@sjcrh/proteinpaint-client 2.166.0 → 2.167.0

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 (882) hide show
  1. package/dist/2dmaf-VLW5XJ4O.js +1364 -0
  2. package/dist/AIProjectAdmin-X3TBCRPR.js +780 -0
  3. package/dist/AppHeader-YA7FCKVM.js +813 -0
  4. package/dist/BoxPlot-PAZYARCX.js +44 -0
  5. package/dist/CorrelationVolcano-S35GWKV5.js +616 -0
  6. package/dist/DifferentialAnalysis-DTDFAUXT.js +237 -0
  7. package/dist/Disco-OE6YY3MH.js +3089 -0
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  823. /package/dist/{profile.spec-A6EADWEC.js.map → profile.spec-DOQYKG6P.js.map} +0 -0
  824. /package/dist/{profileBarchart-EFLPJK2P.js.map → profileBarchart-A4UWV2YA.js.map} +0 -0
  825. /package/dist/{profileForms-TG35YNLD.js.map → profileForms-VONTWVOF.js.map} +0 -0
  826. /package/dist/{profilePlot-2EW2XVTK.js.map → profilePlot-OK5VKWO4.js.map} +0 -0
  827. /package/dist/{profileRadar-AKUYC2O5.js.map → profileRadar-VLEZJCD7.js.map} +0 -0
  828. /package/dist/{profileRadarFacility-EAT66XTX.js.map → profileRadarFacility-QPSSUTB6.js.map} +0 -0
  829. /package/dist/{qualitative-PHQU5DXE.js.map → qualitative-RJKAWHQR.js.map} +0 -0
  830. /package/dist/{regression-EOMJRRDO.js.map → regression-GV73BYCQ.js.map} +0 -0
  831. /package/dist/{regression.inputs-LIH5X2JM.js.map → regression.inputs-PVIJHCRE.js.map} +0 -0
  832. /package/dist/{regression.inputs.term-OO4RZ3QB.js.map → regression.inputs.term-V5I3EP6M.js.map} +0 -0
  833. /package/dist/{regression.inputs.values.table-E7WCTO2L.js.map → regression.inputs.values.table-Y37EJUQB.js.map} +0 -0
  834. /package/dist/{regression.integration.spec-62VEQP6X.js.map → regression.integration.spec-JD32ODD2.js.map} +0 -0
  835. /package/dist/{regression.results-WAHFJ6NA.js.map → regression.results-AHAYXYGI.js.map} +0 -0
  836. /package/dist/{regression.spec-IBIOTZVX.js.map → regression.spec-FGYEES5G.js.map} +0 -0
  837. /package/dist/{report-MKDJXHGY.js.map → report-JYIEDDW5.js.map} +0 -0
  838. /package/dist/{runChart-ETM2EETF.js.map → runChart-CVAWIBA3.js.map} +0 -0
  839. /package/dist/{runchart.integration.spec-QFA4XBKB.js.map → runchart.integration.spec-5Z4IHQU5.js.map} +0 -0
  840. /package/dist/{sampleScatter.spec-N4N7ZGZF.js.map → sampleScatter.spec-QNFWS2Y7.js.map} +0 -0
  841. /package/dist/{sampleView-JTY3RV7I.js.map → sampleView-GKYHS3WO.js.map} +0 -0
  842. /package/dist/{samplelst-RRUMBVT6.js.map → samplelst-CHBS5BGY.js.map} +0 -0
  843. /package/dist/{samplematrix-L37O664Y.js.map → samplematrix-IK4YDAID.js.map} +0 -0
  844. /package/dist/{scatter-E5QHW32W.js.map → scatter-NDA5YSCP.js.map} +0 -0
  845. /package/dist/{scatter.integration.spec-FNVAJSVU.js.map → scatter.integration.spec-GV3EIFGT.js.map} +0 -0
  846. /package/dist/{selectGenomeWithTklst-J6VXCYGG.js.map → selectGenomeWithTklst-X7RAGKRC.js.map} +0 -0
  847. /package/dist/{singleCellPlot-S6S6CKYX.js.map → singleCellPlot-7F735HTR.js.map} +0 -0
  848. /package/dist/{singlecell-B4TNI23F.js.map → singlecell-EO3WYGS7.js.map} +0 -0
  849. /package/dist/{singlecell-4BMIKFY4.js.map → singlecell-YMYLKTSC.js.map} +0 -0
  850. /package/dist/{snp-PAUQ24NZ.js.map → snp-6KN4AWBB.js.map} +0 -0
  851. /package/dist/{snplocus-HVFYZTEE.js.map → snplocus-CLM4WHVH.js.map} +0 -0
  852. /package/dist/{spliceevent.a53ss.diagram-GGGHVNBF.js.map → spliceevent.a53ss.diagram-PKFVC2N4.js.map} +0 -0
  853. /package/dist/{spliceevent.exonskip.diagram-HLMFD6LJ.js.map → spliceevent.exonskip.diagram-XV2Z7AYB.js.map} +0 -0
  854. /package/dist/{spliceevent.noeventdiagram-CKZ3BZ7Y.js.map → spliceevent.noeventdiagram-L5L2BJL5.js.map} +0 -0
  855. /package/dist/{ssGSEA-UGT4GH55.js.map → ssGSEA-W6N4CXMD.js.map} +0 -0
  856. /package/dist/{stattable-6JWMALGB.js.map → stattable-324FS2HA.js.map} +0 -0
  857. /package/dist/{summarizeCnvGeneexp-BJOQY62E.js.map → summarizeCnvGeneexp-57LZ5B2Q.js.map} +0 -0
  858. /package/dist/{summarizeGeneexpSurvival-4HDHL7PE.js.map → summarizeGeneexpSurvival-UQX3VZUK.js.map} +0 -0
  859. /package/dist/{summarizeMutationDiagnosis-TDWO5CKU.js.map → summarizeMutationDiagnosis-5SWO42E4.js.map} +0 -0
  860. /package/dist/{summarizeMutationSurvival-CJJFABOX.js.map → summarizeMutationSurvival-EOU5QOB6.js.map} +0 -0
  861. /package/dist/{summary-WOAXXIHG.js.map → summary-FRIKVPYZ.js.map} +0 -0
  862. /package/dist/{summary.integration.spec-GM73ERMN.js.map → summary.integration.spec-WSI3JNTO.js.map} +0 -0
  863. /package/dist/{summaryInput-FD4SONTY.js.map → summaryInput-3L7CM52X.js.map} +0 -0
  864. /package/dist/{sunburst-3LCJTBRN.js.map → sunburst-HA7UGSXX.js.map} +0 -0
  865. /package/dist/{survival-A3A7IVXT.js.map → survival-2HZ446Y3.js.map} +0 -0
  866. /package/dist/{survival-XF72VMM6.js.map → survival-LJI5JEZZ.js.map} +0 -0
  867. /package/dist/{survival.integration.spec-AU7MCAQV.js.map → survival.integration.spec-7XVO2WNF.js.map} +0 -0
  868. /package/dist/{svgraph-BEMS4JDJ.js.map → svgraph-TRPAXTNP.js.map} +0 -0
  869. /package/dist/{svmr-CDEMTZPK.js.map → svmr-TJOCKTE2.js.map} +0 -0
  870. /package/dist/{table-WYF6QCGB.js.map → table-35RHJK4M.js.map} +0 -0
  871. /package/dist/{termCollection-BVQMNVY7.js.map → termCollection-JS6N5TAP.js.map} +0 -0
  872. /package/dist/{termInfo-JXLIVCSO.js.map → termInfo-5USFZGDB.js.map} +0 -0
  873. /package/dist/{tk-TGIIJYBO.js.map → tk-4ARNGTEQ.js.map} +0 -0
  874. /package/dist/{tp.ui-USYF67P7.js.map → tp.ui-QZEMGVEH.js.map} +0 -0
  875. /package/dist/{tvs.dtcnv.continuous-7SCTSFK3.js.map → tvs.dtcnv.continuous-4K7B7FXF.js.map} +0 -0
  876. /package/dist/{tvs.numeric-OLVW6US3.js.map → tvs.numeric-FCC2EY62.js.map} +0 -0
  877. /package/dist/{tvs.samplelst-BHZHCX5V.js.map → tvs.samplelst-IUSDLB6P.js.map} +0 -0
  878. /package/dist/{violin-OEOWVIZF.js.map → violin-I5JO56GZ.js.map} +0 -0
  879. /package/dist/{violin.integration.spec-AW2U3RHO.js.map → violin.integration.spec-5WVLT3DW.js.map} +0 -0
  880. /package/dist/{violin.interactivity-3O2UDNPQ.js.map → violin.interactivity-EFFBMTN2.js.map} +0 -0
  881. /package/dist/{violin.renderer-W26FA6M7.js.map → violin.renderer-Z3AIV5RH.js.map} +0 -0
  882. /package/dist/{vocabulary-BIQYDKVY.js.map → vocabulary-4PHACFSG.js.map} +0 -0
@@ -1,217 +0,0 @@
1
- import {
2
- dofetch,
3
- dofetch2
4
- } from "./chunk-5TDKRZN5.js";
5
- import {
6
- contigNameNoChr2
7
- } from "./chunk-ECKWM4HB.js";
8
-
9
- // tracks/hic/data/parseData.ts
10
- async function hicParseFile(hic, debugmode, errList = []) {
11
- if (debugmode) window["hic"] = hic;
12
- if (hic.tklst) {
13
- const lst = [];
14
- for (const t of hic.tklst) {
15
- if (!t.type) {
16
- errList.push("type missing from one of the tracks accompanying HiC");
17
- } else {
18
- t.iscustom = true;
19
- lst.push(t);
20
- }
21
- }
22
- if (lst.length) {
23
- hic.tklst = lst;
24
- } else {
25
- delete hic.tklst;
26
- }
27
- }
28
- if (hic.enzyme) {
29
- if (hic.genome.hicenzymefragment) {
30
- let frag = null;
31
- for (const f of hic.genome.hicenzymefragment) {
32
- if (f.enzyme == hic.enzyme) {
33
- frag = f;
34
- break;
35
- }
36
- }
37
- if (frag) {
38
- hic.enzymefile = frag.file;
39
- } else {
40
- errList.push("unknown enzyme: " + hic.enzyme);
41
- delete hic.enzyme;
42
- }
43
- } else {
44
- errList.push("no enzyme fragment information available for this genome");
45
- delete hic.enzyme;
46
- }
47
- }
48
- try {
49
- if (hic.sv && hic.sv.file) {
50
- const re = await dofetch(hic.hostURL + "/textfile", {
51
- method: "POST",
52
- body: JSON.stringify({ file: hic.sv.file, jwt: hic.jwt })
53
- });
54
- const data2 = re.json();
55
- const [err2, header, items] = parseSV(data2.text);
56
- if (err2) throw { message: "Error parsing SV: " + err2 };
57
- hic.sv.header = header;
58
- hic.sv.items = items;
59
- }
60
- const data = await dofetch2("hicstat?" + (hic.file ? "file=" + hic.file : "url=" + hic.url));
61
- if (data.error) {
62
- errList.push(data.error);
63
- return;
64
- }
65
- const err = hicparsestat(hic, data.out);
66
- if (err) throw { message: err };
67
- } catch (err) {
68
- errList.push(err.message || err);
69
- if (err.stack) {
70
- console.log(err.stack);
71
- }
72
- }
73
- return hic;
74
- }
75
- function parseSV(txt) {
76
- const lines = txt.trim().split(/\r?\n/);
77
- const [err, header] = parseSVheader(lines[0]);
78
- if (err) return ["header error: " + err];
79
- const items = [];
80
- for (let i = 1; i < lines.length; i++) {
81
- const line = lines[i];
82
- if (line[0] == "#") continue;
83
- const [e, m] = parseSVline(line, header);
84
- if (e) return ["line " + (i + 1) + " error: " + e];
85
- items.push(m);
86
- }
87
- return [null, header, items];
88
- }
89
- function parseSVheader(line) {
90
- const header = line.toLowerCase().split(" ");
91
- if (header.length <= 1) return "invalid file header for fusions";
92
- const htry = (...lst) => {
93
- for (const a of lst) {
94
- const j = header.indexOf(a);
95
- if (j != -1) return j;
96
- }
97
- return -1;
98
- };
99
- let i = htry("chr_a", "chr1", "chra");
100
- if (i == -1) return "chr_A missing from header";
101
- header[i] = "chr1";
102
- i = htry("chr_b", "chr2", "chrb");
103
- if (i == -1) return "chr_B missing from header";
104
- header[i] = "chr2";
105
- i = htry("pos_a", "position_a", "position1", "posa");
106
- if (i == -1) return "pos_a missing from header";
107
- header[i] = "position1";
108
- i = htry("pos_b", "position_b", "position2", "posb");
109
- if (i == -1) return "pos_b missing from header";
110
- header[i] = "position2";
111
- i = htry("strand_a", "orta", "orienta");
112
- if (i == -1) return "strand_a missing from header";
113
- header[i] = "strand1";
114
- i = htry("strand_b", "ortb", "orientb");
115
- if (i == -1) return "strand_b missing from header";
116
- header[i] = "strand2";
117
- i = htry("numreadsa");
118
- if (i != -1) header[i] = "reads1";
119
- i = htry("numreadsb");
120
- if (i != -1) header[i] = "reads2";
121
- return [null, header];
122
- }
123
- function parseSVline(line, header) {
124
- const lst = line.split(" ");
125
- const m = {};
126
- for (let j = 0; j < header.length; j++) {
127
- m[header[j]] = lst[j];
128
- }
129
- if (!m.chr1) return ["missing chr1"];
130
- if (m.chr1.toLowerCase().indexOf("chr") != 0) {
131
- m.chr1 = "chr" + m.chr1;
132
- }
133
- if (!m.chr2) return ["missing chr2"];
134
- if (m.chr2.toLowerCase().indexOf("chr") != 0) {
135
- m.chr2 = "chr" + m.chr2;
136
- }
137
- if (!m.position1) return ["missing position1"];
138
- let v = Number.parseInt(m.position1);
139
- if (Number.isNaN(v) || v <= 0) return ["position1 invalid value"];
140
- m.position1 = v;
141
- if (!m.position2) return ["missing position2"];
142
- v = Number.parseInt(m.position2);
143
- if (Number.isNaN(v) || v <= 0) return ["position2 invalid value"];
144
- m.position2 = v;
145
- if (m.reads1) {
146
- v = Number.parseInt(m.reads1);
147
- if (Number.isNaN(v)) return ["reads1 invalid value"];
148
- m.reads1 = v;
149
- }
150
- if (m.reads2) {
151
- v = Number.parseInt(m.reads2);
152
- if (Number.isNaN(v)) return ["reads2 invalid value"];
153
- m.reads2 = v;
154
- }
155
- return [null, m];
156
- }
157
- function hicparsestat(hic, j) {
158
- if (!j) return "cannot stat hic file";
159
- hic.normalization = j.normalization;
160
- hic.version = j.version;
161
- if (!j.Chromosomes) return "Chromosomes not found in file stat";
162
- if (!Array.isArray(j.chrorder)) return ".chrorder[] missing";
163
- if (j.chrorder.length == 0) return ".chrorder[] empty array";
164
- hic.chrorder = j.chrorder;
165
- if (!j["Base pair-delimited resolutions"]) return "Base pair-delimited resolutions not found in file stat";
166
- if (!Array.isArray(j["Base pair-delimited resolutions"])) return "Base pair-delimited resolutions should be array";
167
- hic.bpresolution = j["Base pair-delimited resolutions"];
168
- if (!j["Fragment-delimited resolutions"]) return "Fragment-delimited resolutions not found in file stat";
169
- if (!Array.isArray(j["Fragment-delimited resolutions"])) return "Fragment-delimited resolutions is not array";
170
- hic.fragresolution = j["Fragment-delimited resolutions"];
171
- const chrlst = [];
172
- for (const chr in j.Chromosomes) {
173
- chrlst.push(chr);
174
- }
175
- const [nochrcount, haschrcount] = contigNameNoChr2(hic.genome, chrlst);
176
- if (nochrcount + haschrcount == 0) return "chromosome names do not match with genome build";
177
- if (nochrcount > 0) {
178
- hic.nochr = true;
179
- for (let i = 0; i < hic.chrorder.length; i++) hic.chrorder[i] = "chr" + hic.chrorder[i];
180
- }
181
- hic.chrlst = [];
182
- for (const chr of hic.genome.majorchrorder) {
183
- const c2 = hic.nochr ? chr.replace("chr", "") : chr;
184
- if (chrlst.indexOf(c2) != -1) {
185
- hic.chrlst.push(chr);
186
- }
187
- }
188
- }
189
- function hicparsefragdata(items) {
190
- const id2coord = /* @__PURE__ */ new Map();
191
- let min = null, max;
192
- for (const i of items) {
193
- if (!i.rest || !i.rest[0]) {
194
- return ["items[].rest data problem"];
195
- }
196
- const id = Number.parseInt(i.rest[0]);
197
- if (Number.isNaN(id)) {
198
- return [i.start + "." + i.stop + " invalid fragment id: " + i.rest[0]];
199
- }
200
- id2coord.set(id, [i.start, i.stop]);
201
- if (min == null) {
202
- min = id;
203
- max = id;
204
- } else {
205
- min = Math.min(min, id);
206
- max = Math.max(max, id);
207
- }
208
- }
209
- return [null, id2coord, min, max];
210
- }
211
-
212
- export {
213
- hicParseFile,
214
- hicparsestat,
215
- hicparsefragdata
216
- };
217
- //# sourceMappingURL=chunk-VALBVQXS.js.map
@@ -1,444 +0,0 @@
1
- import {
2
- rehydrateFilter
3
- } from "./chunk-SKMFMGCD.js";
4
- import {
5
- getFilter,
6
- getSamplelstTW
7
- } from "./chunk-N5VBIEH5.js";
8
- import {
9
- importPlot
10
- } from "./chunk-FOXJTDTH.js";
11
- import {
12
- findParent,
13
- getFilterItemByTag
14
- } from "./chunk-UT6W4ZZL.js";
15
- import {
16
- StoreApi,
17
- StoreBase
18
- } from "./chunk-FYTZCTJC.js";
19
-
20
- // mass/store.ts
21
- var idPrefix = "_MASS_AUTOID_" + Math.random().toString().slice(-6);
22
- var id = 0;
23
- function getId() {
24
- return idPrefix + "_" + id++;
25
- }
26
- var navHeaderModes = /* @__PURE__ */ new Set([
27
- "with_tabs",
28
- // default, shows tabs cohort/charts/filter etc
29
- "hidden",
30
- // no header
31
- "search_only",
32
- // ?
33
- "hide_search",
34
- // ?
35
- "with_cohortHtmlSelect",
36
- // only show cohort toggle as <select>
37
- "only_buttons"
38
- ]);
39
- var defaultState = {
40
- nav: {
41
- header_mode: "with_tabs",
42
- activeTab: 0
43
- // -1 for no active tab and all closed
44
- },
45
- // will be ignored if there is no dataset termdb.selectCohort
46
- // or value will be set to match a filter node that has been tagged
47
- // as 'cohortfilter' in state.termfilter.filter
48
- activeCohort: 0,
49
- search: { isVisible: true },
50
- plots: [],
51
- termfilter: {
52
- filter: {
53
- type: "tvslst",
54
- in: true,
55
- join: "",
56
- lst: []
57
- }
58
- },
59
- reuse: {
60
- customTermQ: {
61
- byId: {},
62
- // non-dictionary terms do not have a term.id,
63
- // save by term.type + name?
64
- byName: {}
65
- }
66
- },
67
- groups: [],
68
- // element: {name=str, filter={}}, to show in Groups tab
69
- customTerms: [],
70
- // element: {name=str, term={}}, able to attach more attr to object if needed
71
- autoSave: true
72
- };
73
- var MassStore = class extends StoreBase {
74
- constructor(opts, api) {
75
- super(opts);
76
- // expected class-specific props
77
- this.defaultState = defaultState;
78
- this.app = opts.app;
79
- this.api = api;
80
- this.type = "store";
81
- this.state = this.copyMerge(this.toJson(defaultState), opts.state);
82
- this.prevGeneratedId = 0;
83
- }
84
- static {
85
- this.type = "store";
86
- }
87
- validateOpts(opts) {
88
- const s = opts.state;
89
- if (s.vocab.dslabel) {
90
- if (!s.vocab.genome) throw ".state[.vocab].genome missing";
91
- } else {
92
- if (!Array.isArray(s.vocab.terms)) throw "vocab.terms must be an array of objects";
93
- }
94
- return opts;
95
- }
96
- validateState() {
97
- if (!navHeaderModes.has(this.state.nav.header_mode)) throw "invalid state.nav.header_mode";
98
- }
99
- async init() {
100
- try {
101
- this.state.termdbConfig = await this.app.vocabApi.getTermdbConfig();
102
- await this.setTermfilter();
103
- await this.rehydrateGroups();
104
- await this.app.vocabApi.main({
105
- termfilter: JSON.parse(JSON.stringify(this.state.termfilter)),
106
- termdbConfig: this.state.termdbConfig
107
- });
108
- const invalidPlots = [];
109
- for (const [i, savedPlot] of this.state.plots.entries()) {
110
- let plot;
111
- try {
112
- const _ = await importPlot(savedPlot.chartType);
113
- plot = await _.getPlotConfig(savedPlot, this.app, this.state.activeCohort);
114
- } catch (e) {
115
- this.app.printError(e);
116
- console.error(`getPlotConfig() failed: ${e}`);
117
- }
118
- if (!plot) {
119
- invalidPlots.push(i);
120
- continue;
121
- }
122
- this.state.plots[i] = plot;
123
- if (!("id" in plot)) plot.id = `_AUTOID_${id++}_${i}`;
124
- if (plot.mayAdjustConfig) plot.mayAdjustConfig(plot);
125
- }
126
- if (invalidPlots.length) {
127
- for (const i of invalidPlots) {
128
- this.state.plots.splice(i, 1);
129
- }
130
- }
131
- } catch (e) {
132
- console.log("store.init() error", e);
133
- throw e;
134
- }
135
- }
136
- setId(item) {
137
- item.$id = this.prevGeneratedId++;
138
- if (item.$lst) {
139
- for (const subitem of item.$lst) {
140
- this.setId(subitem);
141
- }
142
- }
143
- }
144
- async setTermfilter() {
145
- let filterUiRoot = getFilterItemByTag(this.state.termfilter.filter, "filterUiRoot");
146
- if (!filterUiRoot) {
147
- this.state.termfilter.filter.tag = "filterUiRoot";
148
- filterUiRoot = this.state.termfilter.filter;
149
- }
150
- await Promise.all(rehydrateFilter(this.state.termfilter.filter, this.app.vocabApi));
151
- if (!this.state.termdbConfig.selectCohort) {
152
- this.state.activeCohort = -1;
153
- if (this.state.activeTab === 0) this.state.activeTab = 1;
154
- if (this.state.nav.header_mode === "with_cohortHtmlSelect") {
155
- console.warn(`no termdbConfig.selectCohort to use for nav.header_mode = 'with_cohortHtmlSelect'`);
156
- this.state.nav.header_mode = "search_only";
157
- }
158
- } else {
159
- let cohortFilter = getFilterItemByTag(this.state.termfilter.filter, "cohortFilter");
160
- if (!cohortFilter) {
161
- cohortFilter = {
162
- tag: "cohortFilter",
163
- type: "tvs",
164
- tvs: {
165
- term: JSON.parse(JSON.stringify(this.state.termdbConfig.selectCohort.term)),
166
- values: this.state.activeCohort == -1 ? [] : this.state.termdbConfig.selectCohort.values[this.state.activeCohort].keys.map((key) => {
167
- return { key, label: key };
168
- })
169
- }
170
- };
171
- this.state.termfilter.filter = {
172
- type: "tvslst",
173
- in: true,
174
- join: "and",
175
- lst: [cohortFilter, filterUiRoot]
176
- };
177
- } else {
178
- const sorter = (a, b) => a < b ? -1 : 1;
179
- cohortFilter.tvs.values.sort((a, b) => a.key < b.key ? -1 : 1);
180
- const keysStr = JSON.stringify(cohortFilter.tvs.values.map((v) => v.key).sort(sorter));
181
- const i = this.state.termdbConfig.selectCohort.values.findIndex(
182
- (v) => keysStr == JSON.stringify(v.keys.sort(sorter))
183
- );
184
- if (this.state.activeCohort !== -1 && this.state.activeCohort !== 0 && i !== this.state.activeCohort) {
185
- console.log("Warning: cohortFilter will override the state.activeCohort due to mismatch");
186
- }
187
- this.state.activeCohort = i;
188
- }
189
- }
190
- }
191
- async rehydrateGroups() {
192
- const lst = [];
193
- for (const g of this.state.groups) {
194
- lst.push(...rehydrateFilter(g.filter, this.app.vocabApi));
195
- }
196
- await Promise.all(lst);
197
- }
198
- };
199
- MassStore.prototype.actions = {
200
- // Type '{ app_refresh(this: MassStore, action?: {}): Promise<void>; tab_set(action: any): void; cohort_set(action: any): void; plot_prep(action: any): Promise<void>; ... 13 more ...; delete_group({ name }: { ...; }): void; }' is not assignable to type '(action: { [prop: string]: any; type: string; }) => void | Promise<void>'.
201
- // Object literal may only specify known properties, and 'app_refresh' does not exist in type '(action: { [prop: string]: any; type: string; }) => void | Promise<void>'.
202
- async app_refresh(action) {
203
- this.state = this.copyMerge(this.toJson(this.state), action.state || {});
204
- const subactionPlotIds = /* @__PURE__ */ new Set();
205
- const promises = [];
206
- if (action.subactions) {
207
- for (const a of action.subactions) {
208
- promises.push(this.actions[a.type].call(this, a));
209
- if (a.type.startsWith("plot_")) subactionPlotIds.add(a.id);
210
- }
211
- }
212
- await Promise.all(promises);
213
- for (const plot of this.state.plots) {
214
- if (plot.mayAdjustConfig && !subactionPlotIds.has(plot.id)) {
215
- plot.mayAdjustConfig(plot, action.config);
216
- }
217
- }
218
- },
219
- tab_set(action) {
220
- this.state.nav.activeTab = action.activeTab;
221
- },
222
- cohort_set(action) {
223
- this.state.activeCohort = action.activeCohort;
224
- const cohort = this.state.termdbConfig.selectCohort.values[action.activeCohort];
225
- const cohortFilter = getFilterItemByTag(this.state.termfilter.filter, "cohortFilter");
226
- if (!cohortFilter) throw `No item tagged with 'cohortFilter'`;
227
- cohortFilter.tvs.values = cohort.keys.map((key) => {
228
- return { key, label: key };
229
- });
230
- },
231
- // dispatch "plot_prep" action to produce a 'initiating' UI of this plot, for user to fill in additional details to launch the plot
232
- // example: table, scatterplot which requires user to select two terms
233
- async plot_prep(action) {
234
- const plot = {
235
- id: "id" in action ? action.id : getId()
236
- };
237
- if (!action.config) throw ".config{} missing for plot_prep";
238
- if (action.config.chartType && Object.keys(action.config).length == 1) {
239
- const _ = await importPlot(action.config.chartType);
240
- const config = await _.getPlotConfig(action.config, this.app, this.state.activeCohort);
241
- action.config = Object.assign(config, action.config);
242
- }
243
- Object.assign(plot, action.config);
244
- this.state.plots.push(plot);
245
- },
246
- async plot_create(action) {
247
- const _ = await importPlot(action.config.chartType);
248
- const plot = await _.getPlotConfig(action.config, this.app, this.state.activeCohort);
249
- if (!("id" in action)) action.id = getId();
250
- plot.id = action.id;
251
- if (plot.mayAdjustConfig) {
252
- plot.mayAdjustConfig(plot, action.config);
253
- }
254
- this.state.plots.push(plot);
255
- if (plot.sections) {
256
- for (const section of plot.sections) {
257
- for (const p of section.plots) {
258
- p.parentId = plot.id;
259
- if (!p.id) p.id = getId();
260
- const _2 = await importPlot(p.chartType);
261
- const config = await _2.getPlotConfig(p, this.app, this.state.activeCohort);
262
- this.state.plots.push(config);
263
- }
264
- }
265
- }
266
- },
267
- plot_edit(action) {
268
- const plot = this.state.plots.find((p) => p.id === action.id);
269
- if (!plot) throw `missing plot id='${action.id}' in store.plot_edit()`;
270
- this.copyMerge(plot, action.config, action.opts ? action.opts : {});
271
- if (plot.mayAdjustConfig) {
272
- plot.mayAdjustConfig(plot, action.config);
273
- }
274
- if (action.config && "cutoff" in action.config) {
275
- plot.cutoff = action.config.cutoff;
276
- } else {
277
- delete plot.cutoff;
278
- }
279
- if (!action.parentId && plot.parentId) action.parentId = plot.parentId;
280
- },
281
- plot_delete(action) {
282
- const i = this.state.plots.findIndex((p) => p.id === action.id);
283
- if (i !== -1) {
284
- this.state.plots.splice(i, 1);
285
- const plot = this.state.plots[i];
286
- if (!action.parentId && plot?.parentId) action.parentId = plot.parentId;
287
- }
288
- },
289
- plot_nestedEdits(action) {
290
- const plot = this.state.plots.find((p) => p.id === action.id);
291
- if (!plot) throw `missing plot id='${action.id}' in store.plot_edit_nested`;
292
- for (const edit of action.edits) {
293
- const lastKey = edit.nestedKeys.pop();
294
- const obj = edit.nestedKeys.reduce((obj2, key) => obj2[key], plot);
295
- obj[lastKey] = edit.value;
296
- }
297
- if (!action.parentId && plot.parentId) action.parentId = plot.parentId;
298
- },
299
- // TODO: delete this action? does not seem to be used
300
- async plot_splice(action) {
301
- for (const a of action.subactions) {
302
- await this.actions[a.type].call(this, a);
303
- }
304
- },
305
- filter_replace(action) {
306
- if ("filter0" in action) {
307
- this.state.termfilter.filter0 = action.filter0;
308
- return;
309
- }
310
- const replacementFilter = action.filter ? action.filter : { type: "tvslst", join: "", in: 1, lst: [] };
311
- if (!action.filter.tag) {
312
- this.state.termfilter.filter = replacementFilter;
313
- } else {
314
- const filter = getFilterItemByTag(this.state.termfilter.filter, action.filter.tag);
315
- if (!filter) throw `cannot replace missing filter with tag '${action.filter.tag}'`;
316
- const parent = findParent(this.state.termfilter.filter, filter.$id);
317
- if (parent == filter) {
318
- this.state.termfilter.filter = replacementFilter;
319
- } else {
320
- const i = parent.lst.indexOf(filter);
321
- parent.lst[i] = replacementFilter;
322
- }
323
- }
324
- if (this.app.opts.app?.onFilterChange) this.app.opts.app.onFilterChange(this.state.plots);
325
- },
326
- cache_termq({ termId, q }) {
327
- if (!termId) throw `missing termId for caching custom term.q`;
328
- if (!q?.reuseId) throw `missing or empty tw.q.reuseId as cache identifier for term='${termId}'`;
329
- const cache = this.state.reuse.customTermQ.byId;
330
- if (!cache[termId]) cache[termId] = {};
331
- cache[termId][q.reuseId] = q;
332
- for (const plot of this.state.plots) {
333
- if (!(plot.chartType in getTwsByChartType)) continue;
334
- const twlst = getTwsByChartType[plot.chartType](plot);
335
- for (const tw of twlst) {
336
- if (tw?.q?.reuseId === q.reuseId) tw.q = q;
337
- }
338
- }
339
- },
340
- uncache_termq({ term, q }) {
341
- if (!term.id) throw `missing term.id for uncaching custom term.q`;
342
- if (!q.reuseId) throw `missing qname as uncache identifier for term.id='${term.id}'`;
343
- const cache = this.state.reuse.customTermQ.byId[term.id];
344
- if (!cache) throw `missing term.q cache for term.id='${term.id}`;
345
- if (!(q.reuseId in cache)) console.warn(`q.reuseId='${q.cacheid}' not cached for term.id='${term.id}'`);
346
- else {
347
- delete cache[q.reuseId];
348
- for (const plot of this.state.plots) {
349
- if (!(plot.chartType in getTwsByChartType)) continue;
350
- const twlst = getTwsByChartType[plot.chartType](plot);
351
- for (const tw of twlst) {
352
- if (tw.q.reuseId === q.reuseId) {
353
- delete tw.q.reuseId;
354
- delete tw.q.name;
355
- }
356
- }
357
- }
358
- }
359
- },
360
- add_customTerm(action) {
361
- this.state.customTerms.push(action.obj);
362
- },
363
- delete_customTerm({ name }) {
364
- const i = this.state.customTerms.findIndex((i2) => i2.name == name);
365
- if (i != -1) this.state.customTerms.splice(i, 1);
366
- },
367
- add_group(action) {
368
- if (this.state.nav.header_mode != "hidden") {
369
- const group = action.obj;
370
- const name = `Group ${this.state.groups.length + 1}`;
371
- const samplelstTW = getSamplelstTW([group]);
372
- const appGroup = {
373
- name,
374
- filter: getFilter(samplelstTW),
375
- plotId: group.plotId
376
- };
377
- this.state.groups.push(appGroup);
378
- this.state.nav.activeTab = 1;
379
- } else if ("plotId" in action.obj) {
380
- const plot = this.state.plots.find((p) => p.id == action.obj.plotId);
381
- if (plot.groups) {
382
- action.obj.index = plot.groups.length;
383
- action.obj.name = `Group ${plot.groups.length + 1}`;
384
- plot.groups.push(action.obj);
385
- }
386
- }
387
- },
388
- rename_group(action) {
389
- const index = action.index;
390
- const newName = action.newName;
391
- if (this.state.nav.header_mode != "hidden") {
392
- this.state.groups[index].name = newName;
393
- } else {
394
- for (const plot of this.state.plots) {
395
- if (plot?.groups) {
396
- plot.groups[index].name = newName;
397
- }
398
- }
399
- }
400
- },
401
- change_color_group(action) {
402
- const index = action.index;
403
- const newColor = action.newColor;
404
- if (this.state.nav.header_mode != "hidden") {
405
- this.state.groups[index].color = newColor;
406
- } else {
407
- for (const plot of this.state.plots) {
408
- if (plot?.groups) {
409
- plot.groups[index].color = newColor;
410
- }
411
- }
412
- }
413
- },
414
- delete_group({ name }) {
415
- if (this.state.nav.header_mode != "hidden") {
416
- const i = this.state.groups.findIndex((i2) => i2.name == name);
417
- if (i != -1) this.state.groups.splice(i, 1);
418
- } else {
419
- for (const plot of this.state.plots) {
420
- if (plot?.groups) {
421
- const j = plot.groups.findIndex((j2) => j2.name == name);
422
- if (j != -1) plot.groups.splice(j, 1);
423
- }
424
- }
425
- }
426
- }
427
- };
428
- var getNestedChartSeriesDataTws = (plot) => [plot.term0, plot.term, plot.term2].filter((d) => !!d);
429
- var getTwsByChartType = {
430
- summary: getNestedChartSeriesDataTws,
431
- survival: getNestedChartSeriesDataTws,
432
- cuminc: getNestedChartSeriesDataTws,
433
- regression: (plot) => [plot.outcome, ...plot.independent].filter((d) => !!d),
434
- matrix: (plot) => plot.termgroups.reduce((arr, grp) => {
435
- arr.push(...grp.lst);
436
- return arr;
437
- }, [])
438
- };
439
- var storeInit = StoreApi.getInitFxn(MassStore);
440
-
441
- export {
442
- storeInit
443
- };
444
- //# sourceMappingURL=chunk-VDR5JXI2.js.map