@sjcrh/proteinpaint-client 2.219.1 → 2.221.0

package/dist/chunk-ETXOEP4N.js

@@ -1,184 +0,0 @@
-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-6AKLIWOG.js"),
-  "../plots/controls.config.js": () => import("./controls.config-F7NIPLKB.js"),
-  "../plots/controls.js": () => import("./controls-ZT3GZ667.js"),
-  "../plots/dictionary.js": () => import("./dictionary-U2BWGY6B.js"),
-  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-2XLLIYGA.js"),
-  "../plots/geneExpression.js": () => import("./geneExpression-KPRFXKU7.js"),
-  "../plots/geneORA.js": () => import("./geneORA-R74JPUTC.js"),
-  "../plots/geneset.js": () => import("./geneset-VMBICNCZ.js"),
-  "../plots/hierCluster.js": () => import("./hierCluster-Z4PVNMGS.js"),
-  "../plots/importPlot.js": () => import("./importPlot-GFEFYEHZ.js"),
-  "../plots/matrix.js": () => import("./matrix-W4AX5OBM.js"),
-  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-Q6WUNK2K.js"),
-  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-OGQ3KUY6.js"),
-  "../plots/matrix/hierCluster.js": () => import("./hierCluster-EKGFBQT4.js"),
-  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-3GJZXG75.js"),
-  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-5DAIZ3E5.js"),
-  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-RH4BOM5F.js"),
-  "../plots/matrix/matrix.config.js": () => import("./matrix.config-PK26VPQT.js"),
-  "../plots/matrix/matrix.data.js": () => import("./matrix.data-UK5DGKBK.js"),
-  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-Q5XSAUUH.js"),
-  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-NM4Q5YDN.js"),
-  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-4C37PII5.js"),
-  "../plots/matrix/matrix.js": () => import("./matrix-3UJW6LOA.js"),
-  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-ODV7WXUP.js"),
-  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-5MY7OXWN.js"),
-  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-QA7W7ZUL.js"),
-  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-4FSFJPCK.js"),
-  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-3QLFMBJ5.js"),
-  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-EY3SA6CG.js"),
-  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-2LHSHNFC.js"),
-  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-FGWNBCRR.js"),
-  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-HVOC6IYT.js"),
-  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-OAXWPZZI.js"),
-  "../plots/matrix/test/matrix.unit.spec.js": () => import("./matrix.unit.spec-RAL7AU22.js"),
-  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-HZJKOF5G.js"),
-  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-H3ABPPD3.js"),
-  "../plots/plot.disco.js": () => import("./plot.disco-X7KCDWGX.js"),
-  "../plots/plot.ssgq.js": () => import("./plot.ssgq-GYRVHTC7.js"),
-  "../plots/singleCellPlot.js": () => import("./singleCellPlot-MGOQ7EQV.js"),
-  "../plots/stattable.js": () => import("./stattable-FROSNTJY.js"),
-  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-ZP7XWHQH.js"),
-  "../plots/table.js": () => import("./table-LLCFO4KK.js"),
-  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-QRIRRPO7.js"),
-  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-HRRE3J45.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-LUCTWXHU.js");
-    case "aggregateMatrix":
-      return await import("./AggregateMatrix-JVMF27YL.js");
-    case "animatedBubbleChart":
-      return await import("./animatedBubbleChart-67SY5JGP.js");
-    case "brainImaging":
-      return await import("./brainImaging-ODWHF7WZ.js");
-    case "brainRegions":
-      return await import("./brainRegions-DC7DEA7N.js");
-    case "barchart":
-      return await import("./barchart-IGWRVB6W.js");
-    case "boxplot":
-      return await import("./BoxPlot-22RXMPRL.js");
-    case "bubbleHeatmap":
-      return await import("./bubbleHeatmap-T5ACULRL.js");
-    case "cellTypeBubbleHeatmap":
-      return await import("./cellTypeBubbleHeatmap-RQINXXTK.js");
-    case "correlationVolcano":
-      return await import("./CorrelationVolcano-PBZWPFSN.js");
-    case "cuminc":
-      return await import("./Cuminc-EL74X5GY.js");
-    case "dataDownload":
-      return await import("./dataDownload-CHMPXHBY.js");
-    case "DEinput":
-      return await import("./DEinput-ZKEFJZQU.js");
-    case "dictionary":
-      return await import("./dictionary-U2BWGY6B.js");
-    case "differentialAnalysis":
-      return await import("./DifferentialAnalysis-3JTZ5WCQ.js");
-    case "Disco":
-      return await import("./Disco-ME53U25C.js");
-    case "dmr":
-      return await import("./DmrPlot-OWBXUTON.js");
-    case "facet":
-      return await import("./facet-5VDCSP3S.js");
-    case "GeneExpInput":
-      return await import("./GeneExpInput-BAOC6ICV.js");
-    case "geneRanking":
-      return await import("./geneRanking-IJTXNMHV.js");
-    case "genomeBrowser":
-      return await import("./GB-7X6DBWKS.js");
-    case "geomap":
-      return await import("./Geomap-OZERLL7V.js");
-    case "grin2":
-      return await import("./grin2-Y6KAFVV2.js");
-    case "gsea":
-      return await import("./GSEA-GAZIEGD7.js");
-    case "imagePlot":
-      return await import("./imagePlot-ZJEZPBX7.js");
-    case "numericDictTermCluster":
-      return await import("./numericDictTermCluster-TGL4X6UC.js");
-    case "profileBarchart2":
-      return await import("./barchart2-TT6OBJJP.js");
-    case "profileForms":
-      return await import("./profileForms-FY34KXCL.js");
-    case "profilePlot":
-      return await import("./profilePlot-3FX2TPYC.js");
-    case "profilePolar2":
-      return await import("./polar2-5KNZRLXY.js");
-    case "profileRadar2":
-      return await import("./radar2-X757WR6V.js");
-    case "profileRadarFacility2":
-      return await import("./radarFacility2-GUBAK4Y3.js");
-    case "proteinView":
-      return await import("./proteinView-WSEO3LD3.js");
-    case "proteomeAbundance":
-      return await import("./proteomeAbundance-NH3Y4YC7.js");
-    case "proteomeCohortCompare":
-      return await import("./proteomeCohortCompare-KA2DF3EE.js");
-    case "ProteomeInput":
-      return await import("./ProteomeInput-MOBXHRD5.js");
-    case "regression":
-      return await import("./Regression-XWT4NNTG.js");
-    case "report":
-      return await import("./report-TUAFDGAE.js");
-    case "runChart2":
-    //See frequencyChart
-    case "frequencyChart":
-      return await import("./RunChart2-Q7W5MWJS.js");
-    case "sampleView":
-      return await import("./sampleView-X6YKCBE7.js");
-    case "sampleScatter":
-      return await import("./scatter-FTJ77NUM.js");
-    case "sc":
-      return await import("./SC-MM3JTEVL.js");
-    case "studyCatalog":
-      return await import("./studyCatalog-XIYNJ24U.js");
-    case "cohortSunburst":
-      return await import("./cohortSunburst-AQFSNJ5K.js");
-    case "summarizeCnvGeneexp":
-      return await import("./summarizeCnvGeneexp-N3OFI24L.js");
-    case "summarizeGeneexpSurvival":
-      return await import("./summarizeGeneexpSurvival-J4DO2AL4.js");
-    case "summarizeMutationDiagnosis":
-      return await import("./summarizeMutationDiagnosis-JAEAUFCA.js");
-    case "summarizeMutationSurvival":
-      return await import("./summarizeMutationSurvival-4QZDDXDV.js");
-    case "summarizeMutationCnv":
-      return await import("./summarizeMutationCnv-Y43BBSI4.js");
-    case "summaryInput":
-      return await import("./summaryInput-WCADUZBK.js");
-    case "summary":
-      return await import("./summary-DTJZ7NNA.js");
-    case "sunburst":
-      return await import("./sunburst-DSFFFP33.js");
-    case "swimmer":
-      return await import("./swimmer-2EJZH5PP.js");
-    case "survival":
-      return await import("./survival-ONWZ5RFM.js");
-    case "table":
-      return await import("./table-LLCFO4KK.js");
-    case "violin":
-      return await import("./Violin-XNTBDUPG.js");
-    case "volcano":
-      return await import("./Volcano-GRKXU3WL.js");
-    case "wsi":
-      return await import("./Wsi-22KJSFVH.js");
-    default:
-      if (notFoundMessage) throw notFoundMessage;
-      return await globImport_plots_js(`../plots/${chartType}.js`);
-  }
-}
-
-export {
-  importPlot
-};
-//# sourceMappingURL=chunk-ETXOEP4N.js.map

package/dist/chunk-FOUMNTII.js

@@ -1,134 +0,0 @@
-import {
-  addGeneSearchbox,
-  isoformSelect,
-  pickCollectionFraction,
-  sayerror
-} from "./chunk-BKW35Z4U.js";
-import {
-  Menu
-} from "./chunk-CNFTQSNE.js";
-import {
-  dofetch3
-} from "./chunk-CJHNPYFQ.js";
-import {
-  ISOFORM_EXPRESSION,
-  getColors
-} from "./chunk-ME3HB3V6.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-FOUMNTII.js.map

package/dist/chunk-FTGLS763.js

@@ -1,56 +0,0 @@
-import {
-  sayerror
-} from "./chunk-BKW35Z4U.js";
-import {
-  TermTypeGroups
-} from "./chunk-ME3HB3V6.js";
-
-// termdb/handlers/singleCellCellType.ts
-var SearchHandler = class {
-  async init(opts) {
-    this.validateOpts(opts);
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const scctTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE];
-    if (!scctTerms?.length) {
-      sayerror(
-        holder,
-        `termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`
-      );
-      return;
-    }
-    const usecaseConfig = opts.usecase?.specialCase?.config;
-    const plots = usecaseConfig?.sample?.plots;
-    const isMeta = usecaseConfig?.sample?.isMetaResult;
-    const filtered = plots ? scctTerms.filter((t) => plots.includes(t.plot)) : usecaseConfig?.name ? scctTerms.filter((t) => t.plot === usecaseConfig.name) : scctTerms;
-    const getLabel = (t) => isMeta || plots?.length == 1 ? t.name : `${t.name} (${t.plot})`;
-    const filteredTerms = new Set(
-      plots || !usecaseConfig?.name ? filtered.map((t) => ({ ...t, label: getLabel(t) })) : filtered
-    );
-    for (const t of Array.from(filteredTerms)) {
-      holder.append("div").classed("termdiv", true).style("padding", "0px 5px").append("div").classed("termlabel sja_filter_tag_btn sja_tree_click_term ts_pill", true).style("display", "inline-block").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text(t.label || t.name).on("click", () => {
-        const term = this.makeTerm(t, usecaseConfig);
-        this.callback(term);
-      });
-    }
-  }
-  makeTerm(_term, usecaseConfig) {
-    const term = { ..._term };
-    if (!term.sample && usecaseConfig?.sample) term.sample = usecaseConfig.sample;
-    return term;
-  }
-  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.usecase == null) throw new Error("usecase is required");
-    if (!opts.app.vocabApi.termdbConfig?.termType2terms)
-      throw new Error("termType2terms is required in termdbConfig for singleCellCellType handler");
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-FTGLS763.js.map