@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/chunk-ZZMIDYRE.js

@@ -0,0 +1,197 @@
+import {
+  __glob
+} from "./chunk-HFNDKYVF.js";
+
+// import("../plots/**/*.js") in plots/importPlot.js
+var globImport_plots_js = __glob({
+  "../plots/barchart.data.js": () => import("./barchart.data-VBSWS5N7.js"),
+  "../plots/barchart.events.js": () => import("./barchart.events-F4HSVH6M.js"),
+  "../plots/barchart.js": () => import("./barchart-FSIB3IZZ.js"),
+  "../plots/bars.renderer.js": () => import("./bars.renderer-54UCFLJS.js"),
+  "../plots/bars.settings.js": () => import("./bars.settings-SDU7PZOS.js"),
+  "../plots/brainImaging.js": () => import("./brainImaging-F4GZRF53.js"),
+  "../plots/controls.btns.js": () => import("./controls.btns-KCLXBXSL.js"),
+  "../plots/controls.config.js": () => import("./controls.config-577UCREO.js"),
+  "../plots/controls.js": () => import("./controls-WD5TZITZ.js"),
+  "../plots/cuminc.js": () => import("./cuminc-YJGCKHFM.js"),
+  "../plots/dataDownload.js": () => import("./dataDownload-HBFKARTR.js"),
+  "../plots/dictionary.js": () => import("./dictionary-MWUQYW6W.js"),
+  "../plots/dziviewer/plot.dzi.js": () => import("./plot.dzi-F77KKPIJ.js"),
+  "../plots/facet.js": () => import("./facet-BY6DQRCA.js"),
+  "../plots/gb/test/genomeBrowser.spec.js": () => import("./genomeBrowser.spec-TRREAQCH.js"),
+  "../plots/geneExpression.js": () => import("./geneExpression-SECTPIDT.js"),
+  "../plots/geneORA.js": () => import("./geneORA-CCQGE7QL.js"),
+  "../plots/geneset.js": () => import("./geneset-V2535XGY.js"),
+  "../plots/hierCluster.js": () => import("./hierCluster-5YZOCCTV.js"),
+  "../plots/importPlot.js": () => import("./importPlot-CWMBFQDD.js"),
+  "../plots/matrix.js": () => import("./matrix-AU6NPNID.js"),
+  "../plots/matrix/hierCluster.config.js": () => import("./hierCluster.config-T3Y2LS6V.js"),
+  "../plots/matrix/hierCluster.interactivity.js": () => import("./hierCluster.interactivity-JNBO3MJB.js"),
+  "../plots/matrix/hierCluster.js": () => import("./hierCluster-ZPQCUSVO.js"),
+  "../plots/matrix/hierCluster.renderers.js": () => import("./hierCluster.renderers-FXDCU3PN.js"),
+  "../plots/matrix/matrix.cells.js": () => import("./matrix.cells-CFSI2NWU.js"),
+  "../plots/matrix/matrix.cluster.js": () => import("./matrix.cluster-NU5CYRUT.js"),
+  "../plots/matrix/matrix.config.js": () => import("./matrix.config-VTQ6HL5L.js"),
+  "../plots/matrix/matrix.data.js": () => import("./matrix.data-DBYXSWIN.js"),
+  "../plots/matrix/matrix.dom.js": () => import("./matrix.dom-DDPSUNY2.js"),
+  "../plots/matrix/matrix.groups.js": () => import("./matrix.groups-ZFKWVNMX.js"),
+  "../plots/matrix/matrix.interactivity.js": () => import("./matrix.interactivity-HE2Q6SAO.js"),
+  "../plots/matrix/matrix.js": () => import("./matrix-AT2FFTWO.js"),
+  "../plots/matrix/matrix.layout.js": () => import("./matrix.layout-FD5BPRCX.js"),
+  "../plots/matrix/matrix.legend.js": () => import("./matrix.legend-7MIZZJVB.js"),
+  "../plots/matrix/matrix.renderers.js": () => import("./matrix.renderers-DVM4NB2R.js"),
+  "../plots/matrix/matrix.serieses.js": () => import("./matrix.serieses-7KYX3KAY.js"),
+  "../plots/matrix/matrix.sort.js": () => import("./matrix.sort-CR3J45MQ.js"),
+  "../plots/matrix/matrix.sorterUi.js": () => import("./matrix.sorterUi-4KYRGJT5.js"),
+  "../plots/matrix/test/hierCluster.integration.spec.js": () => import("./hierCluster.integration.spec-PTXVQH77.js"),
+  "../plots/matrix/test/matrix.integration.spec.js": () => import("./matrix.integration.spec-NJ2AXQAS.js"),
+  "../plots/matrix/test/matrix.sort.unit.spec.js": () => import("./matrix.sort.unit.spec-VQ3TR4S2.js"),
+  "../plots/matrix/test/matrix.sorterUi.unit.spec.js": () => import("./matrix.sorterUi.unit.spec-IEHG3OKN.js"),
+  "../plots/matrix/test/oncomatrix.spec.js": () => import("./oncomatrix.spec-4Z4HKS44.js"),
+  "../plots/plot.brainImaging.js": () => import("./plot.brainImaging-WRMDYYHC.js"),
+  "../plots/plot.disco.js": () => import("./plot.disco-SSGPSM7W.js"),
+  "../plots/plot.ssgq.js": () => import("./plot.ssgq-FVFJOYVO.js"),
+  "../plots/regression.inputs.js": () => import("./regression.inputs-LGA67ESO.js"),
+  "../plots/regression.inputs.term.js": () => import("./regression.inputs.term-UCQKXC5D.js"),
+  "../plots/regression.inputs.values.table.js": () => import("./regression.inputs.values.table-2RRE7SMS.js"),
+  "../plots/regression.js": () => import("./regression-XOVSVC7S.js"),
+  "../plots/regression.results.js": () => import("./regression.results-T3HB6CBH.js"),
+  "../plots/sampleView.js": () => import("./sampleView-P5JZHEKY.js"),
+  "../plots/singleCellPlot.js": () => import("./singleCellPlot-MGSS4O3L.js"),
+  "../plots/stattable.js": () => import("./stattable-55YGV5B4.js"),
+  "../plots/survival/test/survival.integration.spec.js": () => import("./survival.integration.spec-FXPCZJSS.js"),
+  "../plots/table.js": () => import("./table-NHS2WLWT.js"),
+  "../plots/test/barchart.integration.spec.js": () => import("./barchart.integration.spec-AXE7BRKX.js"),
+  "../plots/test/cuminc.integration.spec.js": () => import("./cuminc.integration.spec-V46K57GV.js"),
+  "../plots/test/dataDownload.integration.spec.js": () => import("./dataDownload.integration.spec-TEOJOMYK.js"),
+  "../plots/test/expclust.gdc.spec.js": () => import("./expclust.gdc.spec-2R7T7JPY.js"),
+  "../plots/test/regression.integration.spec.js": () => import("./regression.integration.spec-BKM5UI7H.js"),
+  "../plots/test/regression.spec.js": () => import("./regression.spec-W7IVCYVZ.js"),
+  "../plots/test/summary.integration.spec.js": () => import("./summary.integration.spec-VFCYU2V6.js"),
+  "../plots/test/violin.integration.spec.js": () => import("./violin.integration.spec-GBW3VBHW.js"),
+  "../plots/violin.interactivity.js": () => import("./violin.interactivity-N3JVI2AQ.js"),
+  "../plots/violin.js": () => import("./violin-D4EX3ZFV.js"),
+  "../plots/violin.renderer.js": () => import("./violin.renderer-2NYRUXUY.js"),
+  "../plots/volcano/test/testData.js": () => import("./testData-LEJ53F2K.js"),
+  "../plots/wsiviewer/plot.wsi.js": () => import("./plot.wsi-OSZU2PQ5.js")
+});
+
+// plots/importPlot.js
+async function importPlot(chartType, notFoundMessage = "") {
+  switch (chartType) {
+    case "aggregateMatrix":
+      return await import("./AggregateMatrix-7L7OKUXI.js");
+    case "AIProjectAdmin":
+      return await import("./AIProjectAdmin-2W4WNV65.js");
+    case "barchart":
+      return await import("./barchart-FSIB3IZZ.js");
+    case "boxplot":
+      return await import("./BoxPlot-AF72DMSS.js");
+    case "correlationVolcano":
+      return await import("./CorrelationVolcano-H6DHMTYZ.js");
+    case "DEinput":
+      return await import("./DEinput-3HVHJE2I.js");
+    case "dictionary":
+      return await import("./dictionary-MWUQYW6W.js");
+    case "differentialAnalysis":
+      return await import("./DifferentialAnalysis-NBC222Q6.js");
+    case "Disco":
+      return await import("./Disco-B6E3ALAV.js");
+    case "dmr":
+      return await import("./DmrPlot-R3S4PCAE.js");
+    case "DziViewer":
+      return await import("./DziViewer-QYLZ4EMQ.js");
+    case "GeneExpInput":
+      return await import("./GeneExpInput-RESMBEM3.js");
+    case "genomeBrowser":
+      return await import("./GB-PV4RI5DG.js");
+    case "geomap":
+      return await import("./Geomap-2WACSP77.js");
+    case "grin2":
+      return await import("./grin2-GOO7H3RC.js");
+    case "gsea":
+      return await import("./GSEA-DHUOROST.js");
+    case "imagePlot":
+      return await import("./imagePlot-AH2JIGVN.js");
+    case "report":
+      return await import("./report-HRGU3XKL.js");
+    case "runChart2":
+    //See frequencyChart
+    case "frequencyChart":
+      return await import("./RunChart2-YEAOBR2L.js");
+    case "profileBarchart2":
+      return await import("./barchart2-DRNQQJE2.js");
+    case "profileForms":
+      return await import("./profileForms-F7LXHITE.js");
+    case "profilePlot":
+      return await import("./profilePlot-JU7SFYYY.js");
+    case "profilePolar2":
+      return await import("./polar2-R4ZKXKEV.js");
+    case "profileRadar2":
+      return await import("./radar2-EBOTTAMC.js");
+    case "profileRadarFacility2":
+      return await import("./radarFacility2-PAGNJR6D.js");
+    case "proteinView":
+      return await import("./proteinView-VU4SVO5I.js");
+    case "numericDictTermCluster":
+      return await import("./numericDictTermCluster-3HXLMURH.js");
+    case "proteomeAbundance":
+      return await import("./proteomeAbundance-NQ4635NL.js");
+    case "animatedBubbleChart":
+      return await import("./animatedBubbleChart-VJ6EQDQP.js");
+    case "bubbleHeatmap":
+      return await import("./bubbleHeatmap-ZOS2ME3T.js");
+    case "cellTypeBubbleHeatmap":
+      return await import("./cellTypeBubbleHeatmap-BEVDWLHJ.js");
+    case "brainRegions":
+      return await import("./brainRegions-ONUXPD7P.js");
+    case "studyCatalog":
+      return await import("./studyCatalog-AXWH7IOH.js");
+    case "proteomeCohortCompare":
+      return await import("./proteomeCohortCompare-2U537GOK.js");
+    case "geneRanking":
+      return await import("./geneRanking-NVR7ZZIP.js");
+    case "ProteomeInput":
+      return await import("./ProteomeInput-6A7UB4CI.js");
+    case "sampleScatter":
+      return await import("./scatter-WYP2NPNB.js");
+    case "sc":
+      return await import("./SC-C3MJQBI5.js");
+    case "summarizeCnvGeneexp":
+      return await import("./summarizeCnvGeneexp-DRBIXOAP.js");
+    case "summarizeGeneexpSurvival":
+      return await import("./summarizeGeneexpSurvival-4PATAUSN.js");
+    case "summarizeMutationDiagnosis":
+      return await import("./summarizeMutationDiagnosis-UATVI5BK.js");
+    case "summarizeMutationSurvival":
+      return await import("./summarizeMutationSurvival-CZXGM3AA.js");
+    case "summarizeMutationCnv":
+      return await import("./summarizeMutationCnv-UGSIGZDJ.js");
+    case "summaryInput":
+      return await import("./summaryInput-AFZSASTM.js");
+    case "summary":
+      return await import("./summary-IGTXNQ5I.js");
+    case "survival":
+      return await import("./survival-GIRR5ML4.js");
+    case "table":
+      return await import("./table-NHS2WLWT.js");
+    case "violin":
+      return await import("./violin-D4EX3ZFV.js");
+    case "volcano":
+      return await import("./Volcano-N6MXAQDZ.js");
+    case "wsi":
+      return await import("./Wsi-CMLKCEG3.js");
+    case "WSISamplesPlot":
+      return await import("./WsiSamplesPlot-ET7LGNJW.js");
+    case "WSIViewer":
+      return await import("./WSIViewer-OVJ2QS7P.js");
+    default:
+      if (notFoundMessage) throw notFoundMessage;
+      return await globImport_plots_js(`../plots/${chartType}.js`);
+  }
+}
+
+export {
+  importPlot
+};
+//# sourceMappingURL=chunk-ZZMIDYRE.js.map

package/dist/chunk-ZZMIDYRE.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../plots/importPlot.js"],
+  "sourcesContent": ["export async function importPlot(chartType, notFoundMessage = '') {\n\t// TODO: move to dynamic import of exact plot names here, instead of string-pattern,\n\t// so that the bundler does not have to guess code file extension, directory names and letter casing\n\tswitch (chartType) {\n\t\tcase 'aggregateMatrix':\n\t\t\treturn await import('./aggregateMatrix/AggregateMatrix.ts')\n\n\t\tcase 'AIProjectAdmin':\n\t\t\treturn await import('./aiProjectAdmin/AIProjectAdmin.ts')\n\n\t\tcase 'barchart':\n\t\t\treturn await import(`./barchart.js`)\n\n\t\tcase 'boxplot':\n\t\t\treturn await import(`./boxplot/BoxPlot.ts`)\n\n\t\tcase 'correlationVolcano':\n\t\t\treturn await import(`./corrVolcano/CorrelationVolcano.ts`)\n\n\t\tcase 'DEinput':\n\t\t\treturn await import(`./DEinput.ts`)\n\n\t\tcase 'dictionary':\n\t\t\treturn await import(`./dictionary.js`)\n\n\t\tcase 'differentialAnalysis':\n\t\t\treturn await import(`./diffAnalysis/DifferentialAnalysis.ts`)\n\n\t\tcase 'Disco':\n\t\t\treturn await import('./disco/Disco.ts')\n\n\t\tcase 'dmr':\n\t\t\treturn await import('./dmr/DmrPlot.ts')\n\n\t\tcase 'DziViewer':\n\t\t\treturn await import(`./dziviewer/DziViewer.ts`)\n\n\t\tcase 'GeneExpInput':\n\t\t\treturn await import(`./GeneExpInput.ts`)\n\n\t\tcase 'genomeBrowser':\n\t\t\treturn await import('./gb/GB.ts')\n\n\t\tcase 'geomap':\n\t\t\treturn await import('./geomap/Geomap.ts')\n\n\t\tcase 'grin2':\n\t\t\treturn await import('./grin2/grin2')\n\n\t\tcase 'gsea':\n\t\t\treturn await import(`./gsea/GSEA.ts`)\n\n\t\tcase 'imagePlot':\n\t\t\treturn await import('./imagePlot.ts')\n\n\t\tcase 'report':\n\t\t\treturn await import(`./report/report.ts`)\n\n\t\tcase 'runChart2': //See frequencyChart\n\t\tcase 'frequencyChart':\n\t\t\treturn await import(`./runChart2/RunChart2.ts`)\n\n\t\tcase 'profileBarchart2':\n\t\t\treturn await import('./profile/barchart2.ts')\n\n\t\tcase 'profileForms':\n\t\t\treturn await import('./profile/profileForms.ts')\n\n\t\tcase 'profilePlot':\n\t\t\treturn await import('./profile/profilePlot.ts')\n\n\t\tcase 'profilePolar2':\n\t\t\treturn await import('./profile/polar2.ts')\n\n\t\tcase 'profileRadar2':\n\t\t\treturn await import('./profile/radar2.ts')\n\n\t\tcase 'profileRadarFacility2':\n\t\t\treturn await import('./profile/radarFacility2.ts')\n\n\t\tcase 'proteinView':\n\t\t\treturn await import(`./proteinView.ts`)\n\n\t\tcase 'numericDictTermCluster':\n\t\t\treturn await import(`./numericDictTermCluster.ts`)\n\n\t\tcase 'proteomeAbundance':\n\t\t\treturn await import(`./proteomeAbundance.ts`)\n\n\t\tcase 'animatedBubbleChart':\n\t\t\treturn await import(`./animatedBubbleChart.ts`)\n\n\t\tcase 'bubbleHeatmap':\n\t\t\treturn await import('./bubbleHeatmap.ts')\n\n\t\tcase 'cellTypeBubbleHeatmap':\n\t\t\treturn await import('./cellTypeBubbleHeatmap.ts')\n\n\t\tcase 'brainRegions':\n\t\t\treturn await import('./brainRegions.ts')\n\n\t\tcase 'studyCatalog':\n\t\t\treturn await import('./studyCatalog.ts')\n\n\t\tcase 'proteomeCohortCompare':\n\t\t\treturn await import('./proteomeCohortCompare.ts')\n\n\t\tcase 'geneRanking':\n\t\t\treturn await import(`./geneRanking.ts`)\n\n\t\tcase 'ProteomeInput':\n\t\t\treturn await import('./ProteomeInput.ts')\n\n\t\tcase 'sampleScatter':\n\t\t\treturn await import(`./scatter/scatter.js`)\n\n\t\tcase 'sc':\n\t\t\treturn await import('./sc/SC.ts')\n\n\t\tcase 'summarizeCnvGeneexp':\n\t\t\treturn await import(`./summarizeCnvGeneexp.ts`)\n\n\t\tcase 'summarizeGeneexpSurvival':\n\t\t\treturn await import(`./summarizeGeneexpSurvival.ts`)\n\n\t\tcase 'summarizeMutationDiagnosis':\n\t\t\treturn await import(`./summarizeMutationDiagnosis.ts`)\n\n\t\tcase 'summarizeMutationSurvival':\n\t\t\treturn await import(`./summarizeMutationSurvival.ts`)\n\n\t\tcase 'summarizeMutationCnv':\n\t\t\treturn await import(`./summarizeMutationCnv.ts`)\n\n\t\tcase 'summaryInput':\n\t\t\treturn await import(`./summaryInput.ts`)\n\n\t\tcase 'summary':\n\t\t\treturn await import(`./summary.ts`)\n\n\t\tcase 'survival':\n\t\t\treturn await import(`./survival/survival.js`)\n\n\t\tcase 'table':\n\t\t\treturn await import(`./table.js`)\n\n\t\tcase 'violin':\n\t\t\treturn await import(`./violin.js`)\n\n\t\tcase 'volcano':\n\t\t\treturn await import(`./volcano/Volcano.ts`)\n\n\t\tcase 'wsi':\n\t\t\treturn await import('./w2/Wsi.ts')\n\n\t\tcase 'WSISamplesPlot':\n\t\t\treturn await import('./wsisamples/WsiSamplesPlot.ts')\n\n\t\tcase 'WSIViewer':\n\t\t\treturn await import('./wsiviewer/WSIViewer.ts')\n\n\t\tdefault:\n\t\t\t// temporary option to force an error, to bypass the default filename matching\n\t\t\tif (notFoundMessage) throw notFoundMessage\n\n\t\t\t// TODO: should always throw here once all chart types are handled separately as cases;\n\t\t\t// the pattern matching below is problematic because:\n\t\t\t// - it matches non-plot code file names\n\t\t\t// - it assumes a non-typescript, .js file extension\n\t\t\t// - it doesn't handle plot code that are organized under its own subdirectory\n\t\t\treturn await import(`../plots/${chartType}.js`)\n\t}\n}\n"],
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+  "names": []
+}

package/dist/cohort-R743ZSCR.js

@@ -0,0 +1,75 @@
+import {
+  appInit,
+  vocabInit
+} from "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import {
+  TermTypes
+} from "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// termdb/handlers/cohort.ts
+var SearchHandler = class {
+  init(opts) {
+    this.callback = opts.callback;
+    this.app = opts.app;
+    const holder = opts.holder.append("div").style("padding", "10px 0px");
+    const cohorts = this.app.vocabApi.app?.opts?.opts?.cohorts0;
+    if (!cohorts?.length) return;
+    const terms = cohorts.map((cohort) => {
+      const term = {
+        id: cohort.id,
+        name: cohort.name,
+        type: TermTypes.COHORT,
+        filter0: cohort.filter,
+        isleaf: true,
+        parent_id: null
+      };
+      return term;
+    });
+    const vocabApi = vocabInit({ vocab: { terms } });
+    appInit({
+      holder,
+      vocabApi,
+      state: {
+        nav: { header_mode: "hide_search" }
+      },
+      tree: {
+        click_term: (term) => {
+          this.callback(term);
+        }
+      }
+    });
+  }
+};
+export {
+  SearchHandler
+};
+//# sourceMappingURL=cohort-R743ZSCR.js.map

package/dist/condition-MPZIRRGP.js

@@ -0,0 +1,332 @@
+import {
+  getPillNameDefault,
+  make_radios,
+  sayerror,
+  set_hiddenvalues,
+  throwMsgWithFilePathAndFnName
+} from "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import {
+  copyMerge
+} from "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+
+// termsetting/handlers/condition.ts
+var cutoffGrades = [1, 2, 3, 4, 5];
+function getHandler(self) {
+  return {
+    getPillName(d) {
+      return getPillNameDefault(self, d);
+    },
+    getPillStatus() {
+      return getPillStatus(self);
+    },
+    showEditMenu(div) {
+      if (self.q.mode == "discrete") {
+        return showMenu_discrete(self, div);
+      }
+      if (self.q.mode == "binary" || self.q.mode == "cuminc" || self.q.mode == "cox") {
+        return showMenu_cutoff(self, div);
+      }
+      console.error("invalid q.mode:", self.q.mode);
+      throw "invalid q.mode";
+    }
+    // async postMain() {
+    // 	const body = self.opts.getBodyParams?.() || {} //make sure term1_q is added
+    // 	const data = await self.vocabApi.getCategories(self.term, self.filter!, body)
+    // 	//not really sure this is necessary but it's consistent across other handlers
+    // 	self.category2samplecount = []
+    // 	for (const d of data.lst) {
+    // 		self.category2samplecount.push({
+    // 			key: d.key,
+    // 			label: d.label,
+    // 			count: d.samplecount
+    // 		})
+    // 		// }
+    // 	}
+    // }
+  };
+}
+function getPillStatus(self) {
+  const text = self.q?.name || self.q?.reuseId;
+  if (text) return { text };
+  if (self.q.mode == "discrete") {
+    if (self.q.breaks?.length) {
+      return { text: self.q.breaks.length + 1 + " groups" };
+    } else {
+      if (self.q.bar_by_grade) {
+        if (self.q.value_by_max_grade) return { text: "Max. Grade" };
+        if (self.q.value_by_most_recent) return { text: "Most Recent Grade" };
+        if (self.q.value_by_computable_grade) return { text: "Any Grade" };
+        return { text: "Error: unknown grade setting", bgcolor: "red" };
+      }
+      if (self.q.bar_by_children) return { text: "Sub-condition" };
+    }
+  }
+  if (self.q.mode == "binary") {
+    return {
+      text: self.usecase?.target == "regression" ? self.data.q.groups.find((x) => x.name != self.data.refGrp).name : "binary"
+    };
+  }
+  if (self.q.mode == "cuminc" || self.q.mode == "cox") {
+    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
+    return { text: `Grades ${self.q.breaks[0]}-5` };
+  }
+  return {};
+}
+async function showMenu_discrete(self, div) {
+  const value_type_div = div.append("div").style("margin", "10px 0px 10px 5px").style("border-left", "solid 1px #ededed");
+  value_type_div.append("div").style("display", "inline-block").style("margin", "0px 0px 5px 5px").style("color", "rgb(136, 136, 136)").text("Grade type:");
+  const value_type_select = value_type_div.append("select").style("display", "inline").style("margin", "0px 10px").on("change", () => {
+    const i = value_type_select.property("selectedIndex");
+    self.q.bar_by_grade = i != 3;
+    self.q.bar_by_children = i == 3;
+    self.q.value_by_max_grade = i == 0;
+    self.q.value_by_most_recent = i == 1;
+    self.q.value_by_computable_grade = i == 2 || i == 3;
+    self.dom.tip.hide();
+    self.api.runCallback();
+  });
+  value_type_select.append("option").text("Max grade per patient");
+  value_type_select.append("option").text("Most recent grade per patient");
+  value_type_select.append("option").text("Any grade per patient");
+  if (self.term.subconditions) {
+    value_type_select.append("option").text("Sub-conditions");
+  }
+  value_type_select.property(
+    "selectedIndex",
+    self.q.bar_by_children ? 3 : self.q.value_by_computable_grade ? 2 : self.q.value_by_most_recent ? 1 : 0
+  );
+  if (self.q.bar_by_children) {
+    return;
+  }
+  const breaksSelectorDiv = div.append("div").style("margin", "20px 0px 10px 5px").style("border-left", "solid 1px #ededed");
+  breaksSelectorDiv.append("div").text("Divide grades into groups (optional):").style("margin", "0px 0px 10px 5px").style("color", "rgb(136, 136, 136)");
+  const holder = breaksSelectorDiv.append("div").style("display", "flex").style("align-items", "start").style("margin-left", "10px").style("width", "100%");
+  const gradeValuesDiv = holder.append("div").style("margin-right", "20px");
+  const rangeNameDiv = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center").style("margin-right", "5px");
+  gradeValuesDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Cutoff grades");
+  const textarea = gradeValuesDiv.append("textarea").style("width", "100px").style("height", "70px").on("keyup", textarea2gradeUI);
+  gradeValuesDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
+  if (self.q.breaks?.length) {
+    textarea.property("value", self.q.breaks.join("\n"));
+  }
+  textarea2gradeUI();
+  function textarea2gradeUI() {
+    rangeNameDiv.selectAll("*").remove();
+    const breaks = textarea2breaks();
+    if (!breaks.length) {
+      delete self.q.breaks;
+      delete self.q.groups;
+      return;
+    }
+    if (!self.term.values) throwMsgWithFilePathAndFnName(`Missing term values`);
+    const grades = Object.keys(self.term.values).filter((g) => !self.term.values?.[g].uncomputable).map(Number).sort((a, b) => a - b);
+    const groups = getGroups(grades, breaks);
+    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
+    rangeNameDiv.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Label");
+    for (const [i, g] of groups.entries()) {
+      rangeNameDiv.append("div").text(g.name.replace(/Grades* /, ""));
+      rangeNameDiv.append("div").append("input").attr("type", "text").property("value", g.name).style("margin", "2px 0px").on("change", function() {
+        groups[i].name = this.value;
+      });
+    }
+    self.q.breaks = breaks;
+    self.q.groups = groups;
+  }
+  function textarea2breaks() {
+    const str = textarea.property("value").trim();
+    if (!str) return [];
+    const lst = [...new Set(str.split("\n"))];
+    const breaks = [];
+    for (const x of lst) {
+      const b = Number(x);
+      if (!Number.isInteger(b)) {
+        sayerror(div, "cutoff grade must be an integer value");
+        return [];
+      }
+      if (b < 1 || b > 5) {
+        sayerror(div, `cutoff grade must be within grades 1-5`);
+        return [];
+      }
+      breaks.push(b);
+    }
+    if (!breaks.length) return [];
+    return breaks.sort((i, j) => i - j);
+  }
+  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
+    event.target.disabled = true;
+    event.target.innerHTML = "Loading...";
+    self.api.runCallback();
+  });
+}
+function showMenu_cutoff(self, div) {
+  const holder = div.append("div").style("margin", "10px").style("display", "grid").style("grid-template-columns", "auto auto").style("gap", "20px");
+  holder.append("div").text("Grade cutoff").style("opacity", 0.4);
+  const sd = holder.append("div");
+  const gradeSelect = sd.append("select").on("change", changeGradeSelect);
+  for (const i of cutoffGrades) {
+    gradeSelect.append("option").text(self.term.values?.[i].label);
+  }
+  gradeSelect.property("selectedIndex", self.q.breaks[0] - 1);
+  holder.append("div").text(self.q.mode == "binary" ? "Group 1" : "Censored").style("opacity", 0.4);
+  const g1n = holder.append("div").style("opacity", 0.4);
+  holder.append("div").text(self.q.mode == "binary" ? "Group 2" : "Event").style("opacity", 0.4);
+  const g2n = holder.append("div").style("opacity", 0.4);
+  changeGradeSelect();
+  function changeGradeSelect() {
+    const grade = gradeSelect.property("selectedIndex") + 1;
+    g1n.selectAll("*").remove();
+    g2n.selectAll("*").remove();
+    const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
+    for (const i of grades) {
+      if (i < grade) {
+        g1n.append("div").text(self.term.values?.[i].label);
+      } else {
+        g2n.append("div").text(self.term.values?.[i].label);
+      }
+    }
+  }
+  const timeUnit = self.vocabApi.termdbConfig.timeUnit;
+  let timeScaleChoice;
+  if (self.q.mode == "cox") {
+    timeScaleChoice = self.q.timeScale;
+    holder.append("div").text("Time axis").style("opacity", 0.4);
+    const options = [
+      {
+        label: timeUnit.charAt(0).toUpperCase() + timeUnit.slice(1),
+        value: "time"
+      },
+      { label: "Age", value: "age" }
+    ];
+    if (self.q.timeScale == "age") {
+      options[1].checked = true;
+    } else {
+      options[0].checked = true;
+    }
+    make_radios({
+      holder: holder.append("div"),
+      options,
+      styles: { padding: "" },
+      callback: (v) => timeScaleChoice = v
+    });
+  }
+  div.append("button").text("Apply").style("margin", "10px").on("click", (event) => {
+    if (!self.q.breaks || self.q.breaks.length == 0) throwMsgWithFilePathAndFnName("Missing q.breaks");
+    const grade = gradeSelect.property("selectedIndex") + 1;
+    self.q.breaks[0] = grade;
+    if (self.q.mode == "binary") {
+      const grades = Object.keys(self.term.values).map(Number).sort((a, b) => a - b);
+      self.q.groups = getGroups(grades, self.q.breaks);
+      self.refGrp = self.q.groups[0].name;
+    }
+    if (self.q.mode == "cox") self.q.timeScale = timeScaleChoice;
+    event.target.disabled = true;
+    event.target.innerHTML = "Loading...";
+    self.api.runCallback();
+  });
+}
+function getGroups(grades, breaks) {
+  grades.sort((a, b2) => a - b2);
+  const groups = [];
+  let group = { values: [] };
+  let b;
+  for (const g of grades) {
+    if (breaks.includes(g)) {
+      b = g;
+      const max = Math.max(...group.values);
+      if (!groups.length) {
+        if (group.values.length == 1) {
+          if (group.values[0] !== 0) throw "unexpected group value";
+          group.name = "Grade 0";
+        } else {
+          if (group.values.length == 2 && group.values.includes(-1) && group.values.includes(0)) {
+            group.name = "Not tested/Grade 0";
+          } else {
+            group.name = group.values.includes(-1) ? `Not tested/Grade 0 - Grade ${max}` : `Grades 0-${max}`;
+          }
+        }
+      } else {
+        group.name = group.values.length == 1 ? `Grade ${group.values[0]}` : `${group.name}-${max}`;
+      }
+      groups.push(group);
+      group = {
+        name: `Grade ${b}`,
+        values: [g]
+      };
+    } else {
+      group.values.push(g);
+    }
+  }
+  group.name = `Grades ${b}-5`;
+  groups.push(group);
+  return groups;
+}
+function fillTW(tw, vocabApi, defaultQ) {
+  set_hiddenvalues(tw.q, tw.term);
+  if (defaultQ) {
+    copyMerge(tw.q, defaultQ);
+  }
+  if (!Object.keys(tw.q).includes("mode")) tw.q.mode = "discrete";
+  if (!tw.q.valueFor) {
+    const q = tw.q;
+    if (!q.bar_by_grade && !q.bar_by_children) q.bar_by_grade = true;
+    tw.q.valueFor = tw.q.bar_by_children ? "children" : "grade";
+  }
+  if (tw.q.valueFor == "grade") {
+    if (tw.q.value_by_max_grade || tw.q.value_by_most_recent || tw.q.value_by_computable_grade) {
+    } else {
+      tw.q.value_by_max_grade = true;
+    }
+  }
+  if (tw.q.mode == "binary" || tw.q.mode == "cox" || tw.q.mode == "cuminc") {
+    const defaultBreak = tw.q.mode == "binary" ? 1 : 3;
+    if (!tw.q.breaks?.length) tw.q.breaks = [defaultBreak];
+    if (tw.q.breaks.length != 1 || ![1, 2, 3, 4, 5].includes(tw.q.breaks[0])) throw "invalid tw.q.breaks";
+  }
+  if (tw.q.valueFor == "grade") {
+    if (tw.q.breaks?.length) {
+      if (!tw.term.values) throw "missing term.values";
+      if (tw.q.mode == "discrete" || tw.q.mode == "binary") {
+        const grades = Object.keys(tw.term.values).filter((g) => tw.q.mode == "discrete" ? !tw.term.values?.[g].uncomputable : g).map(Number).sort((a, b) => a - b);
+        tw.q.groups = getGroups(grades, tw.q.breaks);
+      }
+    }
+    if (tw.q.mode == "cox") {
+      if (!tw.q.timeScale) tw.q.timeScale = "time";
+      if (!["age", "time"].includes(tw.q.timeScale)) throw "invalid q.timeScale";
+    }
+  }
+}
+export {
+  fillTW,
+  getHandler
+};
+//# sourceMappingURL=condition-MPZIRRGP.js.map

package/dist/controls-WD5TZITZ.js

@@ -0,0 +1,39 @@
+import {
+  controlsInit,
+  renderTerm1Label
+} from "./chunk-73PFJ2VF.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-XFAL46LZ.js";
+import "./chunk-ZZMIDYRE.js";
+import "./chunk-HYOEWQ5P.js";
+import "./chunk-6QCYT6G2.js";
+import "./chunk-FN5XPUPH.js";
+import "./chunk-VSSZJHOR.js";
+import "./chunk-5RUVBYLK.js";
+import "./chunk-ZFJUVP2N.js";
+import "./chunk-R3ARQMM4.js";
+import "./chunk-X4QQRHFB.js";
+import "./chunk-4WF3XDQP.js";
+import "./chunk-X6VTVZY7.js";
+import "./chunk-H6INPPUC.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-L44P5N4U.js";
+import "./chunk-GEQUQ3GG.js";
+import "./chunk-WPHUM5S5.js";
+import "./chunk-75T7ESEO.js";
+import "./chunk-2KXLYFAO.js";
+import "./chunk-LOZEKOES.js";
+import "./chunk-VQZ2Z5YU.js";
+import "./chunk-UJELJXJG.js";
+import "./chunk-FXQXCOII.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-DQC5FFGV.js";
+import "./chunk-HFNDKYVF.js";
+export {
+  controlsInit,
+  renderTerm1Label
+};
+//# sourceMappingURL=controls-WD5TZITZ.js.map