@sjcrh/proteinpaint-client 2.191.3 → 2.191.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/2dmaf-Z3D2M3FB.js +1373 -0
- package/dist/AIProjectAdmin-2OQOQXH4.js +956 -0
- package/dist/AppHeader-PXLGVCVS.js +835 -0
- package/dist/BoxPlot-PUZKHACO.js +1211 -0
- package/dist/CorrelationVolcano-RO6CFLZA.js +619 -0
- package/dist/DE-CCA5SBJG.js +95 -0
- package/dist/DEinput-MRUQW6X6.js +301 -0
- package/dist/DifferentialAnalysis-5YQQLJKR.js +245 -0
- package/dist/Disco-4FTOJBLG.js +3237 -0
- package/dist/Disco.UI-IWVSK3RN.js +245 -0
- package/dist/DmrPlot-FPJJHTM5.js +642 -0
- package/dist/GB-H6JETPRC.js +1130 -0
- package/dist/GeneExpInput-Q42COANS.js +366 -0
- package/dist/HicApp-BBD2YOMT.js +2250 -0
- package/dist/NumBinaryEditor-WMSF7HIO.js +271 -0
- package/dist/NumBinaryEditor.unit.spec-QQATLHF7.js +286 -0
- package/dist/NumContEditor-4CSTHVRX.js +109 -0
- package/dist/NumContEditor.unit.spec-2YF3OS3A.js +169 -0
- package/dist/NumCustomBinEditor-KFAYUWYV.js +38 -0
- package/dist/NumCustomBinEditor.unit.spec-YHAUSGPN.js +284 -0
- package/dist/NumDiscreteEditor-F46H5CME.js +179 -0
- package/dist/NumDiscreteEditor.unit.spec-5BIAWAVN.js +202 -0
- package/dist/NumRegularBinEditor-G7KOA7NR.js +38 -0
- package/dist/NumRegularBinEditor.unit.spec-Y6CBCWLN.js +227 -0
- package/dist/NumSplineEditor-JP2V2L4Y.js +198 -0
- package/dist/NumSplineEditor.unit.spec-N34QBZN3.js +199 -0
- package/dist/NumericDensity-JOPHLURB.js +38 -0
- package/dist/NumericDensity.unit.spec-N45PCLOT.js +221 -0
- package/dist/NumericHandler-SIM4E2Z5.js +39 -0
- package/dist/NumericHandler.unit.spec-NKLYDVTG.js +219 -0
- package/dist/ProteomeInput-5KMNE3PZ.js +396 -0
- package/dist/RunChart2-N7AZVQXJ.js +758 -0
- package/dist/SC-M6RGALZM.js +936 -0
- package/dist/Volcano-YH4RJTT5.js +1379 -0
- package/dist/WSIViewer-7LOVM3AU.js +48508 -0
- package/dist/WsiSamplesPlot-QPPB7OOD.js +165 -0
- package/dist/adSandbox-R2QP74P7.js +38 -0
- package/dist/app-AIIN4WDE.js +37 -0
- package/dist/app-FJT5VXMF.js +49 -0
- package/dist/app.js +15 -15
- package/dist/bam-QBO22VQB.js +860 -0
- package/dist/barchart-VDOP6FQU.js +47 -0
- package/dist/barchart.data-Z2E72EET.js +22 -0
- package/dist/barchart.events-NUYQBI5S.js +47 -0
- package/dist/barchart.integration.spec-COVZPXMH.js +1980 -0
- package/dist/barchart2-KMSU4ROO.js +311 -0
- package/dist/block-TTN2IQAH.js +6202 -0
- package/dist/block.init-RRHHCNSR.js +38 -0
- package/dist/block.mds.expressionrank-7NWBRUII.js +359 -0
- package/dist/block.mds.geneboxplot-4BAJJWCC.js +828 -0
- package/dist/block.mds.junction-XRUIHAF5.js +1545 -0
- package/dist/block.mds.svcnv-YZ7PL733.js +6801 -0
- package/dist/block.svg-FUMP2J7A.js +164 -0
- package/dist/block.tk.aicheck-AIZEND45.js +283 -0
- package/dist/block.tk.ase-H26PKO5U.js +365 -0
- package/dist/block.tk.bam-XNZFHSDQ.js +1906 -0
- package/dist/block.tk.bedgraphdot-QTDBLBO2.js +384 -0
- package/dist/block.tk.bigwig.ui-OSRCPTQC.js +212 -0
- package/dist/block.tk.hicstraw-7GH6LVIH.js +823 -0
- package/dist/block.tk.junction-AJYML4AW.js +2364 -0
- package/dist/block.tk.junction.textmatrixui-4RIH3EZI.js +199 -0
- package/dist/block.tk.ld-AJYQ4C6T.js +99 -0
- package/dist/block.tk.menu-57OP5UW5.js +1029 -0
- package/dist/block.tk.pgv-XO7HP5MM.js +944 -0
- package/dist/brainImaging-65QDNR4D.js +423 -0
- package/dist/chunk-2XCUERHJ.js +102 -0
- package/dist/chunk-322QC6R4.js +222 -0
- package/dist/chunk-35SCELN4.js +217 -0
- package/dist/chunk-36EHIPV4.js +514 -0
- package/dist/chunk-3SZ6GKLB.js +14 -0
- package/dist/chunk-3ZLJDFJU.js +368 -0
- package/dist/chunk-4DXZGZOB.js +54 -0
- package/dist/chunk-4UWS5Y3N.js +1438 -0
- package/dist/chunk-4UWS5Y3N.js.map +7 -0
- package/dist/chunk-54EMVNPW.js +102 -0
- package/dist/chunk-57RBC6IZ.js +302 -0
- package/dist/chunk-5OUTR67M.js +37 -0
- package/dist/chunk-67DBIM6H.js +293 -0
- package/dist/chunk-6A3IPDE2.js +1943 -0
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- package/dist/chunk-7EMWHCVW.js +1825 -0
- package/dist/chunk-7EMWHCVW.js.map +7 -0
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- package/dist/chunk-QNETLNPB.js.map +7 -0
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- package/dist/chunk-R2MMURGK.js +2786 -0
- package/dist/chunk-SA7APTJR.js +20792 -0
- package/dist/chunk-SA7APTJR.js.map +7 -0
- package/dist/chunk-SHWLROJG.js +283 -0
- package/dist/chunk-SKREEF3H.js +184 -0
- package/dist/chunk-UGVNZMLU.js +4274 -0
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- package/dist/chunk-UJKW42DI.js +6364 -0
- package/dist/chunk-ULPMYS5B.js +100 -0
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- package/dist/chunk-VGJSASRT.js +446 -0
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- package/dist/chunk-ZTYNN6G5.js +2327 -0
- package/dist/chunk-ZXTHADSC.js +158 -0
- package/dist/condition-HDVYPJJD.js +332 -0
- package/dist/controls-YEEW46C6.js +41 -0
- package/dist/controls.config-C535H5DL.js +39 -0
- package/dist/correlation-AOSSSSL3.js +99 -0
- package/dist/cuminc-II7NFIFP.js +1149 -0
- package/dist/cuminc.integration.spec-B4N6OMBJ.js +678 -0
- package/dist/customdata.inputui-AI4ZBIEP.js +289 -0
- package/dist/dataDownload-ZQYLXN6D.js +330 -0
- package/dist/dataDownload.integration.spec-2PKYZ2AY.js +193 -0
- package/dist/databrowser.ui-WGD7D3XV.js +433 -0
- package/dist/dictionary-RYM4WP2W.js +111 -0
- package/dist/dnaMethylation-WGJMJL5B.js +38 -0
- package/dist/dnaMethylation.integration.spec-DO3PV4MO.js +203 -0
- package/dist/dofetch-RADX3AFU.js +51 -0
- package/dist/e2pca-KOAAU2JX.js +350 -0
- package/dist/ep-CXCATXYH.js +1256 -0
- package/dist/expclust.gdc.spec-UJO2R3CW.js +307 -0
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- package/dist/forms2-ZBT5BZW3.js +534 -0
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- package/dist/geneExpClustering-FUNS6D2P.js +249 -0
- package/dist/geneExpression-2BWWGYL4.js +38 -0
- package/dist/geneExpression-2OPFWV2K.js +313 -0
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- package/dist/geneORA-S3KQMBYL.js +278 -0
- package/dist/geneRanking-UZ36XAL7.js +551 -0
- package/dist/geneVariant-OOZ2SBXO.js +41 -0
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- package/dist/geneset-SNM4M6UM.js +208 -0
- package/dist/genomeBrowser.spec-DJIRW2X7.js +281 -0
- package/dist/grin2-7AOJP5QJ.js +1560 -0
- package/dist/grin2-RKJXYWJ5.js +821 -0
- package/dist/gsea-SPTQJW67.js +47 -0
- package/dist/hierCluster-KDE5SMYP.js +63 -0
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- package/dist/imagePlot-M5JSHEY4.js +163 -0
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- package/dist/isoformExpression-EV27MKYZ.js +40 -0
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- package/dist/launch.adhoc-NOISOX5E.js +42 -0
- package/dist/leftlabel.sample-42AX4KTV.js +260 -0
- package/dist/lollipop-LQCQBTSX.js +171 -0
- package/dist/maf-U237OWZ3.js +452 -0
- package/dist/maftimeline-NLZLMHT2.js +593 -0
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- /package/dist/{spliceevent.a53ss.diagram-CEFGK2LA.js.map → spliceevent.a53ss.diagram-LLJSPV7M.js.map} +0 -0
- /package/dist/{spliceevent.exonskip.diagram-A24TZTQ7.js.map → spliceevent.exonskip.diagram-LAOIOIST.js.map} +0 -0
- /package/dist/{spliceevent.noeventdiagram-USD42ZZB.js.map → spliceevent.noeventdiagram-MVA7Q3HT.js.map} +0 -0
- /package/dist/{ssGSEA-A5X56E7U.js.map → ssGSEA-7T6S3DSE.js.map} +0 -0
- /package/dist/{ssGSEA.unit.spec-6WMGKWNI.js.map → ssGSEA.unit.spec-XJ3W4NWX.js.map} +0 -0
- /package/dist/{summarizeCnvGeneexp-FZJL4Q7O.js.map → summarizeCnvGeneexp-RRP6JUV6.js.map} +0 -0
- /package/dist/{summarizeGeneexpSurvival-LRJZBHRW.js.map → summarizeGeneexpSurvival-AFLHDD6Q.js.map} +0 -0
- /package/dist/{summarizeMutationCnv-L64CVMHI.js.map → summarizeMutationCnv-NABUYHMX.js.map} +0 -0
- /package/dist/{summarizeMutationDiagnosis-S55CKGBO.js.map → summarizeMutationDiagnosis-2LQ7JU3K.js.map} +0 -0
- /package/dist/{summarizeMutationSurvival-AM7BZVDP.js.map → summarizeMutationSurvival-3WBT5TXG.js.map} +0 -0
- /package/dist/{summary-ANZTET2T.js.map → summary-FRDKOFXW.js.map} +0 -0
- /package/dist/{summary.integration.spec-TW3CJTDA.js.map → summary.integration.spec-ZLRIA7G2.js.map} +0 -0
- /package/dist/{summaryInput-3JHKZU62.js.map → summaryInput-4JO6MHP4.js.map} +0 -0
- /package/dist/{sunburst-ABDTE22P.js.map → sunburst-DRCVSC2X.js.map} +0 -0
- /package/dist/{survival-HROP7OR7.js.map → survival-AK75COPY.js.map} +0 -0
- /package/dist/{survival-KZDESA36.js.map → survival-IF5NI3A6.js.map} +0 -0
- /package/dist/{survival.integration.spec-CMZTALBF.js.map → survival.integration.spec-7IWBTPJG.js.map} +0 -0
- /package/dist/{svgraph-TLRXKVWQ.js.map → svgraph-QBDF2SLB.js.map} +0 -0
- /package/dist/{svmr-R4QOXWQW.js.map → svmr-O4GJJUT2.js.map} +0 -0
- /package/dist/{table-QM3RZQ5R.js.map → table-FQAIXKLE.js.map} +0 -0
- /package/dist/{termCollection-WVYJHPIH.js.map → termCollection-GMDDL3L7.js.map} +0 -0
- /package/dist/{termCollection-B2A3MSCD.js.map → termCollection-ZO5PZ7E3.js.map} +0 -0
- /package/dist/{termCollection.unit.spec-TCPEEZHW.js.map → termCollection.unit.spec-5JBCTXHX.js.map} +0 -0
- /package/dist/{tk-DGFFDV7C.js.map → tk-GJX23IV7.js.map} +0 -0
- /package/dist/{tp.ui-BEESUHHF.js.map → tp.ui-T7FVMTGQ.js.map} +0 -0
- /package/dist/{tvs.dt-UZW3L4MO.js.map → tvs.dt-X7L7NSU6.js.map} +0 -0
- /package/dist/{tvs.dtcnv.categorical-OH5NXCDN.js.map → tvs.dtcnv.categorical-73G2V6CH.js.map} +0 -0
- /package/dist/{tvs.dtcnv.continuous-VWWTWAX2.js.map → tvs.dtcnv.continuous-DWFJL3X7.js.map} +0 -0
- /package/dist/{tvs.dtfusion-YKYYCDJN.js.map → tvs.dtfusion-HQADHCSV.js.map} +0 -0
- /package/dist/{tvs.dtsnvindel-Y3WAHLKK.js.map → tvs.dtsnvindel-PY5OBMGW.js.map} +0 -0
- /package/dist/{tvs.dtsv-UFLR2XRY.js.map → tvs.dtsv-OTBEEWSW.js.map} +0 -0
- /package/dist/{tvs.samplelst-BPWZHD62.js.map → tvs.samplelst-LCXSU5MG.js.map} +0 -0
- /package/dist/{tvs.termCollection-JLA3JQFX.js.map → tvs.termCollection-L527XN4X.js.map} +0 -0
- /package/dist/{violin-TFNQIETS.js.map → violin-6VKRUQV3.js.map} +0 -0
- /package/dist/{violin.integration.spec-XKNZQVN7.js.map → violin.integration.spec-RJATDLQH.js.map} +0 -0
- /package/dist/{violin.interactivity-R2EYNWI6.js.map → violin.interactivity-SKF5H7MN.js.map} +0 -0
- /package/dist/{violin.renderer-5WA4YLGB.js.map → violin.renderer-GB4TPX3B.js.map} +0 -0
- /package/dist/{vocabulary-D2XUEKI6.js.map → vocabulary-D3W44IWE.js.map} +0 -0
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import {
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DownloadMenu,
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PlotBase,
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controlsInit,
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fillTermWrapper,
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fillTwLst,
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getCategoricalTermFilter,
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getCombinedTermFilter
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} from "./chunk-SA7APTJR.js";
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import {
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importPlot
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} from "./chunk-SKREEF3H.js";
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import {
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Menu
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} from "./chunk-HYOEWQ5P.js";
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import {
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icons
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} from "./chunk-IIT367QZ.js";
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import {
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select_default
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} from "./chunk-I6Y4O3RR.js";
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// plots/profile/profilePlot.ts
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var orderedIncomes = ["Low income", "Lower middle income", "Upper middle income", "High income"];
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var orderedVolumes = [
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"Small (1-25 annual newly diagnoses)",
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"Medium (26-80 annual newly diagnoses)",
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"Large (81-120 annual newly diagnoses)",
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"Very large (>120 annual newly diagnoses)"
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];
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var ABBREV_COHORT = 0;
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var FULL_COHORT = 1;
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var profilePlot = class extends PlotBase {
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constructor(opts, type) {
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super(opts);
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this.type = type;
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this.downloadCount = 0;
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this.tip = new Menu({ padding: "4px", offsetX: 10, offsetY: 15 });
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this.scoreTerms = [];
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this.scScoreTerms = [];
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this.isRadarFacility = false;
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this.components = { plots: {} };
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}
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//extracts the relevant state from the appState: config, termfilter, vocab, login info
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getState(appState) {
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const config = appState.plots.find((p) => p.id === this.id);
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if (!config) throw `No plot with id='${this.id}' found`;
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const { logged, sites, user } = getProfileLogin(this.app, appState.activeCohort);
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const site = sites?.[0];
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return {
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config,
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termfilter: appState.termfilter,
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dslabel: appState.vocab.dslabel,
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termdbConfig: appState.termdbConfig,
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vocab: appState.vocab,
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logged,
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//later change to read login info
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site,
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sites,
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user,
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activeCohort: appState.activeCohort,
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//Find plots where I am a parent. Here the child is a second plot for comparison
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plots: appState.plots.filter((p) => p.parentId === this.id)
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//this property is needed to indicate that child plots need to be added to the appState plots
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};
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}
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//refers to the view where all the filters are shown and not the preselected site
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isAggregate() {
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if (!this.state.logged) return true;
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if (this.settings.isAggregate) return true;
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if (this.state.sites?.length > 1 || this.state.user == "admin" || this.isRadarFacility) return true;
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return false;
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}
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//initializes the plot elements
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async init(appState) {
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const config = appState.plots.find((p) => p.id === this.id);
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const state = this.getState(appState);
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if (this.opts.header) {
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let chartName = config.chartType.match(/[A-Z][a-z]+/g);
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chartName = chartName.join(" ");
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chartName = config.headerTitle ? config.headerTitle + ` / ${state.user}` : chartName + ` / ${state.user}`;
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this.opts.header.style("text-transform", "capitalize").text(chartName);
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}
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const div = this.opts.holder.append("div").style("display", "inline-block");
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const leftDiv = div.append("div").style("display", "inline-block").style("vertical-align", "top");
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const rightDiv = div.append("div").style("display", "inline-block").style("vertical-align", "top");
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const controlsDiv = leftDiv.append("div").style("display", "inline-block").style("font-size", "0.9em");
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const iconsDiv = leftDiv.append("div").style("margin-top", "10px").style("padding-left", "12px");
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const holder = rightDiv.insert("div").style("display", "inline-block");
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const plotDiv = holder.append("div");
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this.dom = {
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controlsDiv,
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holder,
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iconsDiv,
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rightDiv,
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plotDiv
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};
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select_default(".sjpp-output-sandbox-content").on("scroll", (event) => {
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if (this.onMouseOut) this.onMouseOut(event);
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});
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this.dom.rightDiv.on("mousemove", (event) => this.onMouseOver(event));
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this.dom.rightDiv.on("mouseleave", (event) => this.onMouseOut(event));
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this.dom.rightDiv.on("mouseout", (event) => this.onMouseOut(event));
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document.addEventListener("scroll", () => this?.tip?.hide());
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const restartDiv = iconsDiv.append("div").style("padding-bottom", "8px");
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icons["restart"](restartDiv, {
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title: "Clear filters",
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handler: async () => {
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this.clearFiltersExcept([]);
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this.app.dispatch({
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type: "plot_edit",
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id: this.id,
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config: { filter: this.getFilter(), settings: { [this.type]: this.settings } }
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});
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}
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});
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if (!config.parentId) {
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const iconDiv = iconsDiv.append("div").style("fill", "#aaa").style("padding", "2px");
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icons["add"](iconDiv, {
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title: "Open another plot for comparison",
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handler: () => {
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const show = !this.isComparison;
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const icon = iconDiv.select("svg");
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icon.style("fill", show ? "orange" : "black");
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if (this.isComparison) {
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const id = this.state.plots.find((p) => p.parentId === this.id)?.id;
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this.app.dispatch({
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type: "plot_delete",
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id,
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parentId: this.id
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});
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return;
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}
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this.legendG.selectAll("*").remove();
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const config2 = structuredClone(this.config);
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config2.parentId = this.id;
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this.app.dispatch({
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type: "plot_create",
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config: config2
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});
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}
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});
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}
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}
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//tooltip handler to hide the tooltip when mouse leaves the plot area
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onMouseOut(_event) {
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this.tip.hide();
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}
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async main() {
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this.config = JSON.parse(JSON.stringify(this.state.config));
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this.settings = this.config.settings[this.type];
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this.dom.plotDiv.selectAll("*").remove();
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this.isComparison = this.config.parentId || this.state.plots.length > 0;
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for (const config of this.state.plots) {
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const plot = structuredClone(config);
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if (this.components.plots[plot.id]) continue;
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const holder = this.opts.holder.append("div").style("display", "inline-block").style("padding", "5px");
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plot.holder = holder.append("div");
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plot.app = this.app;
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const { componentInit } = await importPlot(plot.chartType);
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this.components.plots[plot.id] = await componentInit(plot);
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}
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for (const plotId in this.components.plots) {
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if (!this.state.plots.find((p) => p.id === plotId)) {
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this.components.plots[plotId].destroy();
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delete this.components.plots[plotId];
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}
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}
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}
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async setControls(additionalInputs = []) {
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try {
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const isRadarFacility = this.isRadarFacility;
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const filters = {};
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for (const tw of this.config.filterTWs) {
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filters[tw.term.id] = getCategoricalTermFilter(this.config.filterTWs, this.settings, tw);
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}
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this.filteredTermValues = await this.app.vocabApi.filterTermValues({
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terms: this.config.filterTWs,
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filter: this.state.termfilter.filter,
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filters,
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facilityTW: this.config.facilityTW,
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// safe to pass because the backend code will still compare terms[] with the the dataset's hiddenTermIds,
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// it only affects what will be included in the aggregation and does not disable user access authentication
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filterByUserSites: this.settings.filterByUserSites,
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showAll: true
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});
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const regions = this.filteredTermValues[this.config.regionTW.id];
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const sjgRegions = this.filteredTermValues[this.config.sjgRegionTW.id];
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const countries = this.filteredTermValues[this.config.countryTW.id];
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const incomes = this.filteredTermValues[this.config.incomeTW.id];
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const teachingStates = this.filteredTermValues[this.config.teachingStatusTW.id];
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const referralStates = this.filteredTermValues[this.config.referralStatusTW.id];
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const fundingSources = this.filteredTermValues[this.config.fundingSourceTW.id];
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const hospitalVolumes = this.filteredTermValues[this.config.hospitalVolumeTW.id];
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const yearsOfImplementation = this.filteredTermValues[this.config.yearOfImplementationTW.id];
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incomes.sort((elem1, elem2) => {
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const i1 = orderedIncomes.indexOf(elem1.value);
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const i2 = orderedIncomes.indexOf(elem2.value);
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if (i1 < i2) return -1;
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return 1;
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});
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hospitalVolumes.sort((elem1, elem2) => {
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const i1 = orderedVolumes.indexOf(elem1.value);
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const i2 = orderedVolumes.indexOf(elem2.value);
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if (i1 < i2) return -1;
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return 1;
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});
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const types = this.filteredTermValues[this.config.typeTW.id];
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const isAggregate = this.isAggregate();
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if (!this.settings[this.config.facilityTW?.term?.id] && this.state.sites?.length == 1 && !isAggregate) {
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this.settings[this.config.facilityTW?.term?.id] = [this.state.sites[0]];
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}
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this.filter = this.config.filter || this.getFilter();
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if (this.type == "profileForms")
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this.data = await this.app.vocabApi.getProfileFormScores({
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scoreTerms: this.scoreTerms,
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scScoreTerms: this.scScoreTerms,
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filter: this.filter,
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facilityTW: this.config.facilityTW,
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filterByUserSites: this.settings.filterByUserSites
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});
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else if (this.type == "profileRadarFacility2")
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this.data = await this.fetchRadarFacility2Scores();
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if ((this.type == "profileForms" || this.type == "profileRadarFacility2") && this.data && "error" in this.data)
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throw this.data.error;
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this.sites = this.filteredTermValues[this.config.facilityTW.id]?.filter((s) => !s.disabled && s.value);
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if (this.settings[this.config.facilityTW?.term?.id])
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+
for (const site of this.settings[this.config.facilityTW?.term?.id]) {
|
|
229
|
+
const siteOption = this.sites.find((s) => s.value == site);
|
|
230
|
+
if (siteOption) siteOption.selected = true;
|
|
231
|
+
}
|
|
232
|
+
const chartType = this.type;
|
|
233
|
+
this.dom.controlsDiv.selectAll("*").remove();
|
|
234
|
+
const inputs = [];
|
|
235
|
+
const userSitesFilterInput = {
|
|
236
|
+
label: "Use accessible sites only",
|
|
237
|
+
boxLabel: "",
|
|
238
|
+
type: "checkbox",
|
|
239
|
+
chartType,
|
|
240
|
+
settingsKey: "filterByUserSites"
|
|
241
|
+
};
|
|
242
|
+
if (this.state.sites?.length == 1 && !isRadarFacility) {
|
|
243
|
+
const dataInput = {
|
|
244
|
+
label: "Data",
|
|
245
|
+
type: "radio",
|
|
246
|
+
chartType,
|
|
247
|
+
settingsKey: "isAggregate",
|
|
248
|
+
styles: { display: "inline-block" },
|
|
249
|
+
options: [
|
|
250
|
+
{ label: this.state.site, value: false },
|
|
251
|
+
{ label: "Aggregate", value: true }
|
|
252
|
+
],
|
|
253
|
+
callback: (isAggregate2) => {
|
|
254
|
+
this.settings.isAggregate = isAggregate2;
|
|
255
|
+
const id = this.sites.find((s) => s.value == this.state.site)?.value;
|
|
256
|
+
const value = isAggregate2 ? [] : [id];
|
|
257
|
+
this.setFilterValue(this.config.facilityTW.term.id, value);
|
|
258
|
+
}
|
|
259
|
+
};
|
|
260
|
+
inputs.push(dataInput);
|
|
261
|
+
}
|
|
262
|
+
if (isAggregate || isRadarFacility) {
|
|
263
|
+
inputs.push(
|
|
264
|
+
...[
|
|
265
|
+
{
|
|
266
|
+
label: "WHO Region",
|
|
267
|
+
type: "dropdown",
|
|
268
|
+
chartType,
|
|
269
|
+
settingsKey: this.config.regionTW.term.id,
|
|
270
|
+
options: regions,
|
|
271
|
+
callback: (value) => this.setFilterValue(this.config.regionTW.term.id, value)
|
|
272
|
+
},
|
|
273
|
+
{
|
|
274
|
+
label: "SJG Region",
|
|
275
|
+
type: "dropdown",
|
|
276
|
+
chartType,
|
|
277
|
+
settingsKey: this.config.sjgRegionTW.term.id,
|
|
278
|
+
options: sjgRegions,
|
|
279
|
+
callback: (value) => this.setFilterValue(this.config.sjgRegionTW.term.id, value)
|
|
280
|
+
},
|
|
281
|
+
{
|
|
282
|
+
label: "Country",
|
|
283
|
+
type: "dropdown",
|
|
284
|
+
chartType,
|
|
285
|
+
settingsKey: this.config.countryTW.term.id,
|
|
286
|
+
options: countries,
|
|
287
|
+
callback: (value) => this.setFilterValue(this.config.countryTW.term.id, value)
|
|
288
|
+
},
|
|
289
|
+
{
|
|
290
|
+
label: "Income group",
|
|
291
|
+
type: "dropdown",
|
|
292
|
+
chartType,
|
|
293
|
+
settingsKey: this.config.incomeTW.term.id,
|
|
294
|
+
options: incomes,
|
|
295
|
+
callback: (value) => this.setFilterValue(this.config.incomeTW.term.id, value)
|
|
296
|
+
},
|
|
297
|
+
{
|
|
298
|
+
label: "Facility type",
|
|
299
|
+
type: "dropdown",
|
|
300
|
+
chartType,
|
|
301
|
+
settingsKey: this.config.typeTW.term.id,
|
|
302
|
+
options: types,
|
|
303
|
+
callback: (value) => this.setFilterValue(this.config.typeTW.term.id, value)
|
|
304
|
+
},
|
|
305
|
+
{
|
|
306
|
+
label: this.config.teachingStatusTW.term.name,
|
|
307
|
+
type: "dropdown",
|
|
308
|
+
chartType,
|
|
309
|
+
settingsKey: this.config.teachingStatusTW.term.id,
|
|
310
|
+
options: teachingStates,
|
|
311
|
+
callback: (value) => this.setFilterValue(this.config.teachingStatusTW.term.id, value)
|
|
312
|
+
},
|
|
313
|
+
{
|
|
314
|
+
label: this.config.referralStatusTW.term.name,
|
|
315
|
+
type: "dropdown",
|
|
316
|
+
chartType,
|
|
317
|
+
settingsKey: this.config.referralStatusTW.term.id,
|
|
318
|
+
options: referralStates,
|
|
319
|
+
callback: (value) => this.setFilterValue(this.config.referralStatusTW.term.id, value)
|
|
320
|
+
},
|
|
321
|
+
{
|
|
322
|
+
label: this.config.fundingSourceTW.term.name,
|
|
323
|
+
type: "dropdown",
|
|
324
|
+
chartType,
|
|
325
|
+
settingsKey: this.config.fundingSourceTW.term.id,
|
|
326
|
+
options: fundingSources,
|
|
327
|
+
callback: (value) => this.setFilterValue(this.config.fundingSourceTW.term.id, value)
|
|
328
|
+
},
|
|
329
|
+
{
|
|
330
|
+
label: this.config.hospitalVolumeTW.term.name,
|
|
331
|
+
type: "dropdown",
|
|
332
|
+
chartType,
|
|
333
|
+
settingsKey: this.config.hospitalVolumeTW.term.id,
|
|
334
|
+
options: hospitalVolumes,
|
|
335
|
+
callback: (value) => this.setFilterValue(this.config.hospitalVolumeTW.term.id, value)
|
|
336
|
+
},
|
|
337
|
+
{
|
|
338
|
+
label: this.config.yearOfImplementationTW.term.name,
|
|
339
|
+
type: "dropdown",
|
|
340
|
+
chartType,
|
|
341
|
+
settingsKey: this.config.yearOfImplementationTW.term.id,
|
|
342
|
+
options: yearsOfImplementation,
|
|
343
|
+
callback: (value) => this.setFilterValue(this.config.yearOfImplementationTW.term.id, value)
|
|
344
|
+
}
|
|
345
|
+
]
|
|
346
|
+
);
|
|
347
|
+
}
|
|
348
|
+
if (this.state.logged) {
|
|
349
|
+
if (isAggregate && this.sites.length > 1) {
|
|
350
|
+
const sitesInput = {
|
|
351
|
+
label: "Sites",
|
|
352
|
+
type: "dropdown",
|
|
353
|
+
chartType,
|
|
354
|
+
options: this.sites,
|
|
355
|
+
multiple: true,
|
|
356
|
+
callback: (values) => this.setFilterValue(this.config.facilityTW.term.id, values)
|
|
357
|
+
};
|
|
358
|
+
inputs.push(sitesInput);
|
|
359
|
+
if (this.state.user != "admin") inputs.unshift(userSitesFilterInput);
|
|
360
|
+
}
|
|
361
|
+
if (isRadarFacility) {
|
|
362
|
+
if (this.sampleData?.sites?.length) {
|
|
363
|
+
const facilitySites = this.sampleData.sites;
|
|
364
|
+
const facilitySite = this.settings.facilitySite ? facilitySites.find((s) => s.value == this.settings.facilitySite) : facilitySites[0];
|
|
365
|
+
if (!facilitySite)
|
|
366
|
+
throw new Error(`Access to ${this.settings.facilitySite} facility not allowed`);
|
|
367
|
+
facilitySite.selected = true;
|
|
368
|
+
inputs.unshift({
|
|
369
|
+
label: "Facility site",
|
|
370
|
+
type: "dropdown",
|
|
371
|
+
chartType,
|
|
372
|
+
options: facilitySites,
|
|
373
|
+
callback: (value) => {
|
|
374
|
+
this.setFacilitySite(value);
|
|
375
|
+
}
|
|
376
|
+
});
|
|
377
|
+
}
|
|
378
|
+
}
|
|
379
|
+
}
|
|
380
|
+
inputs.unshift(...additionalInputs);
|
|
381
|
+
this.components.controls = await controlsInit({
|
|
382
|
+
app: this.app,
|
|
383
|
+
id: this.id,
|
|
384
|
+
holder: this.dom.controlsDiv,
|
|
385
|
+
inputs,
|
|
386
|
+
title: "Filters"
|
|
387
|
+
});
|
|
388
|
+
this.components.controls.on(`downloadClick.${chartType}`, (event) => this.download(event));
|
|
389
|
+
this.components.controls.on(`helpClick.${chartType}`, () => {
|
|
390
|
+
const activeCohort = this.state.activeCohort;
|
|
391
|
+
let link;
|
|
392
|
+
if (activeCohort == ABBREV_COHORT) {
|
|
393
|
+
if (chartType == "profileBarchart2")
|
|
394
|
+
link = "https://global.stjude.org/content/dam/global/en-us/documents/no-index/bar-graph-abbr-profiledash.pdf";
|
|
395
|
+
else if (chartType == "profilePolar2")
|
|
396
|
+
link = "https://global.stjude.org/content/dam/global/en-us/documents/no-index/polar-graph-abbr-profiledash.pdf";
|
|
397
|
+
else if (chartType.startsWith("profileRadar"))
|
|
398
|
+
link = "https://global.stjude.org/content/dam/global/en-us/documents/no-index/radar-abbr-profiledash.pdf";
|
|
399
|
+
} else if (activeCohort == FULL_COHORT) {
|
|
400
|
+
if (chartType == "profileBarchart2")
|
|
401
|
+
link = "https://global.stjude.org/content/dam/global/en-us/documents/no-index/bar-graph-full-profiledash.pdf";
|
|
402
|
+
else if (chartType == "profilePolar2")
|
|
403
|
+
link = "https://global.stjude.org/content/dam/global/en-us/documents/no-index/polar-graph-full-profiledash.pdf";
|
|
404
|
+
else if (chartType.startsWith("profileRadar"))
|
|
405
|
+
link = "https://global.stjude.org/content/dam/global/en-us/documents/no-index/radar-full-profiledash.pdf";
|
|
406
|
+
}
|
|
407
|
+
if (link) window.open(link);
|
|
408
|
+
});
|
|
409
|
+
this.filtersCount = 0;
|
|
410
|
+
} catch (e) {
|
|
411
|
+
console.log(e);
|
|
412
|
+
throw e;
|
|
413
|
+
}
|
|
414
|
+
}
|
|
415
|
+
setFilterValue(key, value) {
|
|
416
|
+
const config = this.config;
|
|
417
|
+
this.settings[key] = value;
|
|
418
|
+
config.filter = this.getFilter();
|
|
419
|
+
this.app.dispatch({ type: "plot_edit", id: this.id, config: this.config });
|
|
420
|
+
}
|
|
421
|
+
getFilterWithSettings(settings) {
|
|
422
|
+
let filter = getCategoricalTermFilter(this.config.filterTWs, settings, null);
|
|
423
|
+
filter = getCombinedTermFilter(this.state, filter);
|
|
424
|
+
return filter.filter;
|
|
425
|
+
}
|
|
426
|
+
getFilter() {
|
|
427
|
+
let filter = getCategoricalTermFilter(this.config.filterTWs, this.settings, null);
|
|
428
|
+
filter = getCombinedTermFilter(this.state, filter);
|
|
429
|
+
return filter.filter;
|
|
430
|
+
}
|
|
431
|
+
clearFiltersExcept(ids) {
|
|
432
|
+
for (const tw of this.config.filterTWs) if (!ids.includes(tw.term.id)) this.settings[tw.term.id] = "";
|
|
433
|
+
}
|
|
434
|
+
setFacilitySite(site) {
|
|
435
|
+
this.settings.facilitySite = site;
|
|
436
|
+
this.app.dispatch({ type: "plot_edit", id: this.id, config: this.config });
|
|
437
|
+
}
|
|
438
|
+
addFilterLegend() {
|
|
439
|
+
const hasFilters = this.config.filterTWs.some((tw) => this.settings[tw.term.id]);
|
|
440
|
+
const title = hasFilters ? "Filters" : "No filter applied";
|
|
441
|
+
this.filterG.attr("font-size", "0.9em").append("text").attr("text-anchor", "left").style("font-weight", "bold").text(`${title} (n=${this.data.n})`).attr("transform", `translate(0, -5)`);
|
|
442
|
+
for (const tw of this.config.filterTWs) this.addFilterLegendItem(tw.term.name, this.settings[tw.term.id]);
|
|
443
|
+
}
|
|
444
|
+
addFilterLegendItem(filter, value) {
|
|
445
|
+
if (!value || value?.length === 0) return;
|
|
446
|
+
this.filtersCount++;
|
|
447
|
+
const isArray = Array.isArray(value);
|
|
448
|
+
let text = isArray ? value.join(", ") : value;
|
|
449
|
+
if (text.length > 40) {
|
|
450
|
+
text = text.slice(0, 40) + "...";
|
|
451
|
+
}
|
|
452
|
+
const itemG = this.filterG.append("g").attr("font-size", "0.95em");
|
|
453
|
+
const textElem = itemG.append("text").attr("transform", `translate(0, ${this.filtersCount * 22})`).attr("text-anchor", "left");
|
|
454
|
+
textElem.append("tspan").attr("font-weight", "bold").text(`${filter}: `);
|
|
455
|
+
textElem.append("tspan").text(text);
|
|
456
|
+
}
|
|
457
|
+
addEndUserImpressionNote(uiG) {
|
|
458
|
+
uiG.attr("font-size", "0.9em");
|
|
459
|
+
const textElem = uiG.append("text").attr("transform", `translate(0, 115)`);
|
|
460
|
+
textElem.append("tspan").attr("font-weight", "bold").text("End-user Impression: ");
|
|
461
|
+
textElem.append("tspan").text("It is provided by the local liaison who completed the assessment ");
|
|
462
|
+
uiG.append("text").attr("transform", `translate(0, 140)`).text("in consultation with the PHO medical director or directly by the PHO medical director.");
|
|
463
|
+
uiG.append("text").attr("transform", `translate(0, 165)`).text("The end-user was asked to rate the current status of the domains and subdomains included.");
|
|
464
|
+
}
|
|
465
|
+
addPOCNote(uiG) {
|
|
466
|
+
uiG.attr("font-size", "0.9em");
|
|
467
|
+
const textElem = uiG.append("text").attr("transform", `translate(0, 115)`);
|
|
468
|
+
textElem.append("tspan").attr("font-weight", "bold").text("Point of Care (POC) Staff: ");
|
|
469
|
+
textElem.append("tspan").text("All members of the assessment team, ");
|
|
470
|
+
uiG.append("text").attr("transform", `translate(0, 140)`).text("excluding the Site Coordinator. POC staff provide subjective information based ");
|
|
471
|
+
uiG.append("text").attr("transform", `translate(0, 165)`).text("on their experience and perception about service delivery at the PHO facility.");
|
|
472
|
+
}
|
|
473
|
+
addLegendItem(category, description, index) {
|
|
474
|
+
const text = this.legendG.append("text").attr("font-size", "0.9em").attr("transform", `translate(0, ${index * 20})`).attr("text-anchor", "left");
|
|
475
|
+
text.append("tspan").attr("font-weight", "bold").text(category);
|
|
476
|
+
text.append("tspan").text(`: ${description}`);
|
|
477
|
+
}
|
|
478
|
+
getDownloadFilename() {
|
|
479
|
+
this.downloadCount++;
|
|
480
|
+
let filename = `${this.type}${this.downloadCount}`;
|
|
481
|
+
filename = filename.split(" ").join("_");
|
|
482
|
+
return filename;
|
|
483
|
+
}
|
|
484
|
+
getPercentage(d) {
|
|
485
|
+
if (!d) return 0;
|
|
486
|
+
const score = this.data.term2Score[d.score.term.id];
|
|
487
|
+
return score;
|
|
488
|
+
}
|
|
489
|
+
async download(event) {
|
|
490
|
+
const chartImages = this.getChartImages();
|
|
491
|
+
const menu = new DownloadMenu(chartImages, this.getDownloadFilename());
|
|
492
|
+
menu.show(event.clientX, event.clientY, event.target);
|
|
493
|
+
}
|
|
494
|
+
preApiFreeze(api) {
|
|
495
|
+
api.download = this.download;
|
|
496
|
+
api.getChartImages = () => this.getChartImages();
|
|
497
|
+
}
|
|
498
|
+
getChartImages() {
|
|
499
|
+
const plots = Object.values(this.components.plots);
|
|
500
|
+
const note = "\xA9 2025 St. Jude Children\u2019s Research Hospital";
|
|
501
|
+
let name = plots.length > 0 ? "Original" : "";
|
|
502
|
+
name += ` ${note}`;
|
|
503
|
+
const charts = [{ name, svg: this.dom.svg }];
|
|
504
|
+
let i = 1;
|
|
505
|
+
for (const plot of plots) {
|
|
506
|
+
const chartImages = plot.getChartImages();
|
|
507
|
+
for (const chartImage of chartImages) {
|
|
508
|
+
const svg = chartImage.svg;
|
|
509
|
+
const name2 = chartImages.length > 1 ? `Comparison ${i}. ${chartImage.name} ${note}` : `Comparison ${chartImage.name} ${note}`;
|
|
510
|
+
charts.push({ name: name2, svg });
|
|
511
|
+
}
|
|
512
|
+
i++;
|
|
513
|
+
}
|
|
514
|
+
return charts;
|
|
515
|
+
}
|
|
516
|
+
};
|
|
517
|
+
function makeChartBtnMenu(holder, chartsInstance, chartType) {
|
|
518
|
+
const state = chartsInstance.state;
|
|
519
|
+
const key = state.activeCohort == FULL_COHORT ? "full" : "abbrev";
|
|
520
|
+
const typeConfig = state.termdbConfig?.plotConfigByCohort[key][chartType];
|
|
521
|
+
if (typeConfig.options.length == 1) {
|
|
522
|
+
createPlot(typeConfig.options[0], chartType, chartsInstance);
|
|
523
|
+
return;
|
|
524
|
+
}
|
|
525
|
+
const menuDiv = holder.append("div");
|
|
526
|
+
for (const plotConfig of typeConfig.options) {
|
|
527
|
+
menuDiv.append("div").attr("class", "sja_menuoption sja_sharp_border").text(plotConfig.title).on("click", () => {
|
|
528
|
+
createPlot(plotConfig, chartType, chartsInstance);
|
|
529
|
+
chartsInstance.dom.tip.hide();
|
|
530
|
+
});
|
|
531
|
+
}
|
|
532
|
+
function createPlot(plotConfig, chartType2, chartsInstance2) {
|
|
533
|
+
const config = structuredClone(plotConfig);
|
|
534
|
+
config.chartType = chartType2;
|
|
535
|
+
chartsInstance2.app.dispatch({
|
|
536
|
+
type: "plot_create",
|
|
537
|
+
chartType: chartType2,
|
|
538
|
+
config
|
|
539
|
+
});
|
|
540
|
+
}
|
|
541
|
+
}
|
|
542
|
+
async function getProfilePlotConfig(activeCohort, app, opts) {
|
|
543
|
+
const key = activeCohort == FULL_COHORT ? "full" : "abbrev";
|
|
544
|
+
const config = structuredClone(app.vocabApi.termdbConfig?.plotConfigByCohort[key]?.[opts.chartType]);
|
|
545
|
+
if (!config) throw `No data available for the plot ${opts.chartType} in this dataset`;
|
|
546
|
+
const cohortPreffix = activeCohort == FULL_COHORT ? "F" : "A";
|
|
547
|
+
config.facilityTW = { id: cohortPreffix + "UNIT" };
|
|
548
|
+
config.hidePlotFilter = true;
|
|
549
|
+
await fillTermWrapper(config.facilityTW, app.vocabApi);
|
|
550
|
+
await loadFilterTerms(config, activeCohort, app);
|
|
551
|
+
return config;
|
|
552
|
+
}
|
|
553
|
+
async function loadFilterTerms(config, activeCohort, app) {
|
|
554
|
+
const cohortPreffix = activeCohort == FULL_COHORT ? "F" : "A";
|
|
555
|
+
config.countryTW = { id: cohortPreffix + "country" };
|
|
556
|
+
config.regionTW = { id: cohortPreffix + "WHO_region" };
|
|
557
|
+
config.sjgRegionTW = { id: cohortPreffix + "SJG_region" };
|
|
558
|
+
config.incomeTW = { id: cohortPreffix + "Income_group" };
|
|
559
|
+
config.typeTW = { id: cohortPreffix + "FC_TypeofFacility" };
|
|
560
|
+
config.teachingStatusTW = { id: cohortPreffix + "FC_TeachingFacility" };
|
|
561
|
+
config.referralStatusTW = { id: cohortPreffix + "FC_ReferralFacility" };
|
|
562
|
+
config.fundingSourceTW = { id: cohortPreffix + "FC_FundingSrc" };
|
|
563
|
+
config.hospitalVolumeTW = { id: cohortPreffix + "PO_HospitalVolume" };
|
|
564
|
+
config.yearOfImplementationTW = { id: cohortPreffix + "Year_implementation" };
|
|
565
|
+
const filterTWs = [
|
|
566
|
+
config.facilityTW,
|
|
567
|
+
config.countryTW,
|
|
568
|
+
config.regionTW,
|
|
569
|
+
config.sjgRegionTW,
|
|
570
|
+
config.incomeTW,
|
|
571
|
+
config.typeTW,
|
|
572
|
+
config.teachingStatusTW,
|
|
573
|
+
config.referralStatusTW,
|
|
574
|
+
config.fundingSourceTW,
|
|
575
|
+
config.hospitalVolumeTW,
|
|
576
|
+
config.yearOfImplementationTW
|
|
577
|
+
];
|
|
578
|
+
await fillTwLst(filterTWs, app.vocabApi);
|
|
579
|
+
config.filterTWs = filterTWs;
|
|
580
|
+
}
|
|
581
|
+
function clearLocalFilters(plot) {
|
|
582
|
+
plot.settings = getDefaultProfilePlotSettings();
|
|
583
|
+
}
|
|
584
|
+
function getDefaultProfilePlotSettings() {
|
|
585
|
+
return {
|
|
586
|
+
isAggregate: false,
|
|
587
|
+
filterByUserSites: false
|
|
588
|
+
//if true, the aggregation will be limited to the user sites only
|
|
589
|
+
};
|
|
590
|
+
}
|
|
591
|
+
function getProfileLogin(app, cohort = FULL_COHORT) {
|
|
592
|
+
const auth = app.vocabApi.getClientAuthResult();
|
|
593
|
+
if (!auth) return { logged: false, sites: [], user: "public" };
|
|
594
|
+
const auth_info = cohort == FULL_COHORT ? auth.full : auth.abbrev;
|
|
595
|
+
const logged = auth_info?.role != "public";
|
|
596
|
+
if (!auth_info) return { logged: false, sites: [], user: "public" };
|
|
597
|
+
const user = auth_info?.role || "public";
|
|
598
|
+
const sites = user == "admin" ? null : auth_info.sites;
|
|
599
|
+
return { logged, sites, user };
|
|
600
|
+
}
|
|
601
|
+
|
|
602
|
+
export {
|
|
603
|
+
ABBREV_COHORT,
|
|
604
|
+
FULL_COHORT,
|
|
605
|
+
profilePlot,
|
|
606
|
+
makeChartBtnMenu,
|
|
607
|
+
getProfilePlotConfig,
|
|
608
|
+
loadFilterTerms,
|
|
609
|
+
clearLocalFilters,
|
|
610
|
+
getDefaultProfilePlotSettings,
|
|
611
|
+
getProfileLogin
|
|
612
|
+
};
|
|
613
|
+
//# sourceMappingURL=chunk-P3IENRWJ.js.map
|
|
@@ -0,0 +1,26 @@
|
|
|
1
|
+
import {
|
|
2
|
+
plotColor
|
|
3
|
+
} from "./chunk-4UWS5Y3N.js";
|
|
4
|
+
|
|
5
|
+
// plots/boxplot/defaults.ts
|
|
6
|
+
function getDefaultBoxplotSettings(app, overrides = {}) {
|
|
7
|
+
const defaults = {
|
|
8
|
+
plotLength: 550,
|
|
9
|
+
color: plotColor,
|
|
10
|
+
displayMode: "default",
|
|
11
|
+
labelPad: 10,
|
|
12
|
+
isLogScale: false,
|
|
13
|
+
isVertical: false,
|
|
14
|
+
orderByMedian: false,
|
|
15
|
+
rowHeight: 50,
|
|
16
|
+
rowSpace: 15,
|
|
17
|
+
removeOutliers: false,
|
|
18
|
+
showAssocTests: true
|
|
19
|
+
};
|
|
20
|
+
return Object.assign(defaults, overrides);
|
|
21
|
+
}
|
|
22
|
+
|
|
23
|
+
export {
|
|
24
|
+
getDefaultBoxplotSettings
|
|
25
|
+
};
|
|
26
|
+
//# sourceMappingURL=chunk-PCZNTK74.js.map
|