapper,
-  getT0T2defaultQ
-} from "./chunk-PC4MFDHP.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-HPAW7XDM.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-BZN2O76M.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-52QHIKH2.js";
-import "./chunk-A2ORIMUJ.js";
-import "./chunk-PPSWNLMG.js";
-import "./chunk-RUBZCKIX.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./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 "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// plots/summaryInput.ts
-var SummaryInputPlot = class _SummaryInputPlot extends PlotBase {
-  constructor(opts, api) {
-    super(opts, api);
-    this.components = {};
-    // expected class-specific props
-    // the *_surv keys are the overlay/divide-by held aside for a survival term1, and are
-    // filled by getPlotConfig() like the others, so they route the same way
-    this.configTermKeys = ["term", "term0", "term2", "term0_surv", "term2_surv"];
-    this.type = _SummaryInputPlot.type;
-    this.dom = {
-      header: opts.header.html("Correlation Input"),
-      holder: opts.holder,
-      controls: opts.holder.append("div"),
-      submit: opts.holder.append("div").style("position", "relative").style("margin", "10px").style("max-width", "200px")
-    };
-  }
-  static {
-    this.type = "summaryInput";
-  }
-  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 {
-      termfilter: appState.termfilter,
-      config,
-      // quick fix to skip history tracking as needed
-      _scope_: appState._scope_
-    };
-  }
-  async init(appState) {
-    const state = this.getState(appState);
-    this.renderSubmit();
-    await this.setControls(state.config);
-  }
-  async setControls(config) {
-    const controlLabels = config.controlLabels;
-    const inputs = [
-      {
-        type: "term",
-        configKey: "term",
-        testids: {
-          suffix: "summaryInputControlTerm"
-        },
-        usecase: { target: "summaryInput", detail: "term" },
-        label: controlLabels.term1?.label || "Primary variable",
-        processConfig: (config2) => {
-          const { term, term2, term0, term2_surv, term0_surv } = this.state.config;
-          const editedType = config2.term?.term?.type;
-          if (editedType === term?.term?.type) return;
-          if (editedType == "survival") {
-            if (term2 && term2.term?.name != term2_surv?.term?.name)
-              config2.term2 = { term: structuredClone(term2.term), q: {} };
-            if (term0 && term0.term?.name != term0_surv?.term?.name)
-              config2.term0 = { term: structuredClone(term0.term), q: {} };
-          } else {
-            if (term2_surv && term2_surv.term?.name != term2?.term?.name)
-              config2.term2 = { term: structuredClone(term2_surv.term), q: {} };
-            if (term0_surv && term0_surv.term.name != term0?.term?.name)
-              config2.term0 = { term: structuredClone(term0_surv.term), q: {} };
-          }
-          if (editedType == "multivalue" && config2.term?.term?.valueMeaning == "membership") {
-            if (term2 || config2.term2) config2.term2 = null;
-          }
-        }
-      },
-      {
-        type: "term",
-        configKey: "term2",
-        testids: {
-          suffix: "summaryInputControlTerm2"
-        },
-        usecase: { target: "summaryInput", detail: "term2" },
-        label: controlLabels.term2.label,
-        defaultQ4fillTW: getT0T2defaultQ(),
-        // hidden for survival term1 and for
-        // membership multivalue term1 (overlapping bars invalidate the barchart's
-        // association tests, so no real overlay is offered)
-        getDisplayStyle: (plot) => plot.config.term?.term.type == "survival" || plot.config.term?.term.type == "multivalue" && plot.config.term.term.valueMeaning == "membership" ? "none" : "table-row"
-      },
-      {
-        type: "term",
-        configKey: "term0",
-        testids: {
-          suffix: "summaryInputControlTerm0"
-        },
-        usecase: { target: "summaryInput", detail: "term0" },
-        label: controlLabels.term0.label,
-        defaultQ4fillTW: getT0T2defaultQ(),
-        numericEditMenuVersion: this.opts.numericEditMenuVersion || ["discrete"],
-        getDisplayStyle: (plot) => plot.config.term?.term.type == "survival" ? "none" : "table-row"
-      },
-      {
-        type: "term",
-        configKey: "term2_surv",
-        testids: {
-          suffix: "summaryInputControlTerm2surv"
-        },
-        usecase: { target: "summaryInput", detail: "term2" },
-        label: controlLabels.term2.label,
-        defaultQ4fillTW: getT0T2defaultQ(true),
-        getDisplayStyle: (plot) => plot.config.term?.term.type == "survival" ? "table-row" : "none"
-      },
-      {
-        type: "term",
-        configKey: "term0_surv",
-        testids: {
-          suffix: "summaryInputControlTerm0surv"
-        },
-        usecase: { target: "summaryInput", detail: "term0" },
-        label: controlLabels.term0.label,
-        defaultQ4fillTW: getT0T2defaultQ(true),
-        numericEditMenuVersion: this.opts.numericEditMenuVersion || ["discrete"],
-        getDisplayStyle: (plot) => plot.config.term?.term.type == "survival" ? "table-row" : "none"
-      }
-    ];
-    this.components.controls = await controlsInit({
-      app: this.app,
-      id: this.id,
-      holder: this.dom.controls.style("display", "inline-block"),
-      isOpen: true,
-      showTopBar: false,
-      inputs,
-      // may comment out loadingMasks option to be able to click the submit button and
-      // manually test submitting before a config tw is fully filled, there should only be
-      // a console warning and no displayed error messages in the app
-      loadingMasks: [this.dom.submitMask]
-    });
-  }
-  renderSubmit() {
-    this.dom.submitBtn = this.dom.submit.append("button").property("disabled", true).style("border", "none").style("border-radius", "20px").style("padding", "10px 15px").attr("data-testid", "sjpp-summaryInput-submitBtn").text("Submit").on("click", () => {
-      const { term, term2, term0, term2_surv, term0_surv, filter } = structuredClone(this.config);
-      if (!term) throw "config.term is missing";
-      const chartType = term.term.type == "survival" ? "survival" : "summary";
-      this.app.dispatch({
-        type: "app_refresh",
-        subactions: [
-          {
-            type: "plot_create",
-            config: {
-              chartType,
-              term,
-              term2: chartType == "survival" ? term2_surv : term2,
-              term0: chartType == "survival" ? term0_surv : term0,
-              filter
-            }
-          },
-          {
-            type: "plot_delete",
-            id: this.id
-          }
-        ]
-      });
-    });
-    this.dom.submitMask = this.dom.submit.append("div").style("position", "absolute").style("top", 0).style("left", 0).style("height", "100%").style("width", "100%").style("background-color", `rgba(255,255,255,0.7)`).style("display", "none");
-  }
-  async main() {
-    this.config = await this.getMutableConfig();
-    this.dom.submitBtn.property("disabled", !this.config.term).style("cursor", this.config.term ? "pointer" : "default");
-    this.dom.submitMask.style("display", "none");
-  }
-};
-var summaryInputInit = getCompInit(SummaryInputPlot);
-var componentInit = summaryInputInit;
-async function getPlotConfig(opts, app) {
-  try {
-    if (opts.term) {
-      const defaultQ = opts.term.bins || opts.term.q ? void 0 : { geneVariant: { type: "predefined-groupset" } };
-      await fillTermWrapper(opts.term, app.vocabApi, defaultQ);
-    }
-    const asBinary = opts.term?.term.type == "survival";
-    if (opts.term2) {
-      const defaultQ = opts.term2.bins || opts.term2.q ? void 0 : getT0T2defaultQ(asBinary);
-      await fillTermWrapper(opts.term2, app.vocabApi, defaultQ);
-    }
-    if (opts.term0) {
-      const defaultQ = opts.term0.bins || opts.term0.q ? void 0 : getT0T2defaultQ(asBinary);
-      await fillTermWrapper(opts.term0, app.vocabApi, defaultQ);
-    }
-    if (opts.term2_surv) {
-      const defaultQ = opts.term2_surv.bins || opts.term2_surv.q ? void 0 : getT0T2defaultQ(true);
-      await fillTermWrapper(opts.term2_surv, app.vocabApi, defaultQ);
-    }
-    if (opts.term0_surv) {
-      const defaultQ = opts.term0_surv.bins || opts.term0_surv.q ? void 0 : getT0T2defaultQ(true);
-      await fillTermWrapper(opts.term0_surv, app.vocabApi, defaultQ);
-    }
-  } catch (e) {
-    if (e.stack) console.log(e.stack);
-    throw `${e} [summaryInput getPlotConfig()]`;
-  }
-  const config = {
-    chartType: "summaryInput",
-    settings: {},
-    controlLabels: Object.assign({}, defaultUiLabels, app.vocabApi.termdbConfig.uiLabels || {})
-  };
-  return copyMerge(config, opts);
-}
-export {
-  componentInit,
-  getPlotConfig,
-  summaryInputInit
-};
-//# sourceMappingURL=summaryInput-UK3TLC7M.js.map