@sjcrh/proteinpaint-client 2.208.0 → 2.209.0

package/dist/chunk-B6UXFX73.js

@@ -0,0 +1,178 @@
+import {
+  __glob
+} from "./chunk-HS5PO5ZQ.js";
+
+// import("../plots/**/*.js") in plots/importPlot.js
+var globImport_plots_js = __glob({
+  "../plots/controls.btns.js": () => import("./controls.btns-BYM4DON4.js"),
+  "../plots/controls.config.js": () => import("./controls.config-FWKV66TU.js"),
+  "../plots/controls.js": () => import("./controls-HBROSXHF.js"),
+  "../plots/dictionary.js": () => import("./dictionary-RBE2CIZI.js"),
+  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-UTAHAU76.js"),
+  "../plots/geneExpression.js": () => import("./geneExpression-XVOLNYVN.js"),
+  "../plots/geneORA.js": () => import("./geneORA-HQ7FLMEJ.js"),
+  "../plots/geneset.js": () => import("./geneset-WKV3X2EJ.js"),
+  "../plots/hierCluster.js": () => import("./hierCluster-LZI6OTRS.js"),
+  "../plots/importPlot.js": () => import("./importPlot-OSTC2GPO.js"),
+  "../plots/matrix.js": () => import("./matrix-XT7LUV5K.js"),
+  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-NCYH3Y7Z.js"),
+  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-4HP3JCON.js"),
+  "../plots/matrix/hierCluster.js": () => import("./hierCluster-VVXPOTQU.js"),
+  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-3F5GMEXA.js"),
+  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-NB7LKKXV.js"),
+  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-RH4BOM5F.js"),
+  "../plots/matrix/matrix.config.js": () => import("./matrix.config-X6HS4UGD.js"),
+  "../plots/matrix/matrix.data.js": () => import("./matrix.data-VLFF34SS.js"),
+  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-2SA43BPT.js"),
+  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-F62TSKIG.js"),
+  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-2FBXB52E.js"),
+  "../plots/matrix/matrix.js": () => import("./matrix-QFKGEW5A.js"),
+  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-6TPVKLSX.js"),
+  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-L4ULBMGX.js"),
+  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-DK6YRLO2.js"),
+  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-DCRJLJ3H.js"),
+  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-XSGPH44J.js"),
+  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-WL5I6S3K.js"),
+  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-ZDOOCTV3.js"),
+  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-7QBYWHW6.js"),
+  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-JF75F4I4.js"),
+  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-66JMV5BK.js"),
+  "../plots/matrix/test/matrix.unit.spec.js": () => import("./matrix.unit.spec-36AR4I43.js"),
+  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-NEMLM2ZN.js"),
+  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-KEOUTYIB.js"),
+  "../plots/plot.disco.js": () => import("./plot.disco-7IDMKNAQ.js"),
+  "../plots/plot.ssgq.js": () => import("./plot.ssgq-IOKUGDC4.js"),
+  "../plots/singleCellPlot.js": () => import("./singleCellPlot-BG7UJOHA.js"),
+  "../plots/stattable.js": () => import("./stattable-LFR3RSD6.js"),
+  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-66UOWSZG.js"),
+  "../plots/table.js": () => import("./table-YAAH7WR6.js"),
+  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-BMN2PTJX.js"),
+  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-6JZAT73L.js"),
+  "../plots/volcano/test/testData.js": () => import("./testData-DRM5HWQB.js")
+});
+
+// plots/importPlot.js
+async function importPlot(chartType, notFoundMessage = "") {
+  switch (chartType) {
+    case "aggMatrixInput":
+      return await import("./AggMatrixInput-CH3RQ2QC.js");
+    case "aggregateMatrix":
+      return await import("./AggregateMatrix-DPCHUOMF.js");
+    case "animatedBubbleChart":
+      return await import("./animatedBubbleChart-GMLNYTQC.js");
+    case "brainImaging":
+      return await import("./brainImaging-MBI4XTTU.js");
+    case "brainRegions":
+      return await import("./brainRegions-YVTAESRP.js");
+    case "barchart":
+      return await import("./barchart-SEC6VKQ2.js");
+    case "boxplot":
+      return await import("./BoxPlot-7Q7SMT26.js");
+    case "bubbleHeatmap":
+      return await import("./bubbleHeatmap-ZKTA3AIG.js");
+    case "cellTypeBubbleHeatmap":
+      return await import("./cellTypeBubbleHeatmap-GJZNXDG4.js");
+    case "correlationVolcano":
+      return await import("./CorrelationVolcano-YV4UHOAX.js");
+    case "cuminc":
+      return await import("./Cuminc-ZN53C3MD.js");
+    case "dataDownload":
+      return await import("./dataDownload-ZPAIAAE4.js");
+    case "DEinput":
+      return await import("./DEinput-SJITUJF2.js");
+    case "dictionary":
+      return await import("./dictionary-RBE2CIZI.js");
+    case "differentialAnalysis":
+      return await import("./DifferentialAnalysis-WE4LBHEF.js");
+    case "Disco":
+      return await import("./Disco-PTZQF7IM.js");
+    case "dmr":
+      return await import("./DmrPlot-QROLI66S.js");
+    case "facet":
+      return await import("./facet-DTJKZOBA.js");
+    case "GeneExpInput":
+      return await import("./GeneExpInput-DYBK54HC.js");
+    case "geneRanking":
+      return await import("./geneRanking-MIABUKTN.js");
+    case "genomeBrowser":
+      return await import("./GB-FEBSFX5U.js");
+    case "geomap":
+      return await import("./Geomap-QRD2WZVL.js");
+    case "grin2":
+      return await import("./grin2-N2QM3XTG.js");
+    case "gsea":
+      return await import("./GSEA-KOXOVC5V.js");
+    case "imagePlot":
+      return await import("./imagePlot-OA4WTMLU.js");
+    case "numericDictTermCluster":
+      return await import("./numericDictTermCluster-FNNVLIWB.js");
+    case "profileBarchart2":
+      return await import("./barchart2-D4FXZCTU.js");
+    case "profileForms":
+      return await import("./profileForms-ZDHG67GM.js");
+    case "profilePlot":
+      return await import("./profilePlot-UUZA2YG6.js");
+    case "profilePolar2":
+      return await import("./polar2-PLPE5TX5.js");
+    case "profileRadar2":
+      return await import("./radar2-2KXBS3Y3.js");
+    case "profileRadarFacility2":
+      return await import("./radarFacility2-JCOKJQQF.js");
+    case "proteinView":
+      return await import("./proteinView-GHS3XARL.js");
+    case "proteomeAbundance":
+      return await import("./proteomeAbundance-NH3Y4YC7.js");
+    case "proteomeCohortCompare":
+      return await import("./proteomeCohortCompare-TQ3BGIPS.js");
+    case "ProteomeInput":
+      return await import("./ProteomeInput-4N2G6IFX.js");
+    case "regression":
+      return await import("./Regression-LIWUWAGQ.js");
+    case "report":
+      return await import("./report-WLLFUA7L.js");
+    case "runChart2":
+    //See frequencyChart
+    case "frequencyChart":
+      return await import("./RunChart2-VAX5JGZY.js");
+    case "sampleView":
+      return await import("./sampleView-LPKSYUNF.js");
+    case "sampleScatter":
+      return await import("./scatter-IGFBIZ3B.js");
+    case "sc":
+      return await import("./SC-UHBZ3HRO.js");
+    case "studyCatalog":
+      return await import("./studyCatalog-RINIZ277.js");
+    case "summarizeCnvGeneexp":
+      return await import("./summarizeCnvGeneexp-ZQFNPR65.js");
+    case "summarizeGeneexpSurvival":
+      return await import("./summarizeGeneexpSurvival-GIS7XMMH.js");
+    case "summarizeMutationDiagnosis":
+      return await import("./summarizeMutationDiagnosis-V5L2OKTK.js");
+    case "summarizeMutationSurvival":
+      return await import("./summarizeMutationSurvival-LAUUF6XN.js");
+    case "summarizeMutationCnv":
+      return await import("./summarizeMutationCnv-FWF7YIGR.js");
+    case "summaryInput":
+      return await import("./summaryInput-QIKL3HDD.js");
+    case "summary":
+      return await import("./summary-OMU3ACNE.js");
+    case "survival":
+      return await import("./survival-H5AWMQ36.js");
+    case "table":
+      return await import("./table-YAAH7WR6.js");
+    case "violin":
+      return await import("./Violin-V23VZR6B.js");
+    case "volcano":
+      return await import("./Volcano-64S4AW66.js");
+    case "wsi":
+      return await import("./Wsi-FOJCKDCP.js");
+    default:
+      if (notFoundMessage) throw notFoundMessage;
+      return await globImport_plots_js(`../plots/${chartType}.js`);
+  }
+}
+
+export {
+  importPlot
+};
+//# sourceMappingURL=chunk-B6UXFX73.js.map

package/dist/chunk-BCCFJYPE.js

@@ -0,0 +1,54 @@
+import {
+  addGeneSearchbox,
+  getSCGEunit,
+  getSampleAssayInfo
+} from "./chunk-C3HEDQPT.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import {
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-SB36AUG7.js";
+
+// termdb/handlers/singleCellGeneExpression.ts
+var SearchHandler = class {
+  async init(opts) {
+    this.validateOpts(opts);
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const sample = opts.usecase?.specialCase?.config?.sample;
+    const { genes: geneList } = await getSampleAssayInfo(this.app.vocabApi, sample);
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      geneList,
+      row: holder,
+      searchOnly: "gene",
+      callback: () => this.selectGene(geneSearch.geneSymbol, sample)
+    });
+  }
+  /**TODO: scge tw handler will validate that a sample is included. Need to resolve issue
+   * with sample info not included.*/
+  async selectGene(gene, sample) {
+    if (!gene) throw new Error("No gene selected");
+    const unit = getSCGEunit(this.app.vocabApi);
+    const name = `${gene} ${unit}`;
+    this.callback({ gene, name, type: SINGLECELL_GENE_EXPRESSION, sample });
+  }
+  validateOpts(opts) {
+    if (opts.callback == null) throw new Error("callback is required");
+    if (opts.app == null) throw new Error("app is required");
+    if (opts.holder == null) throw new Error("holder is required");
+    if (opts.genomeObj == null) throw new Error("genomeObj is required");
+    if (opts.usecase == null) throw new Error("usecase is required");
+    if (!opts.usecase?.specialCase?.config?.sample) {
+      throw new Error("usecase.specialCase.config.sample is required for singleCellGeneExpression handler");
+    }
+  }
+};
+
+export {
+  SearchHandler
+};
+//# sourceMappingURL=chunk-BCCFJYPE.js.map

package/dist/chunk-BG3SGGVB.js

@@ -0,0 +1,134 @@
+import {
+  addGeneSearchbox,
+  isoformSelect,
+  pickCollectionFraction,
+  sayerror
+} from "./chunk-C3HEDQPT.js";
+import {
+  Menu
+} from "./chunk-ELJX3QIQ.js";
+import {
+  dofetch3
+} from "./chunk-OBDIJ4QS.js";
+import {
+  ISOFORM_EXPRESSION,
+  getColors
+} from "./chunk-SB36AUG7.js";
+
+// termdb/handlers/isoformExpression.ts
+var SearchHandler = class {
+  constructor() {
+    this.currentGene = null;
+  }
+  init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    this.termCollectionSelectionMode = opts.termCollectionSelectionMode;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    this.dom = {
+      errDiv: holder.append("div").style("margin", "5px 0px").style("display", "none")
+    };
+    const geneSearch = addGeneSearchbox({
+      tip: new Menu({ padding: "0px" }),
+      genome: opts.genomeObj,
+      row: holder,
+      searchOnly: "gene",
+      callback: async () => {
+        try {
+          this.dom.errDiv.style("display", "none");
+          if (!geneSearch.geneSymbol) throw new Error("No gene selected");
+          if (geneSearch.geneSymbol === this.currentGene) return;
+          this.currentGene = geneSearch.geneSymbol;
+          if (this.dom.isoformDiv) this.dom.isoformDiv.remove();
+          this.dom.isoformDiv = holder.append("div");
+          await this.showIsoforms(geneSearch.geneSymbol, opts.genomeObj);
+        } catch (e) {
+          this.dom.errDiv.style("display", "block");
+          sayerror(this.dom.errDiv, "Error: " + (e instanceof Error ? e.message : String(e)));
+        }
+      }
+    });
+  }
+  async showIsoforms(gene, genomeObj) {
+    if (!gene) throw new Error("No gene selected");
+    const data = await dofetch3("genelookup", { body: { genome: genomeObj.name, input: gene, deep: 1 } });
+    if (!data.gmlst?.length) throw new Error(`No isoforms found for ${gene}`);
+    const enstCandidates = data.gmlst.filter((gm) => gm.isoform?.startsWith("ENST"));
+    if (enstCandidates.length === 0) throw new Error(`No Ensembl transcript isoforms found for ${gene}`);
+    const { available } = await dofetch3("termdb/isoformAvailability", {
+      body: {
+        genome: genomeObj.name,
+        dslabel: this.app.vocabApi.vocab.dslabel,
+        isoforms: enstCandidates.map((gm) => gm.isoform)
+      }
+    });
+    const availableSet = new Set(available || []);
+    const enstModels = enstCandidates.filter((gm) => availableSet.has(gm.isoform));
+    if (enstModels.length === 0) throw new Error(`No isoforms with data found for ${gene}`);
+    if (gene !== this.currentGene) return;
+    const div = this.dom.isoformDiv;
+    div.append("div").style("margin-bottom", "8px").style("opacity", 0.65).text(`${gene} \u2014 select isoform(s):`);
+    isoformSelect({
+      holder: div,
+      allgm: enstModels,
+      multiSelect: true,
+      // a single checked isoform yields an individual term, 2+ yield a collection
+      getSubmitLabel: (selectedCount) => selectedCount === 1 ? "Select One Isoform" : `Create Collection (${selectedCount})`,
+      onMultiSelect: (selected) => {
+        if (selected.length === 1) {
+          this.selectIsoform(selected[0].isoform, gene);
+        } else {
+          this.selectCollection(selected, gene);
+        }
+      }
+    });
+  }
+  getUnit() {
+    return this.app.vocabApi.termdbConfig.queries.isoformExpression?.unit || "TPM";
+  }
+  selectIsoform(isoform, gene) {
+    const name = `${isoform} ${this.getUnit()}`;
+    this.callback({ isoform, gene, name, type: ISOFORM_EXPRESSION });
+  }
+  selectCollection(gms, gene) {
+    const unit = this.getUnit();
+    const termlst = gms.map((gm) => ({
+      id: gm.isoform,
+      name: gm.isoform,
+      type: ISOFORM_EXPRESSION,
+      isoform: gm.isoform
+    }));
+    const colorScale = getColors(termlst.length);
+    const term = {
+      type: "termCollection",
+      isCustom: true,
+      memberType: "numeric",
+      name: `${gene} Isoforms (${unit})`,
+      termlst,
+      propsByTermId: Object.fromEntries(termlst.map((term2) => [term2.id, { color: colorScale(term2.id) }])),
+      isleaf: true
+    };
+    if (this.termCollectionSelectionMode === "fraction") {
+      if (!this.dom?.isoformDiv) throw new Error("isoform result holder is missing");
+      this.dom.fractionDiv?.remove();
+      this.dom.fractionDiv = this.dom.isoformDiv.append("div").style("margin-top", "10px");
+      pickCollectionFraction({
+        holder: this.dom.fractionDiv,
+        term,
+        callback: (tw) => this.callback(tw)
+      });
+      return;
+    }
+    this.callback(term);
+  }
+};
+function filterIsoforms(gmlst, availableItems) {
+  const itemSet = new Set(availableItems);
+  return gmlst.filter((gm) => gm.isoform?.startsWith("ENST") && (itemSet.size === 0 || itemSet.has(gm.isoform)));
+}
+
+export {
+  SearchHandler,
+  filterIsoforms
+};
+//# sourceMappingURL=chunk-BG3SGGVB.js.map