@sjcrh/proteinpaint-client 2.211.0 → 2.212.0

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 (883) hide show
  1. package/dist/2dmaf-R23YQDZC.js +1367 -0
  2. package/dist/AggMatrixInput-4DIGZZN4.js +406 -0
  3. package/dist/AggregateMatrix-TF6XXFUN.js +41 -0
  4. package/dist/AppHeader-JB5HPAOQ.js +830 -0
  5. package/dist/BoxPlot-47TUXQDP.js +1208 -0
  6. package/dist/CorrelationVolcano-G7K5JEPM.js +617 -0
  7. package/dist/Cuminc-LBXPOENU.js +1220 -0
  8. package/dist/Cuminc-LBXPOENU.js.map +7 -0
  9. package/dist/DE-JSWA6HXV.js +89 -0
  10. package/dist/DEinput-LEYRVYK6.js +501 -0
  11. package/dist/DM-332QECUP.js +90 -0
  12. package/dist/DifferentialAnalysis-JGH2OMTH.js +239 -0
  13. package/dist/Disco-36PJXFM6.js +3389 -0
  14. package/dist/Disco.UI-PY2KOGKY.js +243 -0
  15. package/dist/DmrPlot-5WMOBZOJ.js +362 -0
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  17. package/dist/GSEA-GYUVO2XA.js +875 -0
  18. package/dist/GeneExpInput-UABEICGS.js +42 -0
  19. package/dist/Geomap-QB6FNV5R.js +84 -0
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  21. package/dist/IDCViewer-L27ICGR5.js +10812 -0
  22. package/dist/NumBinaryEditor-FHSSXZV4.js +279 -0
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  38. package/dist/ProteomeInput-OS5JWC2O.js +388 -0
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  148. package/dist/cohort-CWGZR37O.js +70 -0
  149. package/dist/condition-B6XBQML4.js +327 -0
  150. package/dist/controls-QPW5HUAY.js +34 -0
  151. package/dist/controls.config-IUYTWRHA.js +34 -0
  152. package/dist/correlation-M2NKGTK2.js +95 -0
  153. package/dist/customdata.inputui-RKYIMOWO.js +284 -0
  154. package/dist/dataDownload-LPBLB7QD.js +329 -0
  155. package/dist/databrowser.ui-VTWHELDY.js +425 -0
  156. package/dist/dictionary-NINKMF3F.js +113 -0
  157. package/dist/dnaMethylation-LSVNG7FK.js +33 -0
  158. package/dist/dnaMethylation.integration.spec-6IT3Y3FS.js +198 -0
  159. package/dist/dofetch-HLMSTOMY.js +48 -0
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  161. package/dist/ep-3RFB6K3B.js +1249 -0
  162. package/dist/expclust.gdc.spec-MEWKHFMD.js +302 -0
  163. package/dist/facet-A4JH7FCW.js +519 -0
  164. package/dist/gb-PTF7CLDG.js +81 -0
  165. package/dist/geneExpClustering-VKUIAYCK.js +244 -0
  166. package/dist/geneExpression-3GQFWVJL.js +310 -0
  167. package/dist/geneExpression-VC7QPM3T.js +33 -0
  168. package/dist/geneExpression.unit.spec-PQS7BOMF.js +128 -0
  169. package/dist/geneORA-FCMFWZTN.js +273 -0
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  171. package/dist/geneVariant-2TQ2JD4K.js +36 -0
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  174. package/dist/genefusion.ui-P7YH32A6.js +303 -0
  175. package/dist/geneset-4J43JA3C.js +203 -0
  176. package/dist/genomeBrowser.spec-T2VFNUAV.js +276 -0
  177. package/dist/grin2-5TH4EBVQ.js +949 -0
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  193. package/dist/lollipop-GMGJPMJN.js +166 -0
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  231. package/dist/proteinView-TTLVQ43H.js +1357 -0
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  812. /package/dist/{plot.vaf2cov-CID7GQB5.js.map → plot.vaf2cov-IF4DEEM5.js.map} +0 -0
  813. /package/dist/{polar2-QTSO2HCB.js.map → polar2-QQ3KHFME.js.map} +0 -0
  814. /package/dist/{profileForms-SRR2M5OS.js.map → profileForms-2US7IYYM.js.map} +0 -0
  815. /package/dist/{profilePlot-NDC4S2SC.js.map → profilePlot-DZQCBKPA.js.map} +0 -0
  816. /package/dist/{proteinView-EFNQL3LD.js.map → proteinView-TTLVQ43H.js.map} +0 -0
  817. /package/dist/{proteomeCohortCompare-WMR53HEL.js.map → proteomeCohortCompare-BUZYOOIA.js.map} +0 -0
  818. /package/dist/{pseudbulk.unit.spec-6MRZNXFI.js.map → pseudbulk.unit.spec-YNXQWDSU.js.map} +0 -0
  819. /package/dist/{pseudobulk-O5EC44RY.js.map → pseudobulk-VSXK2PTM.js.map} +0 -0
  820. /package/dist/{qualitative-W6MFYG7Z.js.map → qualitative-AKIZRNFO.js.map} +0 -0
  821. /package/dist/{radar2-GIQILMWK.js.map → radar2-7GXYLICJ.js.map} +0 -0
  822. /package/dist/{radarFacility2-5YJZ5JCK.js.map → radarFacility2-WFKOWGH2.js.map} +0 -0
  823. /package/dist/{render-2J4LR3UI.js.map → render-F3CBMRD5.js.map} +0 -0
  824. /package/dist/{report-MUMQK6XY.js.map → report-6LHMHUDY.js.map} +0 -0
  825. /package/dist/{sampleView-NKZMNBMH.js.map → sampleView-GWKPMVJH.js.map} +0 -0
  826. /package/dist/{samplelst-X74JZMTR.js.map → samplelst-TH6IBDVG.js.map} +0 -0
  827. /package/dist/{samplematrix-QDQXB5ZG.js.map → samplematrix-RPCWT33H.js.map} +0 -0
  828. /package/dist/{sc-FGHV5CBJ.js.map → sc-BFBHBAXF.js.map} +0 -0
  829. /package/dist/{scatter-QFVRBA7F.js.map → scatter-3IC6HOT7.js.map} +0 -0
  830. /package/dist/{scatter-YXF5VQGZ.js.map → scatter-L6R6J2LC.js.map} +0 -0
  831. /package/dist/{selectGenomeWithTklst-DP4RPV7U.js.map → selectGenomeWithTklst-3ZK7FIOP.js.map} +0 -0
  832. /package/dist/{singleCellCellType-XCHCMRR6.js.map → singleCellCellType-CLJFCBV6.js.map} +0 -0
  833. /package/dist/{singleCellCellType.unit.spec-S3JTP235.js.map → singleCellCellType.unit.spec-W32PSTRO.js.map} +0 -0
  834. /package/dist/{singleCellGeneExpression-FD6REV7Y.js.map → singleCellGeneExpression-L6MG37XE.js.map} +0 -0
  835. /package/dist/{singleCellGeneExpression.unit.spec-PVMZYD4G.js.map → singleCellGeneExpression.unit.spec-SF46JHCU.js.map} +0 -0
  836. /package/dist/{singleCellNumericValue-SIITQPMD.js.map → singleCellNumericValue-7QXK6KVZ.js.map} +0 -0
  837. /package/dist/{singleCellNumericValue.unit.spec-7PJEHLF7.js.map → singleCellNumericValue.unit.spec-VC7NQYM2.js.map} +0 -0
  838. /package/dist/{singleCellPlot-YJCFAYJW.js.map → singleCellPlot-5TRNRKPN.js.map} +0 -0
  839. /package/dist/{singlecell-6R7YK5P3.js.map → singlecell-2YV3UAIQ.js.map} +0 -0
  840. /package/dist/{singlecell-KHMH732Y.js.map → singlecell-I4PHM2LZ.js.map} +0 -0
  841. /package/dist/{snp-HXCVSW2F.js.map → snp-ZIA4YWCZ.js.map} +0 -0
  842. /package/dist/{snp.unit.spec-HXMFR4QS.js.map → snp.unit.spec-MVQHY4WJ.js.map} +0 -0
  843. /package/dist/{snplocus-YQVHAKBC.js.map → snplocus-GM6IEDPR.js.map} +0 -0
  844. /package/dist/{spliceevent.a53ss.diagram-4IBTR3JD.js.map → spliceevent.a53ss.diagram-ZFQDHHPY.js.map} +0 -0
  845. /package/dist/{spliceevent.exonskip.diagram-5ZTG65CE.js.map → spliceevent.exonskip.diagram-ZK6JOUMU.js.map} +0 -0
  846. /package/dist/{spliceevent.noeventdiagram-WO5KSC45.js.map → spliceevent.noeventdiagram-YKTF2VZE.js.map} +0 -0
  847. /package/dist/{ssGSEA-VJ3LVYJV.js.map → ssGSEA-FDN4CH2Y.js.map} +0 -0
  848. /package/dist/{ssGSEA.unit.spec-JQIJ4NZP.js.map → ssGSEA.unit.spec-YEUJBT6Z.js.map} +0 -0
  849. /package/dist/{stattable-COVQSHRZ.js.map → stattable-WIZRSKPH.js.map} +0 -0
  850. /package/dist/{studyCatalog-EXVRH4FI.js.map → studyCatalog-X2IGVJ26.js.map} +0 -0
  851. /package/dist/{summarizeCnvGeneexp-UJBTMXXH.js.map → summarizeCnvGeneexp-H7A5SI3R.js.map} +0 -0
  852. /package/dist/{summarizeGeneexpSurvival-XLQJGDRY.js.map → summarizeGeneexpSurvival-GJF6VD2S.js.map} +0 -0
  853. /package/dist/{summarizeMutationCnv-7RWSXB6F.js.map → summarizeMutationCnv-WQLMD2TR.js.map} +0 -0
  854. /package/dist/{summarizeMutationDiagnosis-42MG737O.js.map → summarizeMutationDiagnosis-3S52IDWF.js.map} +0 -0
  855. /package/dist/{summarizeMutationSurvival-FWVKVEHK.js.map → summarizeMutationSurvival-NTQIUNW7.js.map} +0 -0
  856. /package/dist/{summary-NR26ZPQB.js.map → summary-LMRFRKKI.js.map} +0 -0
  857. /package/dist/{summary.integration.spec-Z7JSUTGK.js.map → summary.integration.spec-KQMZKSEQ.js.map} +0 -0
  858. /package/dist/{summaryInput-DGKUOJVC.js.map → summaryInput-NNHZVHQA.js.map} +0 -0
  859. /package/dist/{sunburst-C5JNGFT7.js.map → sunburst-ICUSGIWV.js.map} +0 -0
  860. /package/dist/{survival-GCEX3EAZ.js.map → survival-K5YBNNVE.js.map} +0 -0
  861. /package/dist/{survival.integration.spec-ZX5RD6VQ.js.map → survival.integration.spec-4LRJW2V2.js.map} +0 -0
  862. /package/dist/{svgraph-XCFZ2WAG.js.map → svgraph-U7MS7YEM.js.map} +0 -0
  863. /package/dist/{svmr-4XTTURHA.js.map → svmr-2JGDBPAI.js.map} +0 -0
  864. /package/dist/{table-FQZ4UAH6.js.map → table-CBWOHYW6.js.map} +0 -0
  865. /package/dist/{termCollection-DN6A6HJU.js.map → termCollection-JFGGXVFI.js.map} +0 -0
  866. /package/dist/{termCollection-5QCR6LED.js.map → termCollection-VE3FFL6V.js.map} +0 -0
  867. /package/dist/{termCollection.unit.spec-RSSSXDHU.js.map → termCollection.unit.spec-XQQTDV4A.js.map} +0 -0
  868. /package/dist/{termCollectionFractionSelection-OSN7FITY.js.map → termCollectionFractionSelection-TFGF27GR.js.map} +0 -0
  869. /package/dist/{termCollectionFractionSelection.unit.spec-UW6D3DVK.js.map → termCollectionFractionSelection.unit.spec-MKGG4JBC.js.map} +0 -0
  870. /package/dist/{tk-4CZCVYBP.js.map → tk-74SGUUZY.js.map} +0 -0
  871. /package/dist/{tk-BIPJNXBZ.js.map → tk-K4JFYIZY.js.map} +0 -0
  872. /package/dist/{tp.ui-NI4U7567.js.map → tp.ui-727EXXMT.js.map} +0 -0
  873. /package/dist/{tvs.dt-YRDNDXUU.js.map → tvs.dt-YB2C3T33.js.map} +0 -0
  874. /package/dist/{tvs.dtcnv.categorical-REP4T33P.js.map → tvs.dtcnv.categorical-NOWMZOE5.js.map} +0 -0
  875. /package/dist/{tvs.dtcnv.continuous-K7OREEP5.js.map → tvs.dtcnv.continuous-3KWUNU76.js.map} +0 -0
  876. /package/dist/{tvs.dtfusion-AB5MPH3Q.js.map → tvs.dtfusion-NOJSTABU.js.map} +0 -0
  877. /package/dist/{tvs.dtitd-AFWU7ACY.js.map → tvs.dtitd-OD5B377P.js.map} +0 -0
  878. /package/dist/{tvs.dtsnvindel-G7XQEKEO.js.map → tvs.dtsnvindel-WIQMZTRH.js.map} +0 -0
  879. /package/dist/{tvs.dtsv-Y6BEY4J2.js.map → tvs.dtsv-HPERDN3R.js.map} +0 -0
  880. /package/dist/{tvs.samplelst-XRRWPC2E.js.map → tvs.samplelst-TC2Z7Z35.js.map} +0 -0
  881. /package/dist/{tvs.termCollection-PL4AN3GA.js.map → tvs.termCollection-F64BHWAL.js.map} +0 -0
  882. /package/dist/{vocabulary-DJZWOO6Q.js.map → vocabulary-ZOYF2VHS.js.map} +0 -0
  883. /package/dist/{wsi.direct-XUWANMKV.js.map → wsi.direct-Z5YUZEXG.js.map} +0 -0
@@ -1,56 +0,0 @@
1
- import {
2
- sayerror
3
- } from "./chunk-K7HFOAR7.js";
4
- import {
5
- TermTypeGroups
6
- } from "./chunk-57Z4VYLM.js";
7
-
8
- // termdb/handlers/singleCellCellType.ts
9
- var SearchHandler = class {
10
- async init(opts) {
11
- this.validateOpts(opts);
12
- this.callback = opts.callback;
13
- this.app = opts.app;
14
- const holder = opts.holder.append("div").style("padding", "10px 0px");
15
- const scctTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.SINGLECELL_CELLTYPE];
16
- if (!scctTerms?.length) {
17
- sayerror(
18
- holder,
19
- `termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`
20
- );
21
- return;
22
- }
23
- const usecaseConfig = opts.usecase?.specialCase?.config;
24
- const plots = usecaseConfig?.sample?.plots;
25
- const isMeta = usecaseConfig?.sample?.isMetaResult;
26
- const filtered = plots ? scctTerms.filter((t) => plots.includes(t.plot)) : usecaseConfig?.name ? scctTerms.filter((t) => t.plot === usecaseConfig.name) : scctTerms;
27
- const getLabel = (t) => isMeta || plots?.length == 1 ? t.name : `${t.name} (${t.plot})`;
28
- const filteredTerms = new Set(
29
- plots || !usecaseConfig?.name ? filtered.map((t) => ({ ...t, label: getLabel(t) })) : filtered
30
- );
31
- for (const t of Array.from(filteredTerms)) {
32
- holder.append("div").classed("termdiv", true).style("padding", "0px 5px").append("div").classed("termlabel sja_filter_tag_btn sja_tree_click_term ts_pill", true).style("display", "inline-block").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text(t.label || t.name).on("click", () => {
33
- const term = this.makeTerm(t, usecaseConfig);
34
- this.callback(term);
35
- });
36
- }
37
- }
38
- makeTerm(_term, usecaseConfig) {
39
- const term = { ..._term };
40
- if (!term.sample && usecaseConfig?.sample) term.sample = usecaseConfig.sample;
41
- return term;
42
- }
43
- validateOpts(opts) {
44
- if (opts.callback == null) throw new Error("callback is required");
45
- if (opts.app == null) throw new Error("app is required");
46
- if (opts.holder == null) throw new Error("holder is required");
47
- if (opts.usecase == null) throw new Error("usecase is required");
48
- if (!opts.app.vocabApi.termdbConfig?.termType2terms)
49
- throw new Error("termType2terms is required in termdbConfig for singleCellCellType handler");
50
- }
51
- };
52
-
53
- export {
54
- SearchHandler
55
- };
56
- //# sourceMappingURL=chunk-UZNFOCE7.js.map
@@ -1,550 +0,0 @@
1
- import {
2
- rehydrateFilter
3
- } from "./chunk-SKMFMGCD.js";
4
- import {
5
- findParent,
6
- getFilter,
7
- getFilterItemByTag,
8
- getGvQLabel,
9
- getSamplelstTW,
10
- isCustomizedGvQ
11
- } from "./chunk-K7HFOAR7.js";
12
- import {
13
- importPlot
14
- } from "./chunk-FSWBNSQD.js";
15
- import {
16
- forEachGvTw,
17
- getGvQCacheKey,
18
- gvQCacheKeyPrefix,
19
- trimGvQForCache
20
- } from "./chunk-CME6DYDH.js";
21
- import {
22
- StoreApi,
23
- StoreBase,
24
- deepEqual
25
- } from "./chunk-WINIL2KN.js";
26
- import {
27
- CustomError
28
- } from "./chunk-W5J3LTYS.js";
29
-
30
- // mass/store.ts
31
- var idPrefix = "_MASS_AUTOID_" + Math.random().toString().slice(-6);
32
- var id = 0;
33
- var usedPlotIds = /* @__PURE__ */ new Set();
34
- function getId() {
35
- return idPrefix + "_" + id++;
36
- }
37
- var navHeaderModes = /* @__PURE__ */ new Set([
38
- "with_tabs",
39
- // default, shows tabs cohort/charts/filter etc
40
- "hidden",
41
- // no header
42
- "search_only",
43
- // ?
44
- "hide_search",
45
- // ?
46
- "with_cohortHtmlSelect",
47
- // only show cohort toggle as <select>
48
- "only_buttons"
49
- ]);
50
- var defaultState = {
51
- nav: {
52
- header_mode: "with_tabs",
53
- activeTab: 0
54
- // -1 for no active tab and all closed
55
- },
56
- // will be ignored if there is no dataset termdb.selectCohort
57
- // or value will be set to match a filter node that has been tagged
58
- // as 'cohortfilter' in state.termfilter.filter
59
- activeCohort: 0,
60
- search: { isVisible: true },
61
- plots: [],
62
- termfilter: {
63
- filter: {
64
- type: "tvslst",
65
- in: true,
66
- join: "",
67
- lst: []
68
- }
69
- },
70
- reuse: {
71
- /* settings a user has built for a geneVariant term, keyed by gene(s) and most recent
72
- first, so that a term built later for the same gene can offer them, see remember_gvq().
73
- Filled as a side effect of building one, unlike the removed Reuse menu that required the
74
- user to save a setting by hand before it could be reused, and seeded from the settings
75
- the opened plots already carry, see seedGvQCache().
76
-
77
- Has to stay a plain object, since state.reuse is serialized into saved sessions, while
78
- it is keyed by gene names a url or an embedder can supply. Both the reads and the writes
79
- below are therefore plain property access on a key that getGvQCacheKey() has prefixed
80
- out of the namespace of Object.prototype -- see there for what an unprefixed '__proto__'
81
- would do to a reopened session, and withMigratedGvQCache() for the incoming states that
82
- have to be normalized before they are merged. */
83
- gvQByGene: {}
84
- },
85
- groups: [],
86
- // element: {name=str, filter={}}, to show in Groups tab
87
- customTerms: [],
88
- // element: {name=str, term={}}, able to attach more attr to object if needed
89
- autoSave: true
90
- };
91
- var maxGvQPerGene = 5;
92
- var maxGvQGenes = 30;
93
- function withMigratedGvQCache(state) {
94
- const cache = state?.reuse?.gvQByGene;
95
- if (!cache || typeof cache != "object" || Array.isArray(cache)) return state;
96
- const migrated = {};
97
- for (const key of Object.getOwnPropertyNames(cache)) {
98
- const lst = Object.getOwnPropertyDescriptor(cache, key)?.value;
99
- if (!Array.isArray(lst)) continue;
100
- const migratedKey = key.startsWith(gvQCacheKeyPrefix) ? key : gvQCacheKeyPrefix + key;
101
- delete migrated[migratedKey];
102
- migrated[migratedKey] = lst.slice(0, maxGvQPerGene);
103
- }
104
- const keys = Object.keys(migrated);
105
- for (const key of keys.slice(0, keys.length - maxGvQGenes)) delete migrated[key];
106
- return { ...state, reuse: { ...state.reuse, gvQByGene: migrated } };
107
- }
108
- var MassStore = class extends StoreBase {
109
- constructor(opts, api) {
110
- super(opts);
111
- // expected class-specific props
112
- this.defaultState = defaultState;
113
- this.plotAdjusters = /* @__PURE__ */ new WeakMap();
114
- this.app = opts.app;
115
- this.api = api;
116
- this.type = "store";
117
- let savedState = {};
118
- try {
119
- const key = window.navigator.webdriver && window["SJPP_E2E_STORAGE_STATES_KEY"];
120
- const savedStateStr = key && window.localStorage.getItem("SJPP_E2E_STORAGE_STATES") || "{}";
121
- savedState = JSON.parse(savedStateStr)[key]?.state || {};
122
- } catch (_) {
123
- savedState = {};
124
- }
125
- this.state = this.copyMerge(
126
- this.toJson(defaultState),
127
- withMigratedGvQCache(opts.state),
128
- withMigratedGvQCache(savedState)
129
- );
130
- this.prevGeneratedId = 0;
131
- }
132
- static {
133
- this.type = "store";
134
- }
135
- validateOpts(opts) {
136
- const s = opts.state;
137
- if (s.vocab.dslabel) {
138
- if (!s.vocab.genome) throw ".state[.vocab].genome missing";
139
- } else {
140
- if (!Array.isArray(s.vocab.terms)) throw "vocab.terms must be an array of objects";
141
- }
142
- return opts;
143
- }
144
- validateState() {
145
- if (!navHeaderModes.has(this.state.nav.header_mode)) throw "invalid state.nav.header_mode";
146
- }
147
- async init() {
148
- try {
149
- this.state.termdbConfig = await this.app.vocabApi.getTermdbConfig();
150
- await this.setTermfilter();
151
- await this.rehydrateGroups();
152
- await this.app.vocabApi.main({
153
- termfilter: JSON.parse(JSON.stringify(this.state.termfilter)),
154
- termdbConfig: this.state.termdbConfig
155
- });
156
- const invalidPlots = [];
157
- for (const [i, savedPlot] of this.state.plots.entries()) {
158
- let plot;
159
- try {
160
- const _ = await importPlot(savedPlot.chartType);
161
- plot = await _.getPlotConfig(savedPlot, this.app, this.state.activeCohort);
162
- } catch (e) {
163
- this.app.printError(e);
164
- console.error(`getPlotConfig() failed: ${e}`);
165
- }
166
- if (!plot) {
167
- invalidPlots.push(i);
168
- continue;
169
- }
170
- this.state.plots[i] = plot;
171
- if (!("id" in plot)) plot.id = `_AUTOID_${id++}_${i}`;
172
- if (plot.mayAdjustConfig) {
173
- plot.mayAdjustConfig(plot);
174
- this.plotAdjusters.set(plot, plot.mayAdjustConfig);
175
- delete plot.mayAdjustConfig;
176
- }
177
- }
178
- if (invalidPlots.length) {
179
- for (const i of invalidPlots) {
180
- this.state.plots.splice(i, 1);
181
- }
182
- }
183
- this.seedGvQCache();
184
- } catch (e) {
185
- console.log("store.init() error", e);
186
- throw e;
187
- }
188
- }
189
- /*
190
- Remember the geneVariant settings that the plots this app opened with already carry, so
191
- that one supplied by a url, by an embedder, or by a session saved before these were
192
- remembered can be offered for a term built later, the same as one built by hand here.
193
- Without this, only the Apply button of the edit menu fills the cache, see remember_gvq().
194
-
195
- Appended rather than unshifted, and skipped when already remembered, since a setting that
196
- merely arrived in the opened state has no recency to claim over what a recovered session
197
- carries in state.reuse: the entries a user built stay in front, and the seeded ones follow
198
- in the order the plots list them.
199
-
200
- Neither cap evicts here for the same reason -- a remembered setting is never dropped to
201
- make room for a seeded one.
202
- */
203
- seedGvQCache() {
204
- const cache = this.state.reuse.gvQByGene;
205
- forEachGvTw(this.state.plots, ({ term, q }) => {
206
- if (!isCustomizedGvQ(q)) return;
207
- const key = getGvQCacheKey(term);
208
- if (!key) return;
209
- if (!cache[key]) {
210
- if (Object.keys(cache).length >= maxGvQGenes) return;
211
- cache[key] = [];
212
- }
213
- const lst = cache[key];
214
- if (lst.length >= maxGvQPerGene) return;
215
- const trimmed = trimGvQForCache(q);
216
- if (lst.some((entry) => deepEqual(entry.q, trimmed))) return;
217
- lst.push({ label: getGvQLabel(term, q), q: trimmed });
218
- });
219
- }
220
- setId(item) {
221
- item.$id = this.prevGeneratedId++;
222
- if (item.$lst) {
223
- for (const subitem of item.$lst) {
224
- this.setId(subitem);
225
- }
226
- }
227
- }
228
- async setTermfilter() {
229
- let filterUiRoot = getFilterItemByTag(this.state.termfilter.filter, "filterUiRoot");
230
- if (!filterUiRoot) {
231
- this.state.termfilter.filter.tag = "filterUiRoot";
232
- filterUiRoot = this.state.termfilter.filter;
233
- }
234
- await Promise.all(rehydrateFilter(this.state.termfilter.filter, this.app.vocabApi));
235
- if (!this.state.termdbConfig.selectCohort) {
236
- this.state.activeCohort = -1;
237
- if (this.state.activeTab === 0) this.state.activeTab = 1;
238
- if (this.state.nav.header_mode === "with_cohortHtmlSelect") {
239
- console.warn(`no termdbConfig.selectCohort to use for nav.header_mode = 'with_cohortHtmlSelect'`);
240
- this.state.nav.header_mode = "search_only";
241
- }
242
- } else {
243
- let cohortFilter = getFilterItemByTag(this.state.termfilter.filter, "cohortFilter");
244
- if (!cohortFilter) {
245
- cohortFilter = {
246
- tag: "cohortFilter",
247
- type: "tvs",
248
- tvs: {
249
- term: JSON.parse(JSON.stringify(this.state.termdbConfig.selectCohort.term)),
250
- values: this.state.activeCohort == -1 ? [] : this.state.termdbConfig.selectCohort.values[this.state.activeCohort].keys.map((key) => {
251
- return { key, label: key };
252
- })
253
- }
254
- };
255
- this.state.termfilter.filter = {
256
- type: "tvslst",
257
- in: true,
258
- join: "and",
259
- lst: [cohortFilter, filterUiRoot]
260
- };
261
- } else {
262
- const sorter = (a, b) => a < b ? -1 : 1;
263
- cohortFilter.tvs.values.sort((a, b) => a.key < b.key ? -1 : 1);
264
- const keysStr = JSON.stringify(cohortFilter.tvs.values.map((v) => v.key).sort(sorter));
265
- const i = this.state.termdbConfig.selectCohort.values.findIndex(
266
- (v) => keysStr == JSON.stringify(v.keys.sort(sorter))
267
- );
268
- if (this.state.activeCohort !== -1 && this.state.activeCohort !== 0 && i !== this.state.activeCohort) {
269
- console.log("Warning: cohortFilter will override the state.activeCohort due to mismatch");
270
- }
271
- this.state.activeCohort = i;
272
- }
273
- }
274
- }
275
- async rehydrateGroups() {
276
- const lst = [];
277
- for (const g of this.state.groups) {
278
- lst.push(...rehydrateFilter(g.filter, this.app.vocabApi));
279
- }
280
- await Promise.all(lst);
281
- }
282
- };
283
- MassStore.prototype.actions = {
284
- // 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>'.
285
- // Object literal may only specify known properties, and 'app_refresh' does not exist in type '(action: { [prop: string]: any; type: string; }) => void | Promise<void>'.
286
- async app_refresh(action) {
287
- this.state = this.copyMerge(this.toJson(this.state), withMigratedGvQCache(action.state || {}));
288
- const subactionPlotIds = /* @__PURE__ */ new Set();
289
- const promises = [];
290
- if (action.subactions) {
291
- for (const a of action.subactions) {
292
- promises.push(this.actions[a.type].call(this, a));
293
- if (a.type.startsWith("plot_")) subactionPlotIds.add(a.id);
294
- }
295
- }
296
- await Promise.all(promises);
297
- for (const plot of this.state.plots) {
298
- const mayAdjustConfig = this.plotAdjusters.get(plot);
299
- if (mayAdjustConfig && !subactionPlotIds.has(plot.id)) {
300
- mayAdjustConfig(plot, action.config);
301
- }
302
- }
303
- },
304
- tab_set(action) {
305
- this.state.nav.activeTab = action.activeTab;
306
- },
307
- cohort_set(action) {
308
- this.state.activeCohort = action.activeCohort;
309
- const cohort = this.state.termdbConfig.selectCohort.values[action.activeCohort];
310
- const cohortFilter = getFilterItemByTag(this.state.termfilter.filter, "cohortFilter");
311
- if (!cohortFilter) throw `No item tagged with 'cohortFilter'`;
312
- cohortFilter.tvs.values = cohort.keys.map((key) => {
313
- return { key, label: key };
314
- });
315
- },
316
- // dispatch "plot_prep" action to produce a 'initiating' UI of this plot, for user to fill in additional details to launch the plot
317
- // example: table, scatterplot which requires user to select two terms
318
- async plot_prep(action) {
319
- if (usedPlotIds.has(action.id)) delete action.id;
320
- const plot = {
321
- // rx.getComponents() relies on parsing dot-separated key names that breaks if a key has a dot,
322
- // the plot.id value should be assumed to be auto-generated and to not have any non-rx usage expectations
323
- id: "id" in action && !action.id.includes(".") ? action.id : getId()
324
- };
325
- usedPlotIds.add(plot.id);
326
- if (!action.config) throw ".config{} missing for plot_prep";
327
- if (action.config.chartType && Object.keys(action.config).length == 1) {
328
- const _ = await importPlot(action.config.chartType);
329
- const config = await _.getPlotConfig(action.config, this.app, this.state.activeCohort);
330
- action.config = Object.assign(config, action.config);
331
- }
332
- Object.assign(plot, action.config);
333
- this.state.plots.push(plot);
334
- },
335
- async plot_create(action) {
336
- if (usedPlotIds.has(action.id)) delete action.id;
337
- const _ = await importPlot(action.config.chartType);
338
- const plot = await _.getPlotConfig(action.config, this.app, this.state.activeCohort);
339
- if (!("id" in action) || action.id.includes(".")) action.id = getId();
340
- plot.id = action.id;
341
- usedPlotIds.add(plot.id);
342
- if (plot.mayAdjustConfig) {
343
- plot.mayAdjustConfig(plot);
344
- this.plotAdjusters.set(plot, plot.mayAdjustConfig);
345
- delete plot.mayAdjustConfig;
346
- }
347
- this.state.plots.push(plot);
348
- if (plot.sections) {
349
- for (const section of plot.sections) {
350
- for (const p of section.plots) {
351
- p.parentId = plot.id;
352
- if (!p.id) p.id = getId();
353
- const _2 = await importPlot(p.chartType);
354
- const config = await _2.getPlotConfig(p, this.app, this.state.activeCohort);
355
- this.state.plots.push(config);
356
- }
357
- }
358
- }
359
- },
360
- plot_edit(action) {
361
- const plot = this.state.plots.find((p) => p.id === action.id);
362
- if (!plot) {
363
- throw new CustomError(`missing plot config for id='${action.id}' in store.plot_edit()`, {
364
- name: "MISSING_PLOT_CONFIG",
365
- level: "warn"
366
- });
367
- }
368
- this.copyMerge(plot, action.config, action.opts ? action.opts : {});
369
- const mayAdjustConfig = this.plotAdjusters.get(plot);
370
- if (mayAdjustConfig) mayAdjustConfig(plot, action.config);
371
- if (action.config && "cutoff" in action.config) {
372
- plot.cutoff = action.config.cutoff;
373
- } else {
374
- delete plot.cutoff;
375
- }
376
- if (!action.parentId && plot.parentId) action.parentId = plot.parentId;
377
- },
378
- plot_delete(action) {
379
- const i = this.state.plots.findIndex((p) => p.id === action.id);
380
- if (i !== -1) {
381
- this.state.plots.splice(i, 1);
382
- const plot = this.state.plots[i];
383
- if (!action.parentId && plot?.parentId) action.parentId = plot.parentId;
384
- }
385
- },
386
- plot_nestedEdits(action) {
387
- const plot = this.state.plots.find((p) => p.id === action.id);
388
- if (!plot) {
389
- throw new CustomError(`missing plot config for id='${action.id}' in store.plot_edit_nested`, {
390
- name: "MISSING_PLOT_CONFIG",
391
- level: "warn"
392
- });
393
- }
394
- for (const edit of action.edits) {
395
- const lastKey = edit.nestedKeys.pop();
396
- const obj = edit.nestedKeys.reduce((obj2, key) => obj2[key], plot);
397
- obj[lastKey] = edit.value;
398
- }
399
- if (!action.parentId && plot.parentId) action.parentId = plot.parentId;
400
- },
401
- /*
402
- Remember a geneVariant setting that the user built, keyed by gene, so that a term built
403
- later for the same gene can offer it instead of making the user rebuild the same grouping.
404
-
405
- Dispatched from the Apply button of the geneVariant edit menu, which is the only place
406
- that builds a custom groupset for such a term -- every other mention of 'custom-groupset'
407
- in client/plots/ reads one. See makeEditMenu() in client/termsetting/handlers/geneVariant.ts
408
- and rememberGvQ() in client/termdb/Vocab.js.
409
-
410
- A setting the user returns to moves back to the front of its gene rather than being stored
411
- twice, so each list reads as most recent first. The settings that arrive already built, in
412
- the plots of an opened state, are seeded behind these by seedGvQCache().
413
-
414
- Keyed by gene and never shared across genes: the tvs of a custom groupset filter by the dt
415
- terms of that gene, so a BCR-ABL1 fusion grouping is meaningless on another gene.
416
- */
417
- remember_gvq({ term, q }) {
418
- if (!isCustomizedGvQ(q)) return;
419
- const key = getGvQCacheKey(term);
420
- if (!key) return;
421
- const cache = this.state.reuse.gvQByGene;
422
- const trimmed = trimGvQForCache(q);
423
- const lst = cache[key] || [];
424
- const i = lst.findIndex((entry) => deepEqual(entry.q, trimmed));
425
- if (i != -1) lst.splice(i, 1);
426
- lst.unshift({ label: getGvQLabel(term, q), q: trimmed });
427
- if (lst.length > maxGvQPerGene) lst.length = maxGvQPerGene;
428
- delete cache[key];
429
- cache[key] = lst;
430
- const keys = Object.keys(cache);
431
- if (keys.length > maxGvQGenes) delete cache[keys[0]];
432
- },
433
- // TODO: delete this action? does not seem to be used
434
- async plot_splice(action) {
435
- for (const a of action.subactions) {
436
- await this.actions[a.type].call(this, a);
437
- }
438
- },
439
- filter_replace(action) {
440
- if ("filter0" in action) {
441
- this.state.termfilter.filter0 = action.filter0;
442
- return;
443
- }
444
- const replacementFilter = action.filter ? action.filter : { type: "tvslst", join: "", in: 1, lst: [] };
445
- if (!action.filter.tag) {
446
- this.state.termfilter.filter = replacementFilter;
447
- } else {
448
- const filter = getFilterItemByTag(this.state.termfilter.filter, action.filter.tag);
449
- if (!filter) throw `cannot replace missing filter with tag '${action.filter.tag}'`;
450
- const parent = findParent(this.state.termfilter.filter, filter.$id);
451
- if (parent == filter) {
452
- this.state.termfilter.filter = replacementFilter;
453
- } else {
454
- const i = parent.lst.indexOf(filter);
455
- parent.lst[i] = replacementFilter;
456
- }
457
- }
458
- if (this.app.opts.app?.onFilterChange) this.app.opts.app.onFilterChange(this.state.plots);
459
- },
460
- add_customTerm(action) {
461
- const i = action.obj.id ? this.state.customTerms.findIndex((term) => term.id === action.obj.id) : -1;
462
- if (i === -1) this.state.customTerms.push(action.obj);
463
- else this.state.customTerms[i] = action.obj;
464
- },
465
- delete_customTerm({ id: id2, name }) {
466
- const i = this.state.customTerms.findIndex((term) => id2 ? term.id === id2 : term.name == name);
467
- if (i != -1) this.state.customTerms.splice(i, 1);
468
- },
469
- add_group(action) {
470
- if (this.state.nav.header_mode != "hidden") {
471
- const group = action.obj;
472
- const name = `Group ${this.state.groups.length + 1}`;
473
- const samplelstTW = getSamplelstTW([group]);
474
- const appGroup = {
475
- name,
476
- filter: getFilter(samplelstTW),
477
- plotId: group.plotId
478
- };
479
- this.state.groups.push(appGroup);
480
- this.state.nav.activeTab = 1;
481
- } else if ("plotId" in action.obj) {
482
- const plot = this.state.plots.find((p) => p.id == action.obj.plotId);
483
- if (plot.groups) {
484
- action.obj.index = plot.groups.length;
485
- action.obj.name = `Group ${plot.groups.length + 1}`;
486
- plot.groups.push(action.obj);
487
- }
488
- }
489
- },
490
- rename_group(action) {
491
- const index = action.index;
492
- const newName = action.newName;
493
- if (this.state.nav.header_mode != "hidden") {
494
- this.state.groups[index].name = newName;
495
- } else {
496
- for (const plot of this.state.plots) {
497
- if (plot?.groups) {
498
- plot.groups[index].name = newName;
499
- }
500
- }
501
- }
502
- },
503
- change_color_group(action) {
504
- const index = action.index;
505
- const newColor = action.newColor;
506
- if (this.state.nav.header_mode != "hidden") {
507
- this.state.groups[index].color = newColor;
508
- } else {
509
- for (const plot of this.state.plots) {
510
- if (plot?.groups) {
511
- plot.groups[index].color = newColor;
512
- }
513
- }
514
- }
515
- },
516
- delete_group({ name }) {
517
- if (this.state.nav.header_mode != "hidden") {
518
- const i = this.state.groups.findIndex((i2) => i2.name == name);
519
- if (i != -1) this.state.groups.splice(i, 1);
520
- } else {
521
- for (const plot of this.state.plots) {
522
- if (plot?.groups) {
523
- const j = plot.groups.findIndex((j2) => j2.name == name);
524
- if (j != -1) plot.groups.splice(j, 1);
525
- }
526
- }
527
- }
528
- }
529
- };
530
- var storeInit = StoreApi.getInitFxn(MassStore);
531
-
532
- // mass/skipPrevActionAbort.ts
533
- var globalStateKeys = ["termfilter", "activeCohort", "plots"];
534
- var isGlobalActionType = (type) => type.startsWith("filter") || type.startsWith("cohort");
535
- function skipPrevActionAbort(action) {
536
- if (!action) return false;
537
- if (isGlobalActionType(action.type)) return false;
538
- if (action.type == "app_refresh") {
539
- if (action.subactions?.find((a) => isGlobalActionType(a.type))) return false;
540
- if (action.state) return !globalStateKeys.find((key) => key in action.state);
541
- return Boolean(action.subactions);
542
- }
543
- return true;
544
- }
545
-
546
- export {
547
- storeInit,
548
- skipPrevActionAbort
549
- };
550
- //# sourceMappingURL=chunk-V7UVHM57.js.map