@sjcrh/proteinpaint-client 2.170.21 → 2.170.23

package/dist/chunk-PZ7WCWYR.js

@@ -0,0 +1,168 @@
+import {
+  __glob
+} from "./chunk-HFNDKYVF.js";
+
+// import("../plots/**/*.js") in plots/importPlot.js
+var globImport_plots_js = __glob({
+  "../plots/DziViewer.js": () => import("./DziViewer-3GAMDKPH.js"),
+  "../plots/alphaGenome.js": () => import("./alphaGenome-XELMXZYP.js"),
+  "../plots/barchart.data.js": () => import("./barchart.data-XHQQSOBI.js"),
+  "../plots/barchart.events.js": () => import("./barchart.events-PN2DFSO6.js"),
+  "../plots/barchart.js": () => import("./barchart-7NKVAMCT.js"),
+  "../plots/bars.renderer.js": () => import("./bars.renderer-4N4QOUNI.js"),
+  "../plots/bars.settings.js": () => import("./bars.settings-SDU7PZOS.js"),
+  "../plots/brainImaging.js": () => import("./brainImaging-FWH2D2DU.js"),
+  "../plots/controls.btns.js": () => import("./controls.btns-UXIUAMXI.js"),
+  "../plots/controls.config.js": () => import("./controls.config-AM4LK4IC.js"),
+  "../plots/controls.js": () => import("./controls-GLYBFGRP.js"),
+  "../plots/cuminc.js": () => import("./cuminc-WZD56GIC.js"),
+  "../plots/dataDownload.js": () => import("./dataDownload-24QHNCXE.js"),
+  "../plots/dictionary.js": () => import("./dictionary-5E7CLLRU.js"),
+  "../plots/dziviewer/plot.dzi.js": () => import("./plot.dzi-MJACI56W.js"),
+  "../plots/facet.js": () => import("./facet-6QNMIO6E.js"),
+  "../plots/frequencyChart.js": () => import("./frequencyChart-I3Q3QVY6.js"),
+  "../plots/frequencyChart/test/frequencyChart.integration.spec.js": () => import("./frequencyChart.integration.spec-TDLFPFR2.js"),
+  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-4T56V22I.js"),
+  "../plots/geneExpression.js": () => import("./geneExpression-RNDWSUNQ.js"),
+  "../plots/geneORA.js": () => import("./geneORA-2Y7CYHTH.js"),
+  "../plots/geneset.js": () => import("./geneset-ECEP5R3U.js"),
+  "../plots/gsea.js": () => import("./gsea-BTM3IJRY.js"),
+  "../plots/hierCluster.js": () => import("./hierCluster-54BKKQ44.js"),
+  "../plots/imagePlot.js": () => import("./imagePlot-UTTJUD4R.js"),
+  "../plots/importPlot.js": () => import("./importPlot-L2J4NM7V.js"),
+  "../plots/matrix.js": () => import("./matrix-WQO4KMUQ.js"),
+  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-GUYZGTEW.js"),
+  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-URC4TOXY.js"),
+  "../plots/matrix/hierCluster.js": () => import("./hierCluster-DLGVELGL.js"),
+  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-GDC6LGYZ.js"),
+  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-B3CCDEG3.js"),
+  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-43E3HCDL.js"),
+  "../plots/matrix/matrix.config.js": () => import("./matrix.config-C33VG7ZQ.js"),
+  "../plots/matrix/matrix.controls.js": () => import("./matrix.controls-OTW7KDWP.js"),
+  "../plots/matrix/matrix.data.js": () => import("./matrix.data-4UAT3IGU.js"),
+  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-KO3RCBVA.js"),
+  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-NKYDENEH.js"),
+  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-KMRUZK22.js"),
+  "../plots/matrix/matrix.js": () => import("./matrix-SFABUCQW.js"),
+  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-R5IJLBZX.js"),
+  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-ONRRVW3M.js"),
+  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-Z7XPW7LE.js"),
+  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-XTEOHKVJ.js"),
+  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-6KRXEOQL.js"),
+  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-DCUNQCSC.js"),
+  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-QPLO6REA.js"),
+  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-7DEVQKQF.js"),
+  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-XT7OSKPO.js"),
+  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-IO4NUU6K.js"),
+  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-CWPLPGHG.js"),
+  "../plots/mutationSignature.js": () => import("./mutationSignature-GRJQLL62.js"),
+  "../plots/numericDictTermCluster.js": () => import("./numericDictTermCluster-3E2BONBG.js"),
+  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-INP467BP.js"),
+  "../plots/plot.disco.js": () => import("./plot.disco-H6LXVUJK.js"),
+  "../plots/plot.ssgq.js": () => import("./plot.ssgq-GUF2P4WC.js"),
+  "../plots/regression.inputs.js": () => import("./regression.inputs-Y47JA57G.js"),
+  "../plots/regression.inputs.term.js": () => import("./regression.inputs.term-K2CBZFIA.js"),
+  "../plots/regression.inputs.values.table.js": () => import("./regression.inputs.values.table-E543YLX2.js"),
+  "../plots/regression.js": () => import("./regression-GIF2TWTH.js"),
+  "../plots/regression.results.js": () => import("./regression.results-2FDKW6OV.js"),
+  "../plots/report.js": () => import("./report-SCPRSEH3.js"),
+  "../plots/runChart.js": () => import("./runChart-7EZTX54Q.js"),
+  "../plots/runchart/test/runchart.integration.spec.js": () => import("./runchart.integration.spec-NLRTXWFJ.js"),
+  "../plots/sampleView.js": () => import("./sampleView-ZUTPY5L2.js"),
+  "../plots/scatter/test/scatter.integration.spec.js": () => import("./scatter.integration.spec-H67MTCSL.js"),
+  "../plots/singleCellPlot.js": () => import("./singleCellPlot-HEEYLAS7.js"),
+  "../plots/stattable.js": () => import("./stattable-LAEJIX2Y.js"),
+  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-2MM5OTD2.js"),
+  "../plots/table.js": () => import("./table-NYNPJQE6.js"),
+  "../plots/test/barchart.integration.spec.js": () => import("./barchart.integration.spec-SPQHQ5RV.js"),
+  "../plots/test/cuminc.integration.spec.js": () => import("./cuminc.integration.spec-CFZ4UO24.js"),
+  "../plots/test/dataDownload.integration.spec.js": () => import("./dataDownload.integration.spec-ZRVUKWZG.js"),
+  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-CY34SALS.js"),
+  "../plots/test/profile.spec.js": () => import("./profile.spec-ZJMY7LJR.js"),
+  "../plots/test/regression.integration.spec.js": () => import("./regression.integration.spec-XVQP42RL.js"),
+  "../plots/test/regression.spec.js": () => import("./regression.spec-YOVJOJ6N.js"),
+  "../plots/test/sampleScatter.spec.js": () => import("./sampleScatter.spec-G57CFW6R.js"),
+  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-6LOR5EZO.js"),
+  "../plots/test/violin.integration.spec.js": () => import("./violin.integration.spec-6AFHD3SD.js"),
+  "../plots/violin.interactivity.js": () => import("./violin.interactivity-LDD54ACO.js"),
+  "../plots/violin.js": () => import("./violin-DDDKSLSA.js"),
+  "../plots/violin.renderer.js": () => import("./violin.renderer-6IGRXYNY.js"),
+  "../plots/volcano/test/testData.js": () => import("./testData-LEJ53F2K.js"),
+  "../plots/wsiviewer/plot.wsi.js": () => import("./plot.wsi-AQHIZFJB.js")
+});
+
+// plots/importPlot.js
+async function importPlot(chartType, notFoundMessage = "") {
+  switch (chartType) {
+    case "AIProjectAdmin":
+      return await import("./AIProjectAdmin-OX7PPAXW.js");
+    case "barchart":
+      return await import("./barchart-7NKVAMCT.js");
+    case "boxplot":
+      return await import("./BoxPlot-KM3EW2SS.js");
+    case "chat":
+      return await import("./chat-3XZGIAON.js");
+    case "correlationVolcano":
+      return await import("./CorrelationVolcano-AOD672SJ.js");
+    case "genomeBrowser":
+      return await import("./GB-AHN7GT3M.js");
+    case "differentialAnalysis":
+      return await import("./DifferentialAnalysis-VTWIRFQG.js");
+    case "Disco":
+      return await import("./Disco-ZD3QJDWR.js");
+    case "grin2":
+      return await import("./grin2-2RLFI6VP.js");
+    case "gsea":
+      return await import("./gsea-BTM3IJRY.js");
+    case "sampleScatter":
+      return await import("./scatter-HM7RI57U.js");
+    case "sc":
+      return await import("./SC-TE7VABQU.js");
+    case "summarizeCnvGeneexp":
+      return await import("./summarizeCnvGeneexp-RRGWIRST.js");
+    case "summarizeGeneexpSurvival":
+      return await import("./summarizeGeneexpSurvival-F4IYUKX5.js");
+    case "summarizeMutationDiagnosis":
+      return await import("./summarizeMutationDiagnosis-TQ73TOH2.js");
+    case "summarizeMutationSurvival":
+      return await import("./summarizeMutationSurvival-T23XPTRO.js");
+    case "summarizeMutationCnv":
+      return await import("./summarizeMutationCnv-LLIWCBAO.js");
+    case "summaryInput":
+      return await import("./summaryInput-INPB6GAR.js");
+    case "summary":
+      return await import("./summary-NZNBNPC2.js");
+    case "survival":
+      return await import("./survival-L4UIFI54.js");
+    case "table":
+      return await import("./table-NYNPJQE6.js");
+    case "violin":
+      return await import("./violin-DDDKSLSA.js");
+    case "volcano":
+      return await import("./Volcano-XQ2H7UYY.js");
+    case "WSISamplesPlot":
+      return await import("./WsiSamplesPlot-VJYDVYX3.js");
+    case "WSIViewer":
+      return await import("./WSIViewer-DNKMSHLX.js");
+    case "profileRadar":
+      return await import("./profileRadar-YPEHROUX.js");
+    case "profileRadarFacility":
+      return await import("./profileRadarFacility-SFG2N5OH.js");
+    case "profileBarchart":
+      return await import("./profileBarchart-4U54MXDT.js");
+    case "profilePolar":
+      return await import("./polar-W2J4F67H.js");
+    case "profileForms":
+      return await import("./profileForms-WJB34G3I.js");
+    case "profilePlot":
+      return await import("./profilePlot-IRL5LWXF.js");
+    default:
+      if (notFoundMessage) throw notFoundMessage;
+      return await globImport_plots_js(`../plots/${chartType}.js`);
+  }
+}
+
+export {
+  importPlot
+};
+//# sourceMappingURL=chunk-PZ7WCWYR.js.map

package/dist/{chunk-NJNNPYMC.js → chunk-Q2PPO2QT.js}

@@ -3,7 +3,7 @@ import {
   fillTermWrapper,
   table2col,
   termsettingInit
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 
 // plots/summarizeMutationDiagnosis.ts
 async function makeChartBtnMenu(holder, chartsInstance) {
@@ -97,4 +97,4 @@ export {
   makeChartBtnMenu,
   launchPlot
 };
-//# sourceMappingURL=chunk-NJNNPYMC.js.map
+//# sourceMappingURL=chunk-Q2PPO2QT.js.map

package/dist/{chunk-O7P4EZHA.js → chunk-QXGUNKDA.js}

@@ -1,9 +1,9 @@
 import {
   getDefaultViolinSettings
-} from "./chunk-PJNCR2WK.js";
+} from "./chunk-BELOVMGO.js";
 import {
   appInit
-} from "./chunk-UWYO26OF.js";
+} from "./chunk-RZWCVHII.js";
 import {
   select_default
 } from "./chunk-NDWTN4U5.js";
@@ -225,4 +225,4 @@ function setRenderers(self) {
 export {
   InputValuesTable
 };
-//# sourceMappingURL=chunk-O7P4EZHA.js.map
+//# sourceMappingURL=chunk-QXGUNKDA.js.map

package/dist/{chunk-BRKQSTPH.js → chunk-RNZFN7TZ.js}

@@ -1,10 +1,10 @@
 import {
   keyupEnter
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 import {
   get_bin_label,
   get_bin_range_equation
-} from "./chunk-QIE5DTBW.js";
+} from "./chunk-ABMFFNR4.js";
 
 // termsetting/handlers/NumCustomBinEditor.ts
 var NumCustomBinEditor = class {
@@ -226,4 +226,4 @@ var NumCustomBinEditor = class {
 export {
   NumCustomBinEditor
 };
-//# sourceMappingURL=chunk-BRKQSTPH.js.map
+//# sourceMappingURL=chunk-RNZFN7TZ.js.map

package/dist/{chunk-PRPEYNVE.js → chunk-RVNIY4SD.js}

@@ -1,7 +1,7 @@
 import {
   fillbar,
   make_table_2col
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 
 // src/block.mds.expressionstat.js
 var color_noinfo = "#858585";
@@ -269,4 +269,4 @@ export {
   ase_color,
   ui_config
 };
-//# sourceMappingURL=chunk-PRPEYNVE.js.map
+//# sourceMappingURL=chunk-RVNIY4SD.js.map

package/dist/{chunk-L2XKBMRK.js → chunk-RVZ6M5MM.js}

@@ -1,13 +1,13 @@
 import {
   vcf2dstk
-} from "./chunk-MWGHZ2OR.js";
+} from "./chunk-2Y7E546M.js";
 import {
   getsjcharts
 } from "./chunk-MKAF2BHB.js";
 import {
   parseheader,
   parseline
-} from "./chunk-XG4HJBT5.js";
+} from "./chunk-XULJ2UUC.js";
 import {
   bulk_badline,
   disappear2 as disappear,
@@ -17,7 +17,7 @@ import {
   renderSandboxFormDiv,
   sayerror,
   tkt
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 import {
   invalidcoord,
   string2pos
@@ -26,7 +26,7 @@ import {
   dofetch,
   init_bulk_flag,
   parsesample
-} from "./chunk-QIE5DTBW.js";
+} from "./chunk-ABMFFNR4.js";
 import {
   dtcloss,
   dtcnv,
@@ -1242,7 +1242,7 @@ function bulkui(x, y, genomes, hostURL, holder, header) {
       visual_holder = visualdiv.append("div").html('<span style="opacity:.5">FILE</span> ' + file.name);
     }
     inputdiv.selectAll("*").remove();
-    import("./tp.ui-6ZAZ36DP.js").then((tpui) => {
+    import("./tp.ui-AQBLNRRY.js").then((tpui) => {
       tpui.default(cohort, visual_holder, hostURL);
     });
     return cohort;
@@ -1725,7 +1725,7 @@ function bulkembed(arg) {
     const err2 = tpinit(cohort);
     if (err2) throw { message: "Error parsing study: " + err2 };
     saydiv.text("");
-    import("./tp.ui-6ZAZ36DP.js").then((p) => {
+    import("./tp.ui-AQBLNRRY.js").then((p) => {
       p.default(cohort, holder, arg.hostURL);
     });
   }).catch((err2) => {
@@ -2069,7 +2069,7 @@ function loadstudycohort(genomes, file, holder, hostURL, jwt, noshow, app) {
       sayerror(wait, err2);
     }
     if (!noshow) {
-      return import("./tp.ui-6ZAZ36DP.js").then(async (p) => {
+      return import("./tp.ui-AQBLNRRY.js").then(async (p) => {
         getsjcharts().catch(console.error);
         p.default(cohort, holder, hostURL, app);
         return app;
@@ -2324,4 +2324,4 @@ export {
   bulkin,
   bulkembed
 };
-//# sourceMappingURL=chunk-L2XKBMRK.js.map
+//# sourceMappingURL=chunk-RVZ6M5MM.js.map

package/dist/{chunk-UWYO26OF.js → chunk-RZWCVHII.js}

@@ -1,23 +1,23 @@
 import {
   storeInit
-} from "./chunk-CENQDG7A.js";
+} from "./chunk-VOUTHIB5.js";
 import {
   recoverInit
-} from "./chunk-JUT2O3BR.js";
+} from "./chunk-5FTNFH4T.js";
 import {
   AppBase,
   sayerror,
   vocabInit
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 import {
   importPlot
-} from "./chunk-DXDHMTY7.js";
+} from "./chunk-PZ7WCWYR.js";
 import {
   Menu
 } from "./chunk-OGVY5ALW.js";
 import {
   AppApi
-} from "./chunk-VGLPN6PS.js";
+} from "./chunk-KZBB7S6A.js";
 
 // plots/plot.app.ts
 var PlotApp = class extends AppBase {
@@ -121,6 +121,17 @@ var PlotApp = class extends AppBase {
     if (e.stack) console.log(e.stack);
     this.bus.emit("error");
   }
+  skipPrevActionAbort(action) {
+    if (!action) return false;
+    if (action.type.startsWith("filter")) return false;
+    if (action.type.startsWith("cohort")) return false;
+    if (action.type == "app_refresh") {
+      if (action.subactions) {
+        return action.subactions.find((a) => a.type.startsWith("filter") || a.type.startsWith("cohort")) ? false : true;
+      }
+    }
+    return true;
+  }
   destroy() {
     if (this.dom?.holder) this.dom.holder.selectAll("*").remove();
   }
@@ -130,4 +141,4 @@ var appInit = AppApi.getInitFxn(PlotApp);
 export {
   appInit
 };
-//# sourceMappingURL=chunk-UWYO26OF.js.map
+//# sourceMappingURL=chunk-RZWCVHII.js.map

package/dist/{chunk-UWYO26OF.js.map → chunk-RZWCVHII.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../plots/plot.app.ts"],
-  "sourcesContent": ["import { AppApi, type RxApp, type ComponentApi } from '../rx'\nimport { AppBase } from '#plots/AppBase.ts'\nimport { storeInit } from '#mass/store'\nimport { vocabInit } from '#termdb/vocabulary'\nimport { recoverInit } from '../rx/src/recover'\nimport { sayerror, Menu } from '#dom'\nimport { importPlot } from '#plots/importPlot.js'\n\n/*\nthe purpose of this wrapper is to allow a mass plot to be used with control options outside of mass app\n\nTODO allow to hide controls. e.g. in the cuminc plot integrated into cox-snplocus, allowing to get rid of duplicating code of Cuminc class in cuminc.js\n\nFIXME convert to ts and fully type opts\n\nconstructor options (opts)\n\n\t.holder\n\t\td3-wrapped DOM container\n\n\t.vocabApi\n\t\trequired if state.vocab is not provided\n\n\t.violin{}\n\t\t.mode='minimal'??\n\n\t.app{}\n\t\t.features{}\n\t\t.getPlotHolder() ??\n\n\t.fetchOpts{}\n\t.state: {\n\t\t\n\t\t// required if opts.vocabApi is not provided\n\t\t.vocab: { \n\t\t\tgenome\n\t\t\tdslabel\n\t\t}\n\t\t\n\t\t// required\n\t\tplots[{}] options for rendering 1 or more plot(s), for example:\n\n\t\t[{\n\t\t\tchartType: 'summary',\n\t\t\tchildType: 'barchart',\n\t\t\tterm: {},\n\t\t\tterm2: {},\n\t\t\tsettings: {\n\t\t\t\tbarchart: {\n\t\t\t\t\tunit: 'pct'\n\t\t\t\t}\n\t\t\t}\n\t\t}]\n\t}\n*/\n\nclass PlotApp extends AppBase implements RxApp {\n\t// expected RxApp, some are already declared/set in AppBase\n\tapi: AppApi\n\ttype: string\n\tparentId?: string\n\tdom!: {\n\t\t[index: string]: any\n\t}\n\tcomponents: {\n\t\t[name: string]: ComponentApi | { [name: string]: ComponentApi }\n\t} = {}\n\n\twasDestroyed = false\n\tstore: any\n\tbus!: any\n\n\tconstructor(opts, api) {\n\t\tsuper(opts)\n\t\tthis.api = api\n\t\tthis.type = 'app'\n\t\tthis.dom = this.getDom(opts)\n\t}\n\n\tgetDom(opts) {\n\t\t// this will create divs in the correct stacking order\n\t\tconst dom: { [index: string]: any } = {\n\t\t\tholder: opts.holder,\n\t\t\terrdiv: opts.holder.append('div'),\n\t\t\tplotDiv: opts.holder.append('div')\n\t\t}\n\t\tconst controls = opts.violin?.mode == 'minimal' ? null : opts.holder.append('div').style('white-space', 'nowrap')\n\t\tif (controls) {\n\t\t\tdom.plotControls = controls.append('div').style('display', 'inline-block')\n\t\t\tdom.recoverControls = controls.append('div').style('display', 'inline-block')\n\t\t}\n\t\treturn dom\n\t}\n\n\tasync preApiFreeze(api) {\n\t\ttry {\n\t\t\tapi.tip = new Menu({ padding: '5px' })\n\t\t\tapi.printError = e => this.printError(e)\n\n\t\t\tconst vocab = this.opts.state.vocab\n\n\t\t\tapi.vocabApi = this.opts.vocabApi\n\t\t\t\t? this.opts.vocabApi\n\t\t\t\t: await vocabInit({\n\t\t\t\t\t\tapp: api,\n\t\t\t\t\t\tstate: {\n\t\t\t\t\t\t\tvocab: {\n\t\t\t\t\t\t\t\t// either (genome + dslabel) XOR (terms) can be undefined\n\t\t\t\t\t\t\t\tgenome: vocab?.genome || this.opts.state.genome,\n\t\t\t\t\t\t\t\tdslabel: vocab?.dslabel || this.opts.state.dslabel,\n\t\t\t\t\t\t\t\tterms: vocab?.terms\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t},\n\t\t\t\t\t\tfetchOpts: this.opts.fetchOpts\n\t\t\t\t  })\n\n\t\t\t// the vocabApi's vocab may be reprocessed from the original input\n\t\t\tthis.opts.state.vocab = api.vocabApi.vocab\n\t\t} catch (e) {\n\t\t\tconsole.log(`preApiFreeze error`, e)\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tasync init() {\n\t\t// catch initialization error\n\t\ttry {\n\t\t\t// this plot.app does not create a this.components.nav, unlike mass/app.js\n\t\t\t// so the nav is always hidden, can be hardcoded here\n\t\t\tthis.opts.state.nav = { header_mode: 'hidden' }\n\t\t\tthis.store = await storeInit({ app: this.api, state: this.opts.state })\n\t\t\tthis.state = await this.store.copyState()\n\t\t\tthis.components = {\n\t\t\t\tplots: {}\n\t\t\t}\n\t\t\tif (this.opts.app?.features?.includes('recover'))\n\t\t\t\tthis.components.recover = await recoverInit({\n\t\t\t\t\tapp: this.api,\n\t\t\t\t\tholder: this.dom.recoverControls,\n\t\t\t\t\t// TODO: ???? may limit the tracked state to only the filter, activeCohort ???\n\t\t\t\t\tgetState: appState => appState,\n\t\t\t\t\t//reactsTo: action => true, //action.type != 'plot_edit' || action.type == 'app_refresh',\n\t\t\t\t\tmaxHistoryLen: 10\n\t\t\t\t})\n\n\t\t\tif (this.opts.app?.doNotAwaitInitRender) {\n\t\t\t\t// do not await to return the instance sooner and allow calling appApi.triggerAbort() before initial render,\n\t\t\t\t// instead of waiting for initial data loading and rendering\n\t\t\t\tthis.api.dispatch()\n\t\t\t} else {\n\t\t\t\tawait this.api.dispatch()\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tthis.printError(e)\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.api.vocabApi.main()\n\n\t\tfor (const id in this.components.plots) {\n\t\t\tconst plot = this.components.plots[id]\n\t\t\tif (!this.state.plots.find(p => p.id === plot.id)) {\n\t\t\t\tplot.destroy()\n\t\t\t\tdelete this.components.plots[id]\n\t\t\t}\n\t\t}\n\n\t\tfor (const plot of this.state.plots.values()) {\n\t\t\tif (!this.components.plots[plot.id]) {\n\t\t\t\tconst holder = this.opts?.app?.getPlotHolder\n\t\t\t\t\t? this.opts.app.getPlotHolder(plot, this.dom.holder)\n\t\t\t\t\t: this.dom.holder.append('div')\n\n\t\t\t\t// quick fix to only track the plotDiv for the first plot\n\t\t\t\t// TODO: reliably handle the case where a plotApp instance may have multiple plots/holders\n\t\t\t\tif (!this.dom.plotDiv) this.dom.plotDiv = holder\n\t\t\t\tconst { componentInit } = await importPlot(plot.chartType)\n\t\t\t\tconst plotApi = await componentInit({\n\t\t\t\t\tid: plot.id,\n\t\t\t\t\tapp: this.api,\n\t\t\t\t\tholder,\n\t\t\t\t\tcontrols: this.dom.plotControls\n\t\t\t\t})\n\t\t\t\tthis.components.plots[plot.id] = plotApi\n\t\t\t}\n\t\t}\n\t}\n\n\tprintError(e) {\n\t\tsayerror(this.dom.errdiv, 'Error: ' + (e.message || e))\n\t\tif (e.stack) console.log(e.stack)\n\t\tthis.bus.emit('error')\n\t}\n\n\tdestroy() {\n\t\tif (this.dom?.holder) this.dom.holder.selectAll('*').remove()\n\t}\n}\n\nexport const appInit = AppApi.getInitFxn(PlotApp)\n"],
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+  "sourcesContent": ["import { AppApi, type RxApp, type ComponentApi } from '../rx'\nimport { AppBase } from '#plots/AppBase.ts'\nimport { storeInit } from '#mass/store'\nimport { vocabInit } from '#termdb/vocabulary'\nimport { recoverInit } from '../rx/src/recover'\nimport { sayerror, Menu } from '#dom'\nimport { importPlot } from '#plots/importPlot.js'\n\n/*\nthe purpose of this wrapper is to allow a mass plot to be used with control options outside of mass app\n\nTODO allow to hide controls. e.g. in the cuminc plot integrated into cox-snplocus, allowing to get rid of duplicating code of Cuminc class in cuminc.js\n\nFIXME convert to ts and fully type opts\n\nconstructor options (opts)\n\n\t.holder\n\t\td3-wrapped DOM container\n\n\t.vocabApi\n\t\trequired if state.vocab is not provided\n\n\t.violin{}\n\t\t.mode='minimal'??\n\n\t.app{}\n\t\t.features{}\n\t\t.getPlotHolder() ??\n\n\t.fetchOpts{}\n\t.state: {\n\t\t\n\t\t// required if opts.vocabApi is not provided\n\t\t.vocab: { \n\t\t\tgenome\n\t\t\tdslabel\n\t\t}\n\t\t\n\t\t// required\n\t\tplots[{}] options for rendering 1 or more plot(s), for example:\n\n\t\t[{\n\t\t\tchartType: 'summary',\n\t\t\tchildType: 'barchart',\n\t\t\tterm: {},\n\t\t\tterm2: {},\n\t\t\tsettings: {\n\t\t\t\tbarchart: {\n\t\t\t\t\tunit: 'pct'\n\t\t\t\t}\n\t\t\t}\n\t\t}]\n\t}\n*/\n\nclass PlotApp extends AppBase implements RxApp {\n\t// expected RxApp, some are already declared/set in AppBase\n\tapi: AppApi\n\ttype: string\n\tparentId?: string\n\tdom!: {\n\t\t[index: string]: any\n\t}\n\tcomponents: {\n\t\t[name: string]: ComponentApi | { [name: string]: ComponentApi }\n\t} = {}\n\n\twasDestroyed = false\n\tstore: any\n\tbus!: any\n\n\tconstructor(opts, api) {\n\t\tsuper(opts)\n\t\tthis.api = api\n\t\tthis.type = 'app'\n\t\tthis.dom = this.getDom(opts)\n\t}\n\n\tgetDom(opts) {\n\t\t// this will create divs in the correct stacking order\n\t\tconst dom: { [index: string]: any } = {\n\t\t\tholder: opts.holder,\n\t\t\terrdiv: opts.holder.append('div'),\n\t\t\tplotDiv: opts.holder.append('div')\n\t\t}\n\t\tconst controls = opts.violin?.mode == 'minimal' ? null : opts.holder.append('div').style('white-space', 'nowrap')\n\t\tif (controls) {\n\t\t\tdom.plotControls = controls.append('div').style('display', 'inline-block')\n\t\t\tdom.recoverControls = controls.append('div').style('display', 'inline-block')\n\t\t}\n\t\treturn dom\n\t}\n\n\tasync preApiFreeze(api) {\n\t\ttry {\n\t\t\tapi.tip = new Menu({ padding: '5px' })\n\t\t\tapi.printError = e => this.printError(e)\n\n\t\t\tconst vocab = this.opts.state.vocab\n\n\t\t\tapi.vocabApi = this.opts.vocabApi\n\t\t\t\t? this.opts.vocabApi\n\t\t\t\t: await vocabInit({\n\t\t\t\t\t\tapp: api,\n\t\t\t\t\t\tstate: {\n\t\t\t\t\t\t\tvocab: {\n\t\t\t\t\t\t\t\t// either (genome + dslabel) XOR (terms) can be undefined\n\t\t\t\t\t\t\t\tgenome: vocab?.genome || this.opts.state.genome,\n\t\t\t\t\t\t\t\tdslabel: vocab?.dslabel || this.opts.state.dslabel,\n\t\t\t\t\t\t\t\tterms: vocab?.terms\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t},\n\t\t\t\t\t\tfetchOpts: this.opts.fetchOpts\n\t\t\t\t  })\n\n\t\t\t// the vocabApi's vocab may be reprocessed from the original input\n\t\t\tthis.opts.state.vocab = api.vocabApi.vocab\n\t\t} catch (e) {\n\t\t\tconsole.log(`preApiFreeze error`, e)\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tasync init() {\n\t\t// catch initialization error\n\t\ttry {\n\t\t\t// this plot.app does not create a this.components.nav, unlike mass/app.js\n\t\t\t// so the nav is always hidden, can be hardcoded here\n\t\t\tthis.opts.state.nav = { header_mode: 'hidden' }\n\t\t\tthis.store = await storeInit({ app: this.api, state: this.opts.state })\n\t\t\tthis.state = await this.store.copyState()\n\t\t\tthis.components = {\n\t\t\t\tplots: {}\n\t\t\t}\n\t\t\tif (this.opts.app?.features?.includes('recover'))\n\t\t\t\tthis.components.recover = await recoverInit({\n\t\t\t\t\tapp: this.api,\n\t\t\t\t\tholder: this.dom.recoverControls,\n\t\t\t\t\t// TODO: ???? may limit the tracked state to only the filter, activeCohort ???\n\t\t\t\t\tgetState: appState => appState,\n\t\t\t\t\t//reactsTo: action => true, //action.type != 'plot_edit' || action.type == 'app_refresh',\n\t\t\t\t\tmaxHistoryLen: 10\n\t\t\t\t})\n\n\t\t\tif (this.opts.app?.doNotAwaitInitRender) {\n\t\t\t\t// do not await to return the instance sooner and allow calling appApi.triggerAbort() before initial render,\n\t\t\t\t// instead of waiting for initial data loading and rendering\n\t\t\t\tthis.api.dispatch()\n\t\t\t} else {\n\t\t\t\tawait this.api.dispatch()\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tthis.printError(e)\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tasync main() {\n\t\tthis.api.vocabApi.main()\n\n\t\tfor (const id in this.components.plots) {\n\t\t\tconst plot = this.components.plots[id]\n\t\t\tif (!this.state.plots.find(p => p.id === plot.id)) {\n\t\t\t\tplot.destroy()\n\t\t\t\tdelete this.components.plots[id]\n\t\t\t}\n\t\t}\n\n\t\tfor (const plot of this.state.plots.values()) {\n\t\t\tif (!this.components.plots[plot.id]) {\n\t\t\t\tconst holder = this.opts?.app?.getPlotHolder\n\t\t\t\t\t? this.opts.app.getPlotHolder(plot, this.dom.holder)\n\t\t\t\t\t: this.dom.holder.append('div')\n\n\t\t\t\t// quick fix to only track the plotDiv for the first plot\n\t\t\t\t// TODO: reliably handle the case where a plotApp instance may have multiple plots/holders\n\t\t\t\tif (!this.dom.plotDiv) this.dom.plotDiv = holder\n\t\t\t\tconst { componentInit } = await importPlot(plot.chartType)\n\t\t\t\tconst plotApi = await componentInit({\n\t\t\t\t\tid: plot.id,\n\t\t\t\t\tapp: this.api,\n\t\t\t\t\tholder,\n\t\t\t\t\tcontrols: this.dom.plotControls\n\t\t\t\t})\n\t\t\t\tthis.components.plots[plot.id] = plotApi\n\t\t\t}\n\t\t}\n\t}\n\n\tprintError(e) {\n\t\tsayerror(this.dom.errdiv, 'Error: ' + (e.message || e))\n\t\tif (e.stack) console.log(e.stack)\n\t\tthis.bus.emit('error')\n\t}\n\n\tskipPrevActionAbort(action) {\n\t\t// may skip aborting previously dispatched actions in AppApi.dispatch()\n\t\t// if the new dispatched action doesn't affect all components; this will\n\t\t// allow plots and control menus to continue rendering while creating,\n\t\t// editing, or deleting another plot\n\t\tif (!action) return false\n\t\tif (action.type.startsWith('filter')) return false\n\t\tif (action.type.startsWith('cohort')) return false\n\t\tif (action.type == 'app_refresh') {\n\t\t\tif (action.subactions) {\n\t\t\t\treturn action.subactions.find(a => a.type.startsWith('filter') || a.type.startsWith('cohort')) ? false : true\n\t\t\t}\n\t\t}\n\t\treturn true\n\t}\n\n\tdestroy() {\n\t\tif (this.dom?.holder) this.dom.holder.selectAll('*').remove()\n\t}\n}\n\nexport const appInit = AppApi.getInitFxn(PlotApp)\n"],
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package/dist/{chunk-XZTUXLC6.js → chunk-TT37XSK5.js}

@@ -5,10 +5,10 @@ import {
   disappear2 as disappear,
   makeNumericAxisConfig,
   rgb2hex
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 import {
   dofetch3
-} from "./chunk-QIE5DTBW.js";
+} from "./chunk-ABMFFNR4.js";
 import {
   axisLeft
 } from "./chunk-LOZEKOES.js";
@@ -294,4 +294,4 @@ export {
   bigwigloadsubpanel,
   bigwigconfigpanel
 };
-//# sourceMappingURL=chunk-XZTUXLC6.js.map
+//# sourceMappingURL=chunk-TT37XSK5.js.map

package/dist/{chunk-2KJMSFOW.js → chunk-TZ25ECOQ.js}

@@ -1,6 +1,6 @@
 import {
   sample_match_termvaluesetting
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 import {
   isDictionaryType
 } from "./chunk-YJWWWCJ6.js";
@@ -75,6 +75,7 @@ async function setData(_data) {
   const opts = this.currRequestOpts?.matrix || this.getMatrixRequestOpts(this.state);
   this.numTerms = opts.terms.length;
   opts.loadingDiv = this.chartType != "hierCluster" && this.dom.loadingDiv;
+  opts.signal = this.api.getAbortSignal();
   const data = await this.app.vocabApi.getAnnotatedSampleData(opts, _data);
   this.data = data;
   this.origData = structuredClone(this.data);
@@ -185,4 +186,4 @@ export {
   applyLegendValueFilter,
   matrix_data_exports
 };
-//# sourceMappingURL=chunk-2KJMSFOW.js.map
+//# sourceMappingURL=chunk-TZ25ECOQ.js.map

package/dist/chunk-TZ25ECOQ.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/matrix/matrix.data.js"],
+  "sourcesContent": ["import { getCompInit, copyMerge, deepEqual } from '#rx'\nimport { sample_match_termvaluesetting } from '#common/termutils'\nimport { isDictionaryType } from '#shared/terms.js'\n\nexport function mayRequireToken(tokenMessage = '') {\n\tconst message = tokenMessage || this.state.tokenVerificationMessage\n\tif (!message && this.state.hasVerifiedToken) {\n\t\tthis.dom.errdiv.style('display', 'none').html()\n\t\tthis.dom.controls.style('display', this.opts.controls ? 'inline-block' : '')\n\t\tthis.dom.svg.style('display', '')\n\t\treturn false\n\t} else {\n\t\tthis.dom.errdiv.style('display', '').html(message || 'Requires login')\n\t\tthis.dom.controls.style('display', 'none')\n\t\tthis.dom.svg.style('display', 'none')\n\t\treturn true\n\t}\n}\n\nexport function getMatrixRequestOpts(state) {\n\t/* requests data for all terms shown in matrix,\n\t\tby creating request argument for getAnnotatedSampleData and run it\n\t\tNOTE this excludes the term group used for hierCluster, as its data request is done separately\n\t\t*/\n\tconst terms = []\n\n\tconst termgroups =\n\t\tthis.chartType == 'hierCluster'\n\t\t\t? state.config.termgroups.filter(grp => grp.type != 'hierCluster')\n\t\t\t: state.config.termgroups\n\tfor (const grp of termgroups) {\n\t\tterms.push(...getNormalizedTwLstCopy(grp.lst))\n\t}\n\tif (state.config.divideBy) terms.push(normalizeTwForRequest(structuredClone(state.config.divideBy)))\n\n\t// !!! NOTE !!!\n\t// all parameters here must remove payload properties that are\n\t// not relevant to the data request, so that the dofetch and/or\n\t// browser caching would work\n\tconst opts = {\n\t\tterms,\n\t\tfilter: state.filter,\n\t\tfilter0: state.filter0,\n\t\tmaxGenes: state.config.settings.matrix.maxGenes,\n\t\t/*********** quick fix\n\t\twhen the flag is true, set artificially large number to ensure all genes are sent in one query\n\t\tthis avoids changing getAnnotatedSampleData()\n\t\tadditional non-matrix app that calls getAnnotatedSampleData will NEED THE SAME FIX\n\t\t*/\n\t\ttermsPerRequest: this.app.vocabApi.termdbConfig.queries?.snvindel?.byisoform?.processTwsInOneQuery ? 1000 : 1\n\t}\n\n\tif (this.chartType == 'hierCluster') {\n\t\t/* quick fix, only needed for gdc\n\t\t\tso backend case query will know this context and pull cases with gene exp data\n\t\t\tis ignored by non-gdc datasets\n\t\t\t*/\n\t\topts.isHierCluster = 1\n\t}\n\n\treturn opts\n}\n\nfunction getNormalizedTwLstCopy(twlst) {\n\tconst lst = structuredClone(twlst)\n\tlst.forEach(normalizeTwForRequest)\n\tlst.sort(sortTwLst)\n\treturn lst\n}\n\nfunction normalizeTwForRequest(tw) {\n\tif (!tw?.term) return\n\t// These props are cohort-dependent and should be ignored like termfilter.filter0.\n\t// Note that state filter, filter0 are always sent to the server for dataset-related requests,\n\t// which indirectly covers the computed properties below that are being deleted.\n\tdelete tw.term.category2samplecount\n\t// for GDC, the term.values may not be known ahead of time\n\t// and only filled in as data comes in, should ignore this\n\t// computed value as to avoid affecting tracked state\n\n\t// for dictionary term, term.values is queryed from terms table\n\tif (isDictionaryType(tw.term.type) && tw.term.type !== 'samplelst') delete tw.term.values\n\treturn tw\n}\n\nfunction sortTwLst(twa, twb) {\n\tconst a = twa?.$id || twa.term?.id || twa?.term?.name\n\tconst b = twb?.$id || twb.term?.id || twb?.term?.name\n\treturn a < b ? -1 : 1\n}\n\nexport async function setData(_data) {\n\tconst opts = this.currRequestOpts?.matrix || this.getMatrixRequestOpts(this.state)\n\tthis.numTerms = opts.terms.length\n\topts.loadingDiv = this.chartType != 'hierCluster' && this.dom.loadingDiv\n\topts.signal = this.api.getAbortSignal()\n\tconst data = await this.app.vocabApi.getAnnotatedSampleData(opts, _data)\n\tthis.data = data\n\tthis.origData = structuredClone(this.data)\n\tthis.sampleIdMap = {}\n\tfor (const d of this.data.lst) {\n\t\t// mapping of sample string name to integer id\n\t\t// TODO: not able to find matching sample names between ASH and termdb?\n\t\tthis.sampleIdMap[d.sample] = d._ref_.label\n\t}\n}\n\nexport function applyLegendValueFilter() {\n\tconst self = this\n\tif (!self.config.legendValueFilter.lst.length && !self.config.legendGrpFilter.lst.length) return\n\n\tfor (const grpFilter of self.config.legendGrpFilter.lst) {\n\t\tif (grpFilter.dt) {\n\t\t\tconst filteredOutCats = new Set() // the classes removed by the grpFilter\n\t\t\tfor (const oneSampleData of self.origData.lst) {\n\t\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\t\tif (annoForOneTerm.values) {\n\t\t\t\t\t\tconst newValues = []\n\t\t\t\t\t\tfor (const v of annoForOneTerm.values) {\n\t\t\t\t\t\t\tif (!(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))) {\n\t\t\t\t\t\t\t\tnewValues.push(v)\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tfilteredOutCats.add(v.class)\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tannoForOneTerm.values = newValues\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t\tgrpFilter.filteredOutCats = [...filteredOutCats]\n\t\t\tfor (const oneSampleData of Object.values(self.origData.samples)) {\n\t\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\t\tif (annoForOneTerm.values)\n\t\t\t\t\t\tannoForOneTerm.values = annoForOneTerm.values.filter(\n\t\t\t\t\t\t\tv => !(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))\n\t\t\t\t\t\t)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\n\tconst geneVariant$ids = Object.values(self.data.refs.byTermId)\n\t\t.filter(v => v.term?.type == 'geneVariant')\n\t\t.map(v => v.$id)\n\tconst data = { samples: {}, lst: [], refs: self.data.refs }\n\n\tconst onlyHardFilter = structuredClone(self.config.legendValueFilter)\n\tonlyHardFilter.lst = onlyHardFilter.lst.filter(\n\t\tl => !l.tvs.legendFilterType || l.tvs.legendFilterType !== 'geneVariant_soft'\n\t)\n\tfor (const row of self.origData.lst) {\n\t\tconst include = sample_match_termvaluesetting(row, onlyHardFilter, geneVariant$ids)\n\t\tif (include || self.chartType == 'hierCluster') {\n\t\t\t// for hierCluster, should not filter out any samples by sample_match_termvaluesetting\n\t\t\t// samples are filtered out by joining legendValueFilter with filter in setHierClusterData\n\t\t\tdata.samples[row.sample] = row\n\t\t\tdata.lst.push(row)\n\t\t}\n\t}\n\n\tfor (const valFilter of self.config.legendValueFilter.lst) {\n\t\tif (valFilter.tvs.legendFilterType !== 'geneVariant_soft') continue\n\t\t// applying each soft filter\n\t\tconst tvsV = valFilter.tvs.values[0]\n\t\tconst filteredOutCats = new Set() // the classes removed by the grpFilter\n\t\tfor (const oneSampleData of data.lst) {\n\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\tif (annoForOneTerm.values) {\n\t\t\t\t\tconst newValues = []\n\t\t\t\t\tfor (const v of annoForOneTerm.values) {\n\t\t\t\t\t\tif (!(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))) {\n\t\t\t\t\t\t\tnewValues.push(v)\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tfilteredOutCats.add(v.class)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tannoForOneTerm.values = newValues\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tvalFilter.filteredOutCats = [...filteredOutCats]\n\t\tfor (const oneSampleData of Object.values(data.samples)) {\n\t\t\tfor (const annoForOneTerm of Object.values(oneSampleData)) {\n\t\t\t\tif (annoForOneTerm.values)\n\t\t\t\t\tannoForOneTerm.values = annoForOneTerm.values.filter(\n\t\t\t\t\t\tv => !(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))\n\t\t\t\t\t)\n\t\t\t}\n\t\t}\n\t}\n\tif (self.chartType !== 'hierCluster' && geneVariant$ids.length && self.app.vocabApi.vocab?.dslabel == 'GDC')\n\t\tremove_empty_sample(data, geneVariant$ids)\n\tself.data = data\n}\n\n// each time gene legend soft filter or gene legend group filter is applied (when cell gene values updated), remove\n// the samples that have empty cells (not even WT or BLANK)\nfunction remove_empty_sample(data) {\n\tfor (const oneSampleData of data.lst) {\n\t\tlet removeSample = true\n\t\tfor (const [key, annoForOneTerm] of Object.entries(oneSampleData)) {\n\t\t\tif (!annoForOneTerm.values) continue\n\t\t\tconst annoType = data.refs.byTermId[key].term.type\n\t\t\tif (annoType != 'geneVariant') continue\n\t\t\tif (annoForOneTerm.values.length) removeSample = false\n\t\t}\n\t\tif (removeSample) {\n\t\t\tdata.lst = data.lst.filter(dl => dl.sample !== oneSampleData.sample)\n\t\t\tdelete data.samples[parseInt(oneSampleData.sample)]\n\t\t}\n\t}\n\treturn data\n}\n"],
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+  "names": []
+}

package/dist/{chunk-JUAB6AWT.js → chunk-VMNJ3CBS.js}

@@ -1,6 +1,6 @@
 import {
   runproteinpaint
-} from "./chunk-ULFFSC6N.js";
+} from "./chunk-XDBGOZED.js";
 
 // test/front.helpers.js
 var serverData = /* @__PURE__ */ Object.create(null);
@@ -139,4 +139,4 @@ export {
   getRunPp,
   rideInit
 };
-//# sourceMappingURL=chunk-JUAB6AWT.js.map
+//# sourceMappingURL=chunk-VMNJ3CBS.js.map

package/dist/{chunk-CENQDG7A.js → chunk-VOUTHIB5.js}

@@ -6,14 +6,14 @@ import {
   getFilter,
   getFilterItemByTag,
   getSamplelstTW
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 import {
   importPlot
-} from "./chunk-DXDHMTY7.js";
+} from "./chunk-PZ7WCWYR.js";
 import {
   StoreApi,
   StoreBase
-} from "./chunk-VGLPN6PS.js";
+} from "./chunk-KZBB7S6A.js";
 import {
   CustomError
 } from "./chunk-BEWDIM6H.js";
@@ -459,4 +459,4 @@ var storeInit = StoreApi.getInitFxn(MassStore);
 export {
   storeInit
 };
-//# sourceMappingURL=chunk-CENQDG7A.js.map
+//# sourceMappingURL=chunk-VOUTHIB5.js.map

package/dist/{chunk-CKY3ZZAO.js → chunk-VU5VYG3S.js}

@@ -5,7 +5,7 @@ import {
   first_genetrack_tolist,
   makeSsmLink,
   sayerror
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 import {
   Menu
 } from "./chunk-OGVY5ALW.js";
@@ -254,7 +254,7 @@ function setRenderers(self) {
       "Cumulative incidence test:"
       /*, 'p-value = ' + result.cuminc.pvalue*/
     );
-    const _ = await import("./cuminc-GGM67RVU.js");
+    const _ = await import("./cuminc-WZD56GIC.js");
     const plotter = new _.Cuminc({
       holder,
       config: {
@@ -1106,7 +1106,7 @@ async function createGenomebrowser(self, input, resultLst) {
       overrideTw.q.chr = chr;
       overrideTw.q.start = start;
       overrideTw.q.stop = stop;
-      const _2 = await import("./snplocus-K6AVLJ4I.js");
+      const _2 = await import("./snplocus-4KJHSX65.js");
       await _2.fillTW(overrideTw, self.app.vocabApi);
       self.hasUnsubmittedEdits_nullify_singleuse = true;
       input.pill.runCallback(overrideTw);
@@ -1143,7 +1143,7 @@ async function createGenomebrowser(self, input, resultLst) {
     }
   });
   first_genetrack_tolist(self.parent.genomeObj, arg.tklst);
-  const _ = await import("./block-CHK3JXWE.js");
+  const _ = await import("./block-6XQF343G.js");
   return new _.Block(arg);
 }
 async function updateMds3Tk(self, input, resultLst) {
@@ -1272,4 +1272,4 @@ export {
   RegressionResults,
   showLDlegend
 };
-//# sourceMappingURL=chunk-CKY3ZZAO.js.map
+//# sourceMappingURL=chunk-VU5VYG3S.js.map

package/dist/{chunk-FPT6OILW.js → chunk-W5IT2MO3.js}

@@ -1,12 +1,12 @@
 import {
   summaryInit
-} from "./chunk-RJVNGG6X.js";
+} from "./chunk-FWHKDQVI.js";
 import {
   navInit
-} from "./chunk-FOD4UOVS.js";
+} from "./chunk-7BXRTSFU.js";
 import {
   storeInit
-} from "./chunk-CENQDG7A.js";
+} from "./chunk-VOUTHIB5.js";
 import {
   AppBase,
   downloadSVGsAsPdf,
@@ -14,10 +14,10 @@ import {
   newSandboxDiv,
   sayerror,
   vocabInit
-} from "./chunk-CTRQJ6M4.js";
+} from "./chunk-IKXK6WW5.js";
 import {
   importPlot
-} from "./chunk-DXDHMTY7.js";
+} from "./chunk-PZ7WCWYR.js";
 import {
   Menu
 } from "./chunk-OGVY5ALW.js";
@@ -25,7 +25,7 @@ import {
   AppApi,
   getCompInit,
   multiInit
-} from "./chunk-VGLPN6PS.js";
+} from "./chunk-KZBB7S6A.js";
 import {
   select_default
 } from "./chunk-NDWTN4U5.js";
@@ -290,6 +290,17 @@ var MassApp = class extends AppBase {
     if (e.stack) console.log(e.stack);
     this.bus.emit("error");
   }
+  skipPrevActionAbort(action) {
+    if (!action) return false;
+    if (action.type.startsWith("filter")) return false;
+    if (action.type.startsWith("cohort")) return false;
+    if (action.type == "app_refresh") {
+      if (action.subactions) {
+        return action.subactions.find((a) => a.type.startsWith("filter") || a.type.startsWith("cohort")) ? false : true;
+      }
+    }
+    return true;
+  }
   async downloadPlots() {
     const chartImagesAll = [];
     let i = 1;
@@ -320,4 +331,4 @@ var appInit = AppApi.getInitFxn(MassApp);
 export {
   appInit
 };
-//# sourceMappingURL=chunk-FPT6OILW.js.map
+//# sourceMappingURL=chunk-W5IT2MO3.js.map