@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/geneset-V2535XGY.js

@@ -0,0 +1,208 @@
+import {
+  GeneSetEditUIwithTabs,
+  fillTermWrapper
+} from "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import {
+  dofetch3
+} from "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import {
+  copyMerge,
+  getCompInit
+} from "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.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-HFNDKYVF.js";
+
+// plots/geneset.js
+var GenesetComp = class _GenesetComp {
+  static type = "geneset";
+  // type: 'geneset'
+  // dom: {
+  // 	[domKey: string]: any // usually a d3-selection
+  // }
+  // opts: {
+  // 	holder: any
+  // 	genes: string[]
+  // 	mode: 'geneVariant' | 'geneExpression'
+  // 	callback: CallbackArg
+  // 	reactsTo?: (action: any) => boolean
+  // 	showWaitMessage?: (waitDiv: any) => void
+  // }
+  constructor(opts) {
+    this.type = _GenesetComp.type;
+    this.dom = {
+      holder: opts.holder.style("position", "relative").style("min-height", "300px").style("margin", "0px 20px").style("max-width", "1000px"),
+      body: opts.holder.append("div"),
+      loadingOverlay: opts.holder.append("div").attr("class", "sjpp-spinner").style("display", "none").style("position", "absolute").style("background-color", "#fff").style("z-index", 10).style("opacity", "0.5")
+      //.style('width', '100%')
+      //.style('height', '100%')
+    };
+  }
+  init() {
+    if (this.opts.reactsTo) this.reactsTo = this.opts.reactsTo;
+  }
+  getState(appState) {
+    const config = appState.plots.find((p) => p.id === this.id);
+    return {
+      vocab: appState.vocab,
+      filter0: appState.termfilter.filter0,
+      config
+    };
+  }
+  async main() {
+    this.dom.body.selectAll("*").remove();
+    this.dom.loadingOverlay.style("display", "");
+    this.noWait().catch(console.warn);
+  }
+  async noWait() {
+    const abortCtrl = new AbortController();
+    try {
+      const [genes, stale] = await this.api.detectStale(() => this.getGenes({ signal: abortCtrl.signal }), {
+        abortCtrl
+      });
+      if (stale) return;
+      if (!genes?.length) this.render();
+      else this.opts.callback(this.api, genes);
+    } catch (e) {
+      if (e == "stale sequenceId" || e.name == "AbortError") return;
+      if (e?.code === "CACHE_BUSY" && this.opts.showWaitMessage) {
+        if (window.confirm(e.message || String(e))) this.main();
+        return;
+      }
+      if (this.opts.showWaitMessage) {
+        this.dom.body.style("margin", "20px").html(e);
+      }
+      throw e;
+    }
+  }
+  async getGenes({ signal }) {
+    const genes = this.opts.genes;
+    const settings = this.state.config.settings;
+    if (this.opts.genes) {
+      if (!Array.isArray(this.opts.genes) || this.opts.genes.length == 0) throw ".genes[] is not non-empty array";
+      return await this.getTwLst(this.opts.genes);
+    }
+    if (this.opts.showEditUI) {
+      return [];
+    }
+    let waitDiv;
+    if (this.opts.showWaitMessage) {
+      waitDiv = this.dom.body.append("div").style("margin", "20px");
+      this.opts.showWaitMessage(waitDiv);
+    }
+    let data;
+    if (this.opts.mode == "geneVariant") {
+      const body = {
+        genome: this.state.vocab.genome,
+        dslabel: this.state.vocab.dslabel
+      };
+      if (settings.maxGenes) body.maxGenes = settings.maxGenes;
+      if (settings.geneFilter) body.geneFilter = settings.geneFilter;
+      if (this.state.filter0) body.filter0 = this.state.filter0;
+      data = await dofetch3("termdb/topMutatedGenes", { body, signal });
+    } else if (this.opts.mode == "geneExpression") {
+      const body = {
+        genome: this.state.vocab.genome,
+        dslabel: this.state.vocab.dslabel,
+        maxGenes: settings.maxGenes
+      };
+      if (this.state.filter0) body.filter0 = this.state.filter0;
+      data = await dofetch3("termdb/topVariablyExpressedGenes", { body, signal });
+    } else {
+      throw "unknown opts.mode [geneset.js]";
+    }
+    if (!data) throw "invalid server response";
+    if (data.error) {
+      if (data.status === 429) throw Object.assign(new Error(data.error), { code: "CACHE_BUSY" });
+      throw data.error;
+    }
+    if (!data.genes) return [];
+    waitDiv.remove();
+    this.dom.loadingOverlay?.style("display", "none");
+    return await this.getTwLst(data.genes);
+  }
+  async getTwLst(genes) {
+    return await Promise.all(
+      // do tempfix of "data.genes.slice(0,3).map" for faster testing
+      genes.map(
+        async (i) => typeof i == "string" ? await fillTermWrapper({ term: { gene: i, type: this.opts.mode } }, this.app.vocabApi) : await fillTermWrapper({ term: { gene: i.gene || i.name, type: this.opts.mode } }, this.app.vocabApi)
+      )
+    );
+  }
+  async render() {
+    if (!this.dom?.holder) return;
+    const settings = this.state.config.settings;
+    this.dom.body.append("p").html(
+      `Define a gene set to launch <span style='text-transform: capitalize'>${this.state.config.toolName.toLowerCase()}</span>.`
+    );
+    new GeneSetEditUIwithTabs(
+      {
+        holder: this.dom.body.append("div"),
+        genome: this.opts.genome,
+        mode: this.opts.mode,
+        vocabApi: this.app.vocabApi,
+        //  await vocabInit({ state: { genome: gdcGenome, dslabel: gdcDslabel } }),
+        maxNumGenes: settings.maxGenes,
+        callback: async (result) => {
+          const twlst = await Promise.all(
+            result.geneList.map(async (i) => {
+              return fillTermWrapper({ term: { gene: i.gene || i.name || i, type: this.opts.mode } }, this.app.vocabApi);
+            })
+          );
+          this.opts.callback(this.api, twlst);
+        }
+      }
+      /*as GeneSetEditArg*/
+    );
+    this.dom.loadingOverlay?.style("display", "none");
+  }
+  destroy() {
+    this.dom.holder.selectAll("*").remove();
+    this.dom.holder.remove();
+    for (const key in this.dom) {
+      delete this.dom[key];
+    }
+  }
+};
+var genesetInit = getCompInit(GenesetComp);
+var componentInit = genesetInit;
+async function getPlotConfig(opts = {}, app) {
+  const config = copyMerge(
+    {
+      chartType: "geneset"
+    },
+    opts
+  );
+  return config;
+}
+export {
+  componentInit,
+  genesetInit,
+  getPlotConfig
+};
+//# sourceMappingURL=geneset-V2535XGY.js.map

package/dist/genomeBrowser.spec-TRREAQCH.js

@@ -0,0 +1,281 @@
+import {
+  detectGt,
+  detectOne
+} from "./chunk-Z2TA7NML.js";
+import {
+  getRunPp
+} from "./chunk-VJCJCDFI.js";
+import {
+  require_tape
+} from "./chunk-TUMA63WX.js";
+import "./chunk-57GCW5SF.js";
+import "./chunk-WGRJEQT7.js";
+import "./chunk-KSA3ND7Z.js";
+import "./chunk-FESRWKYY.js";
+import "./chunk-PRZWSBMA.js";
+import "./chunk-Y45RZL4F.js";
+import "./chunk-MKAF2BHB.js";
+import "./chunk-E2JRANYL.js";
+import "./chunk-E2GHT7RH.js";
+import "./chunk-HOCICSX4.js";
+import "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.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-HFNDKYVF.js";
+
+// plots/gb/test/genomeBrowser.spec.js
+var import_tape = __toESM(require_tape(), 1);
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- plots/genomeBrowser -***-");
+  test.end();
+});
+(0, import_tape.default)("sjlife default setting", (test) => {
+  const holder = getHolder();
+  runpp({
+    holder,
+    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
+  });
+});
+(0, import_tape.default)("Sjlife default, with global mass filter", (test) => {
+  const holder = getHolder();
+  runpp({
+    holder,
+    state: {
+      termfilter: {
+        filter: {
+          type: "tvslst",
+          join: "and",
+          in: true,
+          lst: [
+            {
+              type: "tvs",
+              tvs: {
+                term: { id: "diaggrp_s" },
+                values: [{ key: "Acute lymphoblastic leukemia", label: "Acute lymphoblastic leukemia" }]
+              }
+            },
+            {
+              type: "tvs",
+              tvs: {
+                term: { id: "agedx_s", name: "agedx", type: "float" },
+                ranges: [{ startunbounded: true, stop: 10, stopinclusive: true }]
+              }
+            }
+          ]
+        }
+      }
+    },
+    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
+  });
+});
+(0, import_tape.default)("Two groups: filter + population", (test) => {
+  const holder = getHolder();
+  const p = getPlot([groupFilterAML, groupPopulation1]);
+  runpp({
+    holder,
+    state: { plots: [p] },
+    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
+  });
+});
+(0, import_tape.default)("Two groups: filter + info", (test) => {
+  const holder = getHolder();
+  const p = getPlot([groupFilterAML, groupInfo1]);
+  runpp({
+    holder,
+    state: { plots: [p] },
+    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
+  });
+});
+(0, import_tape.default)("Two groups: filter + filter", (test) => {
+  const holder = getHolder();
+  const p = getPlot([groupFilterAML, groupFilterALLmale]);
+  runpp({
+    holder,
+    state: { plots: [p] },
+    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
+  });
+});
+(0, import_tape.default)("Two groups: info + info", (test) => {
+  const holder = getHolder();
+  const p = getPlot([groupInfo1, groupInfo2]);
+  runpp({
+    holder,
+    state: { plots: [p] },
+    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
+  });
+});
+(0, import_tape.default)("Two groups: info + poulation", (test) => {
+  const holder = getHolder();
+  const p = getPlot([groupInfo1, groupPopulation1]);
+  runpp({
+    holder,
+    state: { plots: [p] },
+    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
+  });
+});
+(0, import_tape.default)("Two groups: population + poulation", (test) => {
+  const holder = getHolder();
+  const p = getPlot([groupPopulation1, groupPopulation2]);
+  runpp({
+    holder,
+    state: { plots: [p] },
+    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
+  });
+});
+(0, import_tape.default)("Single group: population", (test) => {
+  const holder = getHolder();
+  const p = getPlot([groupPopulation1]);
+  runpp({
+    holder,
+    state: { plots: [p] },
+    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
+  });
+});
+(0, import_tape.default)("Single group: filter", (test) => {
+  const holder = getHolder();
+  const p = getPlot([groupFilterALLmale]);
+  runpp({
+    holder,
+    state: { plots: [p] },
+    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
+  });
+});
+(0, import_tape.default)("Single group: info", (test) => {
+  const holder = getHolder();
+  const p = getPlot([groupInfo1]);
+  runpp({
+    holder,
+    state: { plots: [p] },
+    genomeBrowser: { callbacks: { "postRender.test": runTests(test, holder) } }
+  });
+});
+function getHolder() {
+  return select_default("body").append("div").style("border", "1px solid #aaa").style("padding", "5px").style("margin", "5px");
+}
+function getPlot(groups) {
+  const p = {
+    chartType: "genomeBrowser",
+    geneSearchResult: { chr: "chr10", start: 61901683, stop: 62096944 }
+  };
+  if (groups) {
+    p.snvindel = {
+      details: {
+        groups,
+        groupTestMethods: [
+          { name: "Allele frequency difference" },
+          { name: "Fisher's exact test", axisLabel: "-log10(pvalue)" }
+        ],
+        groupTestMethodsIdx: 1
+      }
+    };
+  }
+  return p;
+}
+var runpp = getRunPp("mass", {
+  state: {
+    nav: { activeTab: 1 },
+    vocab: { dslabel: "SJLife", genome: "hg38" },
+    plots: [getPlot()]
+  },
+  debug: 1
+});
+function runTests(test, holder) {
+  return async (gb) => {
+    const div = gb.Inner.dom.holder;
+    const blockDiv = await detectOne({ elem: div.node(), selector: ".sja_Block_div" });
+    test.ok(blockDiv, "Block div is rendered");
+    const tklst = blockDiv.querySelectorAll('[data-testid="sja_sample_menu_opener"]');
+    test.equal(tklst.length, 2, "Block has 2 tracks");
+    const variantTk = tklst[0];
+    const variants = await detectGt({ elem: variantTk, selector: ".sja_aa_discg" });
+    test.ok(variants.length > 0, "Should render variants in variants track");
+    if (test._ok) holder.remove();
+    test.end();
+  };
+}
+var groupFilterAML = {
+  type: "filter",
+  filter: {
+    type: "tvslst",
+    in: true,
+    join: "",
+    lst: [
+      {
+        type: "tvs",
+        tvs: {
+          term: { id: "diaggrp_s", name: "Diagnosis Group", type: "categorical" },
+          values: [{ key: "Acute myeloid leukemia", label: "Acute myeloid leukemia" }]
+        }
+      }
+    ]
+  }
+};
+var groupFilterALLmale = {
+  type: "filter",
+  filter: {
+    type: "tvslst",
+    in: true,
+    join: "and",
+    lst: [
+      {
+        type: "tvs",
+        tvs: {
+          term: { id: "diaggrp_s", name: "Diagnosis Group", type: "categorical" },
+          values: [{ key: "Acute lymphoblastic leukemia", label: "Acute lymphoblastic leukemia" }]
+        }
+      },
+      {
+        type: "tvs",
+        tvs: { term: { id: "sex_s", name: "Sex", type: "categorical" }, values: [{ key: "1", label: "Male" }] }
+      }
+    ]
+  }
+};
+var groupPopulation1 = {
+  type: "population",
+  key: "gnomAD",
+  label: "gnomAD",
+  allowto_adjust_race: true,
+  adjust_race: true
+};
+var groupPopulation2 = {
+  type: "population",
+  key: "TOPMed",
+  label: "TOPMed",
+  allowto_adjust_race: true,
+  adjust_race: true
+};
+var groupInfo1 = { type: "info", infoKey: "AF_sjlife" };
+var groupInfo2 = { type: "info", infoKey: "gnomAD_AF" };
+//# sourceMappingURL=genomeBrowser.spec-TRREAQCH.js.map

package/dist/grin2-6X5GCPBQ.js

@@ -0,0 +1,75 @@
+import {
+  appInit
+} from "./chunk-E732F6XI.js";
+import "./chunk-2TWVFQD2.js";
+import "./chunk-SKMFMGCD.js";
+import "./chunk-UILBQKQ6.js";
+import {
+  vocabInit
+} from "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import {
+  copyMerge
+} from "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.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 "./chunk-HFNDKYVF.js";
+
+// gdc/grin2.ts
+async function gdcGRIN2ui(arg, _holder, genomes) {
+  const toolGenome = arg.genome || "hg38";
+  const toolDslabel = arg.dslabel || "GDC";
+  const genome = genomes[toolGenome];
+  if (!genome) throw toolGenome + " missing";
+  if (arg.filter0 && typeof arg.filter0 != "object") throw "arg.filter0 not object";
+  const vocabApi = await vocabInit({
+    state: { vocab: { genome: toolGenome, dslabel: toolDslabel } }
+  });
+  vocabApi.getTermdbConfig();
+  const plotAppApi = await appInit({
+    holder: select_default(arg.holder).select(".sja_root_holder"),
+    genome,
+    state: copyMerge(
+      {
+        genome: toolGenome,
+        dslabel: toolDslabel,
+        termfilter: { filter0: arg.filter0 },
+        plots: [{ chartType: "grin2" }]
+      },
+      arg.state || {}
+    ),
+    app: arg.opts?.app || {}
+  });
+  return plotAppApi;
+}
+export {
+  gdcGRIN2ui
+};
+//# sourceMappingURL=grin2-6X5GCPBQ.js.map