@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.
Files changed (888) hide show
  1. package/dist/2dmaf-Z3D2M3FB.js +1373 -0
  2. package/dist/AIProjectAdmin-2OQOQXH4.js +956 -0
  3. package/dist/AppHeader-PXLGVCVS.js +835 -0
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  5. package/dist/CorrelationVolcano-RO6CFLZA.js +619 -0
  6. package/dist/DE-CCA5SBJG.js +95 -0
  7. package/dist/DEinput-MRUQW6X6.js +301 -0
  8. package/dist/DifferentialAnalysis-5YQQLJKR.js +245 -0
  9. package/dist/Disco-4FTOJBLG.js +3237 -0
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  159. package/dist/dnaMethylation-WGJMJL5B.js +38 -0
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  813. /package/dist/{plot.disco-BLNU4I6Q.js.map → plot.disco-OUE4RFHL.js.map} +0 -0
  814. /package/dist/{plot.dzi-FKWY6K5Q.js.map → plot.dzi-T3GPUH36.js.map} +0 -0
  815. /package/dist/{plot.ssgq-3GTTOOMK.js.map → plot.ssgq-WJHGMXW5.js.map} +0 -0
  816. /package/dist/{plot.vaf2cov-UAI64HYN.js.map → plot.vaf2cov-NGD5PCV4.js.map} +0 -0
  817. /package/dist/{plot.wsi-QJ52IJXL.js.map → plot.wsi-2MU5BDG3.js.map} +0 -0
  818. /package/dist/{polar2-6S4IHKK4.js.map → polar2-YCWPBPFU.js.map} +0 -0
  819. /package/dist/{profileForms-WXWHZ56N.js.map → profileForms-OV3I6RK7.js.map} +0 -0
  820. /package/dist/{profilePlot-K7ICCFQ3.js.map → profilePlot-OMVO3K4H.js.map} +0 -0
  821. /package/dist/{proteinView-ALZTEKTC.js.map → proteinView-OAR2RC6U.js.map} +0 -0
  822. /package/dist/{qualitative-QMPO7EY6.js.map → qualitative-MEYBRUC6.js.map} +0 -0
  823. /package/dist/{radar2-LDAFJHSI.js.map → radar2-KREAMGVV.js.map} +0 -0
  824. /package/dist/{radarFacility2-3TX3U243.js.map → radarFacility2-DBPEV7VC.js.map} +0 -0
  825. /package/dist/{regression-DUUCJOFW.js.map → regression-ZPDPLI6G.js.map} +0 -0
  826. /package/dist/{regression.inputs-B6SFFVED.js.map → regression.inputs-QOSBAGL6.js.map} +0 -0
  827. /package/dist/{regression.inputs.term-P5NHX7ME.js.map → regression.inputs.term-HMUMPY7X.js.map} +0 -0
  828. /package/dist/{regression.inputs.values.table-MVPP5VAK.js.map → regression.inputs.values.table-VMCTZHLG.js.map} +0 -0
  829. /package/dist/{regression.integration.spec-T7VH46WO.js.map → regression.integration.spec-RP74JTAA.js.map} +0 -0
  830. /package/dist/{regression.results-QEP4T6JO.js.map → regression.results-5XC6M67C.js.map} +0 -0
  831. /package/dist/{regression.spec-BTBCBKMF.js.map → regression.spec-EZYM24J7.js.map} +0 -0
  832. /package/dist/{report-WYCH4DJX.js.map → report-ZOVQCOGQ.js.map} +0 -0
  833. /package/dist/{sampleScatter.spec-LC6K22FF.js.map → sampleScatter.spec-CD52FEOC.js.map} +0 -0
  834. /package/dist/{sampleView-V3JYDTRA.js.map → sampleView-SVTLSWRG.js.map} +0 -0
  835. /package/dist/{samplelst-JO7UROYA.js.map → samplelst-HXF5POJD.js.map} +0 -0
  836. /package/dist/{samplematrix-6526IJRO.js.map → samplematrix-NYDAH74I.js.map} +0 -0
  837. /package/dist/{sc-EUC7G5OV.js.map → sc-JIDT4W4K.js.map} +0 -0
  838. /package/dist/{scatter-UMK37C4M.js.map → scatter-WNRTPSEE.js.map} +0 -0
  839. /package/dist/{scatter.integration.spec-BTOB6Y4H.js.map → scatter.integration.spec-3EYTPY5B.js.map} +0 -0
  840. /package/dist/{selectGenomeWithTklst-JNEOHP4V.js.map → selectGenomeWithTklst-OSB7B6L3.js.map} +0 -0
  841. /package/dist/{singleCellCellType-ZDMKPQ2Q.js.map → singleCellCellType-3BH7LWQ6.js.map} +0 -0
  842. /package/dist/{singleCellCellType.unit.spec-BKGRNHYP.js.map → singleCellCellType.unit.spec-RU4RJXFF.js.map} +0 -0
  843. /package/dist/{singleCellGeneExpression-J5KFX7TD.js.map → singleCellGeneExpression-3UA4YER7.js.map} +0 -0
  844. /package/dist/{singleCellGeneExpression.unit.spec-6F5YFV7K.js.map → singleCellGeneExpression.unit.spec-4ZTBG37H.js.map} +0 -0
  845. /package/dist/{singleCellPlot-VA6SWR5L.js.map → singleCellPlot-ZUAWK5RE.js.map} +0 -0
  846. /package/dist/{singlecell-A4OHBVJD.js.map → singlecell-BGJZB7MF.js.map} +0 -0
  847. /package/dist/{singlecell-2CWHJR2P.js.map → singlecell-RO3BL5OO.js.map} +0 -0
  848. /package/dist/{snp-PJNNPOSF.js.map → snp-HD7VQKBR.js.map} +0 -0
  849. /package/dist/{snp.unit.spec-JKZCYPNA.js.map → snp.unit.spec-ISXCLMWW.js.map} +0 -0
  850. /package/dist/{snplocus-YY6UIS2R.js.map → snplocus-IL5Z4XWV.js.map} +0 -0
  851. /package/dist/{spliceevent.a53ss.diagram-CEFGK2LA.js.map → spliceevent.a53ss.diagram-LLJSPV7M.js.map} +0 -0
  852. /package/dist/{spliceevent.exonskip.diagram-A24TZTQ7.js.map → spliceevent.exonskip.diagram-LAOIOIST.js.map} +0 -0
  853. /package/dist/{spliceevent.noeventdiagram-USD42ZZB.js.map → spliceevent.noeventdiagram-MVA7Q3HT.js.map} +0 -0
  854. /package/dist/{ssGSEA-A5X56E7U.js.map → ssGSEA-7T6S3DSE.js.map} +0 -0
  855. /package/dist/{ssGSEA.unit.spec-6WMGKWNI.js.map → ssGSEA.unit.spec-XJ3W4NWX.js.map} +0 -0
  856. /package/dist/{summarizeCnvGeneexp-FZJL4Q7O.js.map → summarizeCnvGeneexp-RRP6JUV6.js.map} +0 -0
  857. /package/dist/{summarizeGeneexpSurvival-LRJZBHRW.js.map → summarizeGeneexpSurvival-AFLHDD6Q.js.map} +0 -0
  858. /package/dist/{summarizeMutationCnv-L64CVMHI.js.map → summarizeMutationCnv-NABUYHMX.js.map} +0 -0
  859. /package/dist/{summarizeMutationDiagnosis-S55CKGBO.js.map → summarizeMutationDiagnosis-2LQ7JU3K.js.map} +0 -0
  860. /package/dist/{summarizeMutationSurvival-AM7BZVDP.js.map → summarizeMutationSurvival-3WBT5TXG.js.map} +0 -0
  861. /package/dist/{summary-ANZTET2T.js.map → summary-FRDKOFXW.js.map} +0 -0
  862. /package/dist/{summary.integration.spec-TW3CJTDA.js.map → summary.integration.spec-ZLRIA7G2.js.map} +0 -0
  863. /package/dist/{summaryInput-3JHKZU62.js.map → summaryInput-4JO6MHP4.js.map} +0 -0
  864. /package/dist/{sunburst-ABDTE22P.js.map → sunburst-DRCVSC2X.js.map} +0 -0
  865. /package/dist/{survival-HROP7OR7.js.map → survival-AK75COPY.js.map} +0 -0
  866. /package/dist/{survival-KZDESA36.js.map → survival-IF5NI3A6.js.map} +0 -0
  867. /package/dist/{survival.integration.spec-CMZTALBF.js.map → survival.integration.spec-7IWBTPJG.js.map} +0 -0
  868. /package/dist/{svgraph-TLRXKVWQ.js.map → svgraph-QBDF2SLB.js.map} +0 -0
  869. /package/dist/{svmr-R4QOXWQW.js.map → svmr-O4GJJUT2.js.map} +0 -0
  870. /package/dist/{table-QM3RZQ5R.js.map → table-FQAIXKLE.js.map} +0 -0
  871. /package/dist/{termCollection-WVYJHPIH.js.map → termCollection-GMDDL3L7.js.map} +0 -0
  872. /package/dist/{termCollection-B2A3MSCD.js.map → termCollection-ZO5PZ7E3.js.map} +0 -0
  873. /package/dist/{termCollection.unit.spec-TCPEEZHW.js.map → termCollection.unit.spec-5JBCTXHX.js.map} +0 -0
  874. /package/dist/{tk-DGFFDV7C.js.map → tk-GJX23IV7.js.map} +0 -0
  875. /package/dist/{tp.ui-BEESUHHF.js.map → tp.ui-T7FVMTGQ.js.map} +0 -0
  876. /package/dist/{tvs.dt-UZW3L4MO.js.map → tvs.dt-X7L7NSU6.js.map} +0 -0
  877. /package/dist/{tvs.dtcnv.categorical-OH5NXCDN.js.map → tvs.dtcnv.categorical-73G2V6CH.js.map} +0 -0
  878. /package/dist/{tvs.dtcnv.continuous-VWWTWAX2.js.map → tvs.dtcnv.continuous-DWFJL3X7.js.map} +0 -0
  879. /package/dist/{tvs.dtfusion-YKYYCDJN.js.map → tvs.dtfusion-HQADHCSV.js.map} +0 -0
  880. /package/dist/{tvs.dtsnvindel-Y3WAHLKK.js.map → tvs.dtsnvindel-PY5OBMGW.js.map} +0 -0
  881. /package/dist/{tvs.dtsv-UFLR2XRY.js.map → tvs.dtsv-OTBEEWSW.js.map} +0 -0
  882. /package/dist/{tvs.samplelst-BPWZHD62.js.map → tvs.samplelst-LCXSU5MG.js.map} +0 -0
  883. /package/dist/{tvs.termCollection-JLA3JQFX.js.map → tvs.termCollection-L527XN4X.js.map} +0 -0
  884. /package/dist/{violin-TFNQIETS.js.map → violin-6VKRUQV3.js.map} +0 -0
  885. /package/dist/{violin.integration.spec-XKNZQVN7.js.map → violin.integration.spec-RJATDLQH.js.map} +0 -0
  886. /package/dist/{violin.interactivity-R2EYNWI6.js.map → violin.interactivity-SKF5H7MN.js.map} +0 -0
  887. /package/dist/{violin.renderer-5WA4YLGB.js.map → violin.renderer-GB4TPX3B.js.map} +0 -0
  888. /package/dist/{vocabulary-D2XUEKI6.js.map → vocabulary-D3W44IWE.js.map} +0 -0
@@ -0,0 +1,613 @@
1
+ import {
2
+ DownloadMenu,
3
+ PlotBase,
4
+ controlsInit,
5
+ fillTermWrapper,
6
+ fillTwLst,
7
+ getCategoricalTermFilter,
8
+ getCombinedTermFilter
9
+ } from "./chunk-SA7APTJR.js";
10
+ import {
11
+ importPlot
12
+ } from "./chunk-SKREEF3H.js";
13
+ import {
14
+ Menu
15
+ } from "./chunk-HYOEWQ5P.js";
16
+ import {
17
+ icons
18
+ } from "./chunk-IIT367QZ.js";
19
+ import {
20
+ select_default
21
+ } from "./chunk-I6Y4O3RR.js";
22
+
23
+ // plots/profile/profilePlot.ts
24
+ var orderedIncomes = ["Low income", "Lower middle income", "Upper middle income", "High income"];
25
+ var orderedVolumes = [
26
+ "Small (1-25 annual newly diagnoses)",
27
+ "Medium (26-80 annual newly diagnoses)",
28
+ "Large (81-120 annual newly diagnoses)",
29
+ "Very large (>120 annual newly diagnoses)"
30
+ ];
31
+ var ABBREV_COHORT = 0;
32
+ var FULL_COHORT = 1;
33
+ var profilePlot = class extends PlotBase {
34
+ constructor(opts, type) {
35
+ super(opts);
36
+ this.type = type;
37
+ this.downloadCount = 0;
38
+ this.tip = new Menu({ padding: "4px", offsetX: 10, offsetY: 15 });
39
+ this.scoreTerms = [];
40
+ this.scScoreTerms = [];
41
+ this.isRadarFacility = false;
42
+ this.components = { plots: {} };
43
+ }
44
+ //extracts the relevant state from the appState: config, termfilter, vocab, login info
45
+ getState(appState) {
46
+ const config = appState.plots.find((p) => p.id === this.id);
47
+ if (!config) throw `No plot with id='${this.id}' found`;
48
+ const { logged, sites, user } = getProfileLogin(this.app, appState.activeCohort);
49
+ const site = sites?.[0];
50
+ return {
51
+ config,
52
+ termfilter: appState.termfilter,
53
+ dslabel: appState.vocab.dslabel,
54
+ termdbConfig: appState.termdbConfig,
55
+ vocab: appState.vocab,
56
+ logged,
57
+ //later change to read login info
58
+ site,
59
+ sites,
60
+ user,
61
+ activeCohort: appState.activeCohort,
62
+ //Find plots where I am a parent. Here the child is a second plot for comparison
63
+ plots: appState.plots.filter((p) => p.parentId === this.id)
64
+ //this property is needed to indicate that child plots need to be added to the appState plots
65
+ };
66
+ }
67
+ //refers to the view where all the filters are shown and not the preselected site
68
+ isAggregate() {
69
+ if (!this.state.logged) return true;
70
+ if (this.settings.isAggregate) return true;
71
+ if (this.state.sites?.length > 1 || this.state.user == "admin" || this.isRadarFacility) return true;
72
+ return false;
73
+ }
74
+ //initializes the plot elements
75
+ async init(appState) {
76
+ const config = appState.plots.find((p) => p.id === this.id);
77
+ const state = this.getState(appState);
78
+ if (this.opts.header) {
79
+ let chartName = config.chartType.match(/[A-Z][a-z]+/g);
80
+ chartName = chartName.join(" ");
81
+ chartName = config.headerTitle ? config.headerTitle + ` / ${state.user}` : chartName + ` / ${state.user}`;
82
+ this.opts.header.style("text-transform", "capitalize").text(chartName);
83
+ }
84
+ const div = this.opts.holder.append("div").style("display", "inline-block");
85
+ const leftDiv = div.append("div").style("display", "inline-block").style("vertical-align", "top");
86
+ const rightDiv = div.append("div").style("display", "inline-block").style("vertical-align", "top");
87
+ const controlsDiv = leftDiv.append("div").style("display", "inline-block").style("font-size", "0.9em");
88
+ const iconsDiv = leftDiv.append("div").style("margin-top", "10px").style("padding-left", "12px");
89
+ const holder = rightDiv.insert("div").style("display", "inline-block");
90
+ const plotDiv = holder.append("div");
91
+ this.dom = {
92
+ controlsDiv,
93
+ holder,
94
+ iconsDiv,
95
+ rightDiv,
96
+ plotDiv
97
+ };
98
+ select_default(".sjpp-output-sandbox-content").on("scroll", (event) => {
99
+ if (this.onMouseOut) this.onMouseOut(event);
100
+ });
101
+ this.dom.rightDiv.on("mousemove", (event) => this.onMouseOver(event));
102
+ this.dom.rightDiv.on("mouseleave", (event) => this.onMouseOut(event));
103
+ this.dom.rightDiv.on("mouseout", (event) => this.onMouseOut(event));
104
+ document.addEventListener("scroll", () => this?.tip?.hide());
105
+ const restartDiv = iconsDiv.append("div").style("padding-bottom", "8px");
106
+ icons["restart"](restartDiv, {
107
+ title: "Clear filters",
108
+ handler: async () => {
109
+ this.clearFiltersExcept([]);
110
+ this.app.dispatch({
111
+ type: "plot_edit",
112
+ id: this.id,
113
+ config: { filter: this.getFilter(), settings: { [this.type]: this.settings } }
114
+ });
115
+ }
116
+ });
117
+ if (!config.parentId) {
118
+ const iconDiv = iconsDiv.append("div").style("fill", "#aaa").style("padding", "2px");
119
+ icons["add"](iconDiv, {
120
+ title: "Open another plot for comparison",
121
+ handler: () => {
122
+ const show = !this.isComparison;
123
+ const icon = iconDiv.select("svg");
124
+ icon.style("fill", show ? "orange" : "black");
125
+ if (this.isComparison) {
126
+ const id = this.state.plots.find((p) => p.parentId === this.id)?.id;
127
+ this.app.dispatch({
128
+ type: "plot_delete",
129
+ id,
130
+ parentId: this.id
131
+ });
132
+ return;
133
+ }
134
+ this.legendG.selectAll("*").remove();
135
+ const config2 = structuredClone(this.config);
136
+ config2.parentId = this.id;
137
+ this.app.dispatch({
138
+ type: "plot_create",
139
+ config: config2
140
+ });
141
+ }
142
+ });
143
+ }
144
+ }
145
+ //tooltip handler to hide the tooltip when mouse leaves the plot area
146
+ onMouseOut(_event) {
147
+ this.tip.hide();
148
+ }
149
+ async main() {
150
+ this.config = JSON.parse(JSON.stringify(this.state.config));
151
+ this.settings = this.config.settings[this.type];
152
+ this.dom.plotDiv.selectAll("*").remove();
153
+ this.isComparison = this.config.parentId || this.state.plots.length > 0;
154
+ for (const config of this.state.plots) {
155
+ const plot = structuredClone(config);
156
+ if (this.components.plots[plot.id]) continue;
157
+ const holder = this.opts.holder.append("div").style("display", "inline-block").style("padding", "5px");
158
+ plot.holder = holder.append("div");
159
+ plot.app = this.app;
160
+ const { componentInit } = await importPlot(plot.chartType);
161
+ this.components.plots[plot.id] = await componentInit(plot);
162
+ }
163
+ for (const plotId in this.components.plots) {
164
+ if (!this.state.plots.find((p) => p.id === plotId)) {
165
+ this.components.plots[plotId].destroy();
166
+ delete this.components.plots[plotId];
167
+ }
168
+ }
169
+ }
170
+ async setControls(additionalInputs = []) {
171
+ try {
172
+ const isRadarFacility = this.isRadarFacility;
173
+ const filters = {};
174
+ for (const tw of this.config.filterTWs) {
175
+ filters[tw.term.id] = getCategoricalTermFilter(this.config.filterTWs, this.settings, tw);
176
+ }
177
+ this.filteredTermValues = await this.app.vocabApi.filterTermValues({
178
+ terms: this.config.filterTWs,
179
+ filter: this.state.termfilter.filter,
180
+ filters,
181
+ facilityTW: this.config.facilityTW,
182
+ // safe to pass because the backend code will still compare terms[] with the the dataset's hiddenTermIds,
183
+ // it only affects what will be included in the aggregation and does not disable user access authentication
184
+ filterByUserSites: this.settings.filterByUserSites,
185
+ showAll: true
186
+ });
187
+ const regions = this.filteredTermValues[this.config.regionTW.id];
188
+ const sjgRegions = this.filteredTermValues[this.config.sjgRegionTW.id];
189
+ const countries = this.filteredTermValues[this.config.countryTW.id];
190
+ const incomes = this.filteredTermValues[this.config.incomeTW.id];
191
+ const teachingStates = this.filteredTermValues[this.config.teachingStatusTW.id];
192
+ const referralStates = this.filteredTermValues[this.config.referralStatusTW.id];
193
+ const fundingSources = this.filteredTermValues[this.config.fundingSourceTW.id];
194
+ const hospitalVolumes = this.filteredTermValues[this.config.hospitalVolumeTW.id];
195
+ const yearsOfImplementation = this.filteredTermValues[this.config.yearOfImplementationTW.id];
196
+ incomes.sort((elem1, elem2) => {
197
+ const i1 = orderedIncomes.indexOf(elem1.value);
198
+ const i2 = orderedIncomes.indexOf(elem2.value);
199
+ if (i1 < i2) return -1;
200
+ return 1;
201
+ });
202
+ hospitalVolumes.sort((elem1, elem2) => {
203
+ const i1 = orderedVolumes.indexOf(elem1.value);
204
+ const i2 = orderedVolumes.indexOf(elem2.value);
205
+ if (i1 < i2) return -1;
206
+ return 1;
207
+ });
208
+ const types = this.filteredTermValues[this.config.typeTW.id];
209
+ const isAggregate = this.isAggregate();
210
+ if (!this.settings[this.config.facilityTW?.term?.id] && this.state.sites?.length == 1 && !isAggregate) {
211
+ this.settings[this.config.facilityTW?.term?.id] = [this.state.sites[0]];
212
+ }
213
+ this.filter = this.config.filter || this.getFilter();
214
+ if (this.type == "profileForms")
215
+ this.data = await this.app.vocabApi.getProfileFormScores({
216
+ scoreTerms: this.scoreTerms,
217
+ scScoreTerms: this.scScoreTerms,
218
+ filter: this.filter,
219
+ facilityTW: this.config.facilityTW,
220
+ filterByUserSites: this.settings.filterByUserSites
221
+ });
222
+ else if (this.type == "profileRadarFacility2")
223
+ this.data = await this.fetchRadarFacility2Scores();
224
+ if ((this.type == "profileForms" || this.type == "profileRadarFacility2") && this.data && "error" in this.data)
225
+ throw this.data.error;
226
+ this.sites = this.filteredTermValues[this.config.facilityTW.id]?.filter((s) => !s.disabled && s.value);
227
+ if (this.settings[this.config.facilityTW?.term?.id])
228
+ 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