@sjcrh/proteinpaint-client 2.204.0 → 2.205.0

package/dist/geneset-MVXSEOKZ.js

@@ -1,203 +0,0 @@
-import {
-  GeneSetEditUIwithTabs,
-  fillTermWrapper
-} from "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import {
-  dofetch3
-} from "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import "./chunk-S5SOLLGM.js";
-import {
-  copyMerge,
-  getCompInit
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.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/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-MVXSEOKZ.js.map

package/dist/genomeBrowser.spec-QDB4Z2L6.js

@@ -1,276 +0,0 @@
-import {
-  getRunPp
-} from "./chunk-HWMZ2OHD.js";
-import {
-  detectGt,
-  detectOne
-} from "./chunk-FYXIK6Y6.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-56HEUYYM.js";
-import "./chunk-BBYVVPEO.js";
-import "./chunk-XPB2GP3C.js";
-import "./chunk-FUEJFIQX.js";
-import "./chunk-PRZWSBMA.js";
-import "./chunk-MCRWA655.js";
-import "./chunk-MKAF2BHB.js";
-import "./chunk-XHOL37O6.js";
-import "./chunk-4FTH4L3A.js";
-import "./chunk-X7IAKV5Z.js";
-import "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import "./chunk-S5SOLLGM.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.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/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-QDB4Z2L6.js.map

package/dist/grin2-DCU6PLPU.js

@@ -1,70 +0,0 @@
-import {
-  appInit
-} from "./chunk-GQ6T62VJ.js";
-import "./chunk-GTMHDSOQ.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-X46YA4CB.js";
-import {
-  vocabInit
-} from "./chunk-7RX5UEF3.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-L42F5J5C.js";
-import "./chunk-HKQDZKSF.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-FUSTNOQZ.js";
-import "./chunk-VSPUFGDX.js";
-import "./chunk-WVPFLPWB.js";
-import "./chunk-S5SOLLGM.js";
-import {
-  copyMerge
-} from "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.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-HS5PO5ZQ.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-DCU6PLPU.js.map