@sjcrh/proteinpaint-client 2.166.0 → 2.167.1

package/dist/chunk-VDR5JXI2.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../mass/store.ts"],
-  "sourcesContent": ["import { StoreApi, StoreBase, type AppApi, type RxStore } from '#rx'\nimport { getFilterItemByTag, findParent } from '#filter/filter'\nimport { getSamplelstTW, getFilter } from './groups.js'\nimport { rehydrateFilter } from '../filter/rehydrateFilter.js'\nimport { importPlot } from '#plots/importPlot.js'\n\n/*\ntmp comment on plot state. later properly define it in typescript\n\na basic plot:\n{\n\tchartType: string\n\t... other properties\n\tid?: dynamically assigned to identify this plot\n}\n\nSometimes a plot may have sections where each section has a name and an array of plots, like in the report plot. \nAn example of such plot is seeing in sjcares. In that case the plot config will look like this:\n{\n\tid?: dynamically assigned to identify this plot\n\tsections: {\n\t\tname: string\n\t\tplots: {\n\t\t\tchartType: string\n\t\t\t... other properties of this child plot\n\t\t\tparentId?: dynamically assigned to point to plot.id\n\t\t}[]\n\t\t... other properties of a section\n\t}[]\n}\nThe state of each plot is added to the appState plots array, so that these plots can be treated as regular plots and be embedded in a parent plot.\n*/\n\n// to distinguish from IDs assigned by other code or users\nconst idPrefix = '_MASS_AUTOID_' + Math.random().toString().slice(-6)\nlet id = 0 // Number((+new Date()).toString().slice(-8))\n\nfunction getId() {\n\treturn idPrefix + '_' + id++\n}\n\nconst navHeaderModes = new Set([\n\t'with_tabs', // default, shows tabs cohort/charts/filter etc\n\t'hidden', // no header\n\t'search_only', // ?\n\t'hide_search', // ?\n\t'with_cohortHtmlSelect', // only show cohort toggle as <select>\n\t'only_buttons'\n])\n\nconst defaultState = {\n\tnav: {\n\t\theader_mode: 'with_tabs',\n\t\tactiveTab: 0 // -1 for no active tab and all closed\n\t},\n\t// will be ignored if there is no dataset termdb.selectCohort\n\t// or value will be set to match a filter node that has been tagged\n\t// as 'cohortfilter' in state.termfilter.filter\n\tactiveCohort: 0,\n\tsearch: { isVisible: true },\n\tplots: [],\n\ttermfilter: {\n\t\tfilter: {\n\t\t\ttype: 'tvslst',\n\t\t\tin: true,\n\t\t\tjoin: '',\n\t\t\tlst: []\n\t\t}\n\t},\n\treuse: {\n\t\tcustomTermQ: {\n\t\t\tbyId: {},\n\t\t\t// non-dictionary terms do not have a term.id,\n\t\t\t// save by term.type + name?\n\t\t\tbyName: {}\n\t\t}\n\t},\n\tgroups: [], // element: {name=str, filter={}}, to show in Groups tab\n\tcustomTerms: [], // element: {name=str, term={}}, able to attach more attr to object if needed\n\tautoSave: true\n}\n\n// one store for the whole MASS app\nclass MassStore extends StoreBase implements RxStore {\n\tstatic type = 'store'\n\n\t// expected RxStore, some are already declared/set in AppBase\n\tapp: AppApi\n\tapi: StoreApi\n\ttype: string\n\n\t// expected class-specific props\n\tdefaultState = defaultState\n\tactions!: {\n\t\t[actionType: string]: (action: { type: string; [prop: string]: any }) => void | Promise<void>\n\t}\n\n\tconstructor(opts, api) {\n\t\tsuper(opts)\n\t\tthis.app = opts.app\n\t\tthis.api = api\n\t\tthis.type = 'store'\n\t\tthis.state = this.copyMerge(this.toJson(defaultState), opts.state) // opts.state\n\t\tthis.prevGeneratedId = 0\n\t}\n\n\tvalidateOpts(opts) {\n\t\tconst s = opts.state\n\t\t// assume that any vocabulary with a route\n\t\t// will require genome + dslabel\n\t\tif (s.vocab.dslabel) {\n\t\t\tif (!s.vocab.genome) throw '.state[.vocab].genome missing'\n\t\t} else {\n\t\t\tif (!Array.isArray(s.vocab.terms)) throw 'vocab.terms must be an array of objects'\n\t\t}\n\t\treturn opts\n\t}\n\n\tvalidateState() {\n\t\t// nav.header_mode should always be present\n\t\tif (!navHeaderModes.has(this.state.nav.header_mode)) throw 'invalid state.nav.header_mode'\n\t}\n\n\tasync init() {\n\t\ttry {\n\t\t\tthis.state.termdbConfig = await this.app.vocabApi.getTermdbConfig()\n\t\t\tawait this.setTermfilter()\n\t\t\tawait this.rehydrateGroups()\n\n\t\t\t// vocab.state.termfilter may be used in getPlotConfig() when rehydrating terms,\n\t\t\t// so manually set it here\n\t\t\tawait this.app.vocabApi.main({\n\t\t\t\ttermfilter: JSON.parse(JSON.stringify(this.state.termfilter)),\n\t\t\t\ttermdbConfig: this.state.termdbConfig\n\t\t\t})\n\t\t\tconst invalidPlots: any[] = []\n\t\t\tfor (const [i, savedPlot] of this.state.plots.entries()) {\n\t\t\t\tlet plot\n\t\t\t\ttry {\n\t\t\t\t\tconst _ = await importPlot(savedPlot.chartType)\n\t\t\t\t\t// this.state{} is already fully set with initial state, thus okay to pass to getPlotConfig()\n\t\t\t\t\tplot = await _.getPlotConfig(savedPlot, this.app, this.state.activeCohort)\n\t\t\t\t} catch (e) {\n\t\t\t\t\tthis.app.printError(e)\n\t\t\t\t\tconsole.error(`getPlotConfig() failed: ${e}`)\n\t\t\t\t}\n\t\t\t\tif (!plot) {\n\t\t\t\t\tinvalidPlots.push(i)\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tthis.state.plots[i] = plot\n\t\t\t\tif (!('id' in plot)) plot.id = `_AUTOID_${id++}_${i}`\n\t\t\t\tif (plot.mayAdjustConfig) plot.mayAdjustConfig(plot)\n\t\t\t}\n\t\t\tif (invalidPlots.length) {\n\t\t\t\tfor (const i of invalidPlots) {\n\t\t\t\t\tthis.state.plots.splice(i, 1)\n\t\t\t\t}\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tconsole.log('store.init() error', e)\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tsetId(item) {\n\t\titem.$id = this.prevGeneratedId++\n\t\tif (item.$lst) {\n\t\t\tfor (const subitem of item.$lst) {\n\t\t\t\tthis.setId(subitem)\n\t\t\t}\n\t\t}\n\t}\n\n\tasync setTermfilter() {\n\t\tlet filterUiRoot = getFilterItemByTag(this.state.termfilter.filter, 'filterUiRoot')\n\t\tif (!filterUiRoot) {\n\t\t\tthis.state.termfilter.filter.tag = 'filterUiRoot'\n\t\t\tfilterUiRoot = this.state.termfilter.filter\n\t\t}\n\n\t\tawait Promise.all(rehydrateFilter(this.state.termfilter.filter, this.app.vocabApi))\n\n\t\tif (!this.state.termdbConfig.selectCohort) {\n\t\t\tthis.state.activeCohort = -1\n\t\t\t// since the cohort tab will be hidden, default to making the filter tab active\n\t\t\tif (this.state.activeTab === 0) this.state.activeTab = 1\n\t\t\tif (this.state.nav.header_mode === 'with_cohortHtmlSelect') {\n\t\t\t\tconsole.warn(`no termdbConfig.selectCohort to use for nav.header_mode = 'with_cohortHtmlSelect'`)\n\t\t\t\tthis.state.nav.header_mode = 'search_only'\n\t\t\t}\n\t\t} else {\n\t\t\tlet cohortFilter = getFilterItemByTag(this.state.termfilter.filter, 'cohortFilter')\n\t\t\tif (!cohortFilter) {\n\t\t\t\t// support legacy state.termfilter and test scripts that\n\t\t\t\t// that does not specify a cohort when required;\n\t\t\t\t// will use state.activeCohort if not -1\n\t\t\t\tcohortFilter = {\n\t\t\t\t\ttag: 'cohortFilter',\n\t\t\t\t\ttype: 'tvs',\n\t\t\t\t\ttvs: {\n\t\t\t\t\t\tterm: JSON.parse(JSON.stringify(this.state.termdbConfig.selectCohort.term)),\n\t\t\t\t\t\tvalues:\n\t\t\t\t\t\t\tthis.state.activeCohort == -1\n\t\t\t\t\t\t\t\t? []\n\t\t\t\t\t\t\t\t: this.state.termdbConfig.selectCohort.values[this.state.activeCohort].keys.map(key => {\n\t\t\t\t\t\t\t\t\t\treturn { key, label: key }\n\t\t\t\t\t\t\t\t  })\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tthis.state.termfilter.filter = {\n\t\t\t\t\ttype: 'tvslst',\n\t\t\t\t\tin: true,\n\t\t\t\t\tjoin: 'and',\n\t\t\t\t\tlst: [cohortFilter, filterUiRoot]\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tconst sorter = (a, b) => (a < b ? -1 : 1)\n\t\t\t\tcohortFilter.tvs.values.sort((a, b) => (a.key < b.key ? -1 : 1))\n\t\t\t\tconst keysStr = JSON.stringify(cohortFilter.tvs.values.map(v => v.key).sort(sorter))\n\t\t\t\tconst i = this.state.termdbConfig.selectCohort.values.findIndex(\n\t\t\t\t\tv => keysStr == JSON.stringify(v.keys.sort(sorter))\n\t\t\t\t)\n\t\t\t\tif (this.state.activeCohort !== -1 && this.state.activeCohort !== 0 && i !== this.state.activeCohort) {\n\t\t\t\t\tconsole.log('Warning: cohortFilter will override the state.activeCohort due to mismatch')\n\t\t\t\t}\n\t\t\t\tthis.state.activeCohort = i\n\t\t\t}\n\t\t}\n\t}\n\n\tasync rehydrateGroups() {\n\t\t// rehydrate filter terms of each group\n\t\tconst lst: any[] = []\n\t\tfor (const g of this.state.groups) {\n\t\t\tlst.push(...rehydrateFilter(g.filter, this.app.vocabApi))\n\t\t}\n\t\tawait Promise.all(lst)\n\t}\n}\n\n/*\n\tTo clearly indicate the allowed store actions,\n\tsupply a literal \"actions\" object on the \n\tconstructor prototype\n*/\nMassStore.prototype.actions = {\n\t// 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>'.\n\t// Object literal may only specify known properties, and 'app_refresh' does not exist in type '(action: { [prop: string]: any; type: string; }) => void | Promise<void>'.\n\n\tasync app_refresh(this: MassStore, action) {\n\t\t// optional action.state{} may be full or partial overrides\n\t\t// to the current state\n\t\t//\n\t\t// when constructing an app, app_refresh() is called\n\t\t// without action.state as the current state at the\n\t\t// initial render is not meant to be modified yet\n\t\t//\n\t\tthis.state = this.copyMerge(this.toJson(this.state), action.state || {})\n\n\t\t// Subactions cause existing action methods to be called in parallel,\n\t\t// to update unrelated parts of the state.\n\t\t//\n\t\t// Note that an alternative approach of pre-merging actions payloads into\n\t\t// one \"write\" step or action is not as reliable, since that approach may leave\n\t\t// out custom logic that are required and already coded in existing actions.\n\t\t//\n\t\tconst subactionPlotIds = new Set()\n\t\tconst promises: any[] = []\n\t\tif (action.subactions) {\n\t\t\tfor (const a of action.subactions) {\n\t\t\t\tpromises.push(this.actions[a.type].call(this, a))\n\t\t\t\tif (a.type.startsWith('plot_')) subactionPlotIds.add(a.id)\n\t\t\t}\n\t\t}\n\t\tawait Promise.all(promises)\n\n\t\tfor (const plot of this.state.plots) {\n\t\t\tif (plot.mayAdjustConfig && !subactionPlotIds.has(plot.id)) {\n\t\t\t\t// assume that mayAdjustConfig() is not async\n\t\t\t\tplot.mayAdjustConfig(plot, action.config)\n\t\t\t}\n\t\t}\n\t},\n\ttab_set(this: MassStore, action) {\n\t\tthis.state.nav.activeTab = action.activeTab\n\t},\n\tcohort_set(this: MassStore, action) {\n\t\tthis.state.activeCohort = action.activeCohort\n\t\tconst cohort = this.state.termdbConfig.selectCohort.values[action.activeCohort]\n\t\tconst cohortFilter = getFilterItemByTag(this.state.termfilter.filter, 'cohortFilter')\n\t\tif (!cohortFilter) throw `No item tagged with 'cohortFilter'`\n\t\tcohortFilter.tvs.values = cohort.keys.map(key => {\n\t\t\treturn { key, label: key }\n\t\t})\n\t},\n\n\t// dispatch \"plot_prep\" action to produce a 'initiating' UI of this plot, for user to fill in additional details to launch the plot\n\t// example: table, scatterplot which requires user to select two terms\n\tasync plot_prep(this: MassStore, action) {\n\t\tconst plot = {\n\t\t\tid: 'id' in action ? action.id : getId()\n\t\t}\n\t\tif (!action.config) throw '.config{} missing for plot_prep'\n\t\tif (action.config.chartType && Object.keys(action.config).length == 1) {\n\t\t\tconst _ = await importPlot(action.config.chartType)\n\t\t\tconst config = await _.getPlotConfig(action.config, this.app, this.state.activeCohort)\n\t\t\taction.config = Object.assign(config, action.config)\n\t\t}\n\t\tObject.assign(plot, action.config)\n\t\tthis.state.plots.push(plot)\n\t},\n\n\tasync plot_create(this: MassStore, action) {\n\t\tconst _ = await importPlot(action.config.chartType)\n\t\tconst plot = await _.getPlotConfig(action.config, this.app, this.state.activeCohort)\n\t\tif (!('id' in action)) action.id = getId()\n\t\tplot.id = action.id\n\t\tif (plot.mayAdjustConfig) {\n\t\t\tplot.mayAdjustConfig(plot, action.config)\n\t\t}\n\t\tthis.state.plots.push(plot)\n\t\t// Parent plots may have child plots, organized in sections to ease the visualization and analysis. For example the sjcares report,\n\t\t//has the sections Demographics, Diagnosis and Stagind with their respective plots. We go over the plots for each section to add them\n\t\t// to the state.plots array, so that they can be treated as regular plots and be embedded in a parent plot\n\t\tif (plot.sections) {\n\t\t\t// this is handled for embedder convenience,\n\t\t\t// ideally app state.plots would already have all the plot entries\n\t\t\t// instead of having nested plot.sections[] with plots per section in a session state to be rehydrated;\n\t\t\t//\n\t\t\t// nested plot entries are harder to manage:\n\t\t\t// - store methods will need to look in different places\n\t\t\t//   to process a dispatched plot_* action\n\t\t\t// - a plot's `getState()` method will also need to look in different places for the plot config, such as\n\t\t\t// getState(appState) {\n\t\t\t//   const config = appState.plots.find(p => p.id === this.id || (p.id === this.parentId && p.plots?.find(p => p.id === this.id)))\n\t\t\t//    ...\n\t\t\t// }\n\t\t\tfor (const section of plot.sections) {\n\t\t\t\tfor (const p of section.plots) {\n\t\t\t\t\t// by tracking a child plot's parentId, it makes it easier to\n\t\t\t\t\t// - find a plot's config in the app state\n\t\t\t\t\t// - prevent the app from rendering each child plot in it's own sandbox\n\t\t\t\t\t// - prevent counting child plots separately in CHARTS tab\n\t\t\t\t\tp.parentId = plot.id\n\t\t\t\t\tif (!p.id) p.id = getId() // fill in missing child plot id\n\t\t\t\t\tconst _ = await importPlot(p.chartType)\n\t\t\t\t\tconst config = await _.getPlotConfig(p, this.app, this.state.activeCohort)\n\t\t\t\t\t// Move nested state.plot[i].plots[] into the root state.plots[] array\n\t\t\t\t\tthis.state.plots.push(config)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t},\n\n\tplot_edit(this: MassStore, action) {\n\t\tconst plot = this.state.plots.find(p => p.id === action.id)\n\t\tif (!plot) throw `missing plot id='${action.id}' in store.plot_edit()`\n\t\tthis.copyMerge(plot, action.config, action.opts ? action.opts : {})\n\t\tif (plot.mayAdjustConfig) {\n\t\t\tplot.mayAdjustConfig(plot, action.config)\n\t\t}\n\n\t\tif (action.config && 'cutoff' in action.config) {\n\t\t\tplot.cutoff = action.config.cutoff\n\t\t} else {\n\t\t\tdelete plot.cutoff\n\t\t}\n\n\t\t// action.parentId may be used in reactsTo() code\n\t\tif (!action.parentId && plot.parentId) action.parentId = plot.parentId\n\t},\n\n\tplot_delete(this: MassStore, action) {\n\t\tconst i = this.state.plots.findIndex(p => p.id === action.id)\n\t\tif (i !== -1) {\n\t\t\tthis.state.plots.splice(i, 1)\n\t\t\t// action.parentId may be used in reactsTo() code\n\t\t\tconst plot = this.state.plots[i]\n\t\t\tif (!action.parentId && plot?.parentId) action.parentId = plot.parentId\n\t\t}\n\t},\n\n\tplot_nestedEdits(this: MassStore, action) {\n\t\tconst plot = this.state.plots.find(p => p.id === action.id)\n\t\tif (!plot) throw `missing plot id='${action.id}' in store.plot_edit_nested`\n\t\tfor (const edit of action.edits) {\n\t\t\tconst lastKey = edit.nestedKeys.pop()\n\t\t\tconst obj = edit.nestedKeys.reduce((obj, key) => obj[key], plot)\n\t\t\tobj[lastKey] = edit.value\n\t\t}\n\t\t// action.parentId may be used in reactsTo() code\n\t\tif (!action.parentId && plot.parentId) action.parentId = plot.parentId\n\t},\n\n\t// TODO: delete this action? does not seem to be used\n\tasync plot_splice(this: MassStore, action) {\n\t\tfor (const a of action.subactions) {\n\t\t\t// need to await in case the sequence of subactions is relevant\n\t\t\tawait this.actions[a.type].call(this, a)\n\t\t}\n\t},\n\n\tfilter_replace(this: MassStore, action) {\n\t\tif ('filter0' in action) {\n\t\t\t// quick fix since rx.copyMerge() does not work for filter0,\n\t\t\t// as used in app_refresh() and dispatched from GDC matrixApi.update()\n\t\t\tthis.state.termfilter.filter0 = action.filter0\n\t\t\treturn\n\t\t}\n\n\t\tconst replacementFilter = action.filter ? action.filter : { type: 'tvslst', join: '', in: 1, lst: [] }\n\t\tif (!action.filter.tag) {\n\t\t\tthis.state.termfilter.filter = replacementFilter\n\t\t} else {\n\t\t\tconst filter = getFilterItemByTag(this.state.termfilter.filter, action.filter.tag)\n\t\t\tif (!filter) throw `cannot replace missing filter with tag '${action.filter.tag}'`\n\t\t\tconst parent = findParent(this.state.termfilter.filter, filter.$id)\n\t\t\tif (parent == filter) {\n\t\t\t\tthis.state.termfilter.filter = replacementFilter\n\t\t\t} else {\n\t\t\t\tconst i = parent.lst.indexOf(filter)\n\t\t\t\tparent.lst[i] = replacementFilter\n\t\t\t}\n\t\t}\n\t\t//In the profile runproteinpaint this function is passed to clear the local filters when the global filter changes\n\t\tif (this.app.opts.app?.onFilterChange) this.app.opts.app.onFilterChange(this.state.plots)\n\t},\n\n\tcache_termq(this: MassStore, { termId, q }) {\n\t\t// TODO: support caching by term.name\n\t\tif (!termId) throw `missing termId for caching custom term.q`\n\t\tif (!q?.reuseId) throw `missing or empty tw.q.reuseId as cache identifier for term='${termId}'`\n\t\tconst cache = this.state.reuse.customTermQ.byId\n\t\tif (!cache[termId]) cache[termId] = {}\n\t\tcache[termId][q.reuseId] = q\n\n\t\t// apply this change to all plots that use the same term.q cache\n\t\tfor (const plot of this.state.plots) {\n\t\t\tif (!(plot.chartType in getTwsByChartType)) continue\n\t\t\tconst twlst = getTwsByChartType[plot.chartType](plot)\n\t\t\tfor (const tw of twlst) {\n\t\t\t\tif (tw?.q?.reuseId === q.reuseId) tw.q = q\n\t\t\t}\n\t\t}\n\t},\n\n\tuncache_termq(this: MassStore, { term, q }) {\n\t\t// TODO: support uncaching by term.name\n\t\tif (!term.id) throw `missing term.id for uncaching custom term.q`\n\t\tif (!q.reuseId) throw `missing qname as uncache identifier for term.id='${term.id}'`\n\t\tconst cache = this.state.reuse.customTermQ.byId[term.id]\n\t\tif (!cache) throw `missing term.q cache for term.id='${term.id}`\n\t\tif (!(q.reuseId in cache)) console.warn(`q.reuseId='${q.cacheid}' not cached for term.id='${term.id}'`)\n\t\telse {\n\t\t\tdelete cache[q.reuseId]\n\t\t\t// apply this change to all plots that use the same term.q cache\n\t\t\tfor (const plot of this.state.plots) {\n\t\t\t\tif (!(plot.chartType in getTwsByChartType)) continue\n\t\t\t\tconst twlst = getTwsByChartType[plot.chartType](plot)\n\t\t\t\tfor (const tw of twlst) {\n\t\t\t\t\tif (tw.q.reuseId === q.reuseId) {\n\t\t\t\t\t\tdelete tw.q.reuseId\n\t\t\t\t\t\tdelete tw.q.name\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t},\n\n\tadd_customTerm(this: MassStore, action) {\n\t\tthis.state.customTerms.push(action.obj)\n\t},\n\n\tdelete_customTerm(this: MassStore, { name }) {\n\t\tconst i = this.state.customTerms.findIndex(i => i.name == name)\n\t\tif (i != -1) this.state.customTerms.splice(i, 1)\n\t},\n\n\tadd_group(this: MassStore, action) {\n\t\tif (this.state.nav.header_mode != 'hidden') {\n\t\t\tconst group = action.obj\n\t\t\tconst name = `Group ${this.state.groups.length + 1}`\n\n\t\t\tconst samplelstTW = getSamplelstTW([group])\n\t\t\tconst appGroup = {\n\t\t\t\tname: name,\n\t\t\t\tfilter: getFilter(samplelstTW),\n\t\t\t\tplotId: group.plotId\n\t\t\t}\n\t\t\tthis.state.groups.push(appGroup)\n\t\t\tthis.state.nav.activeTab = 1\n\t\t} else if ('plotId' in action.obj) {\n\t\t\tconst plot = this.state.plots.find(p => p.id == action.obj.plotId)\n\t\t\tif (plot.groups) {\n\t\t\t\taction.obj.index = plot.groups.length\n\t\t\t\taction.obj.name = `Group ${plot.groups.length + 1}`\n\t\t\t\tplot.groups.push(action.obj)\n\t\t\t}\n\t\t}\n\t},\n\n\trename_group(this: MassStore, action) {\n\t\tconst index = action.index\n\t\tconst newName = action.newName\n\t\tif (this.state.nav.header_mode != 'hidden') {\n\t\t\tthis.state.groups[index].name = newName\n\t\t} else {\n\t\t\tfor (const plot of this.state.plots) {\n\t\t\t\tif (plot?.groups) {\n\t\t\t\t\tplot.groups[index].name = newName\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t},\n\n\tchange_color_group(this: MassStore, action) {\n\t\tconst index = action.index\n\t\tconst newColor = action.newColor\n\t\tif (this.state.nav.header_mode != 'hidden') {\n\t\t\tthis.state.groups[index].color = newColor\n\t\t} else {\n\t\t\tfor (const plot of this.state.plots) {\n\t\t\t\tif (plot?.groups) {\n\t\t\t\t\tplot.groups[index].color = newColor\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t},\n\n\tdelete_group(this: MassStore, { name }) {\n\t\tif (this.state.nav.header_mode != 'hidden') {\n\t\t\tconst i = this.state.groups.findIndex(i => i.name == name)\n\t\t\tif (i != -1) this.state.groups.splice(i, 1)\n\t\t} else {\n\t\t\tfor (const plot of this.state.plots) {\n\t\t\t\tif (plot?.groups) {\n\t\t\t\t\tconst j = plot.groups.findIndex(j => j.name == name)\n\t\t\t\t\tif (j != -1) plot.groups.splice(j, 1)\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n}\n\n// each chartType should have a getter function\n// to return all the term wrappers in the plot config\nconst getNestedChartSeriesDataTws = plot => [plot.term0, plot.term, plot.term2].filter(d => !!d)\nconst getTwsByChartType = {\n\tsummary: getNestedChartSeriesDataTws,\n\tsurvival: getNestedChartSeriesDataTws,\n\tcuminc: getNestedChartSeriesDataTws,\n\tregression: plot => [plot.outcome, ...plot.independent].filter(d => !!d),\n\tmatrix: plot =>\n\t\tplot.termgroups.reduce((arr, grp) => {\n\t\t\tarr.push(...grp.lst)\n\t\t\treturn arr\n\t\t}, [])\n}\n\n// must use the await keyword when using this storeInit()\nexport const storeInit = StoreApi.getInitFxn(MassStore)\n"],
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-  "names": ["_", "obj", "i", "j"]
-}

package/dist/chunk-W4D2EYE4.js

@@ -1,95 +0,0 @@
-import {
-  getPlotConfig
-} from "./chunk-DA5VGV5L.js";
-import {
-  fillTermWrapper
-} from "./chunk-UT6W4ZZL.js";
-import {
-  TermTypes,
-  numericTypes
-} from "./chunk-RYRCMHYR.js";
-import {
-  copyMerge
-} from "./chunk-FYTZCTJC.js";
-
-// plots/matrix/hierCluster.config.js
-async function getPlotConfig2(opts = {}, app) {
-  opts.chartType = "hierCluster";
-  const config = await getPlotConfig(opts, app);
-  delete config.genes;
-  config.settings.hierCluster = {
-    /* type of data used for clustering
-    exciting todo: (to introduce new dt values)
-    - gene dependency
-    - numeric dic term
-    - non-gene genomic stuff that resolves into numeric quantities (cpg meth)
-    - metabolite
-    */
-    dataType: config.dataType,
-    // adjust the default group name based on automatically detected term types
-    // Done in matrix.cells.js: setHierClusterCellProps
-    // termGroupName: 'Expression',
-    clusterSamples: true,
-    clusterRows: true,
-    clusterMethod: "average",
-    // complete
-    distanceMethod: "euclidean",
-    zScoreCap: 5,
-    zScoreTransformation: true,
-    xDendrogramHeight: 100,
-    yDendrogramHeight: 200,
-    colorScale: "blueWhiteRed"
-  };
-  const overrides = app.vocabApi.termdbConfig.hierCluster || {};
-  const hierClusterSubTypeOverrides = app.vocabApi.termdbConfig[`${config.dataType}Cluster`] || {};
-  copyMerge(
-    config.settings.hierCluster,
-    overrides.settings,
-    opts.settings?.hierCluster || {},
-    hierClusterSubTypeOverrides.settings
-  );
-  {
-    const c = config.settings.hierCluster.colorScale;
-    if (!c) throw "colorScale missing";
-  }
-  config.settings.matrix.collabelpos = "top";
-  const termGroupName = config.settings.hierCluster.termGroupName;
-  const hcTermGroup = config.termgroups.find((g) => g.type == "hierCluster" || g.name == termGroupName) || {
-    name: termGroupName
-  };
-  hcTermGroup.type = "hierCluster";
-  if (!hcTermGroup.lst?.length) {
-    if (!Array.isArray(opts.terms)) throw "opts.terms[] not array (may show geneset edit ui)";
-    const promises = [];
-    for (const i of opts.terms) {
-      const tw = i.term ? i : { term: i };
-      if (!tw.term.type) {
-        if (config.dataType == TermTypes.GENE_EXPRESSION || config.dataType == TermTypes.METABOLITE_INTENSITY) {
-          tw.term.type = config.dataType;
-        } else {
-          throw `term type missing and cannot be assigned by dataType`;
-        }
-      } else if (!numericTypes.has(tw.term.type)) {
-        throw "term type is not numeric";
-      } else if (config.dataType && !canTermBeInHierGrp(config.dataType, tw.term.type)) {
-        throw `cannot have term type ${tw.term.type} in ${config.dataType} term group`;
-      }
-      promises.push(fillTermWrapper(tw, app.vocabApi));
-    }
-    hcTermGroup.lst = await Promise.all(promises);
-    if (config.termgroups.indexOf(hcTermGroup) == -1) config.termgroups.unshift(hcTermGroup);
-  }
-  config.settings.matrix.maxSample = 1e5;
-  return config;
-}
-function canTermBeInHierGrp(grpType, twType) {
-  if (grpType == "numericDictTerm") {
-    if (twType == "float" || twType == "integer") return true;
-  }
-  return twType == grpType;
-}
-
-export {
-  getPlotConfig2 as getPlotConfig
-};
-//# sourceMappingURL=chunk-W4D2EYE4.js.map

package/dist/chunk-XATIKUGU.js

@@ -1,142 +0,0 @@
-import {
-  runproteinpaint
-} from "./chunk-JXHU2FIA.js";
-
-// test/front.helpers.js
-var serverData = /* @__PURE__ */ Object.create(null);
-function getRunPp(appname = "", defaultArgs = {}, _host = "http://localhost:3000") {
-  const host = window.testHost || _host;
-  const arg = {
-    host: window.testHost || _host,
-    noheader: 1,
-    nobox: true,
-    debug: 1,
-    norecover: true
-  };
-  if (appname == "mass" || appname == "termdb") {
-    defaultArgs.debounceInterval = 0;
-  }
-  if (appname) arg[appname] = defaultArgs;
-  else copyMerge(arg, defaultArgs);
-  const argStr = JSON.stringify(arg);
-  return function runpp(overrides = {}) {
-    const argCopy = JSON.parse(argStr);
-    if (appname) copyMerge(argCopy[appname], overrides);
-    else copyMerge(argCopy, overrides);
-    if (appname && defaultArgs.fetchOpts) {
-      argCopy[appname].fetchOpts = defaultArgs.fetchOpts;
-    }
-    return runproteinpaint(Object.assign(argCopy, { serverData }));
-  };
-}
-function copyMerge(base, ...args) {
-  const target = typeof base == "string" ? JSON.parse(base) : base;
-  for (const arg of args) {
-    if (arg) {
-      const source = typeof base == "string" ? JSON.parse(JSON.stringify(arg)) : arg;
-      for (const key in source) {
-        if (!target[key] || Array.isArray(target[key]) || typeof target[key] !== "object") target[key] = source[key];
-        else copyMerge(target[key], source[key]);
-      }
-    }
-  }
-  return target;
-}
-function rideInit(opts = {}) {
-  const self = new Ride(opts);
-  const rideApi = {
-    // ride on the default event bus
-    to(callback, sub = {}) {
-      self.addToThen(callback, Object.assign({}, opts, sub));
-      return rideApi;
-    },
-    use(triggerFxn, sub = {}) {
-      self.addUseThen(triggerFxn, Object.assign({}, opts, sub));
-      return rideApi;
-    },
-    change(sub = {}) {
-      Object.assign(opts, sub);
-      return rideApi;
-    },
-    // run callback without using bus, with or without timeout
-    run(callback, after = 0) {
-      self.addRunThen(callback, after, opts);
-      return rideApi;
-    },
-    // close the event bus
-    done(test) {
-      if (opts.bus) self.resolved.then(() => opts.bus.on(opts.eventType, null));
-      self.resolved.then(() => {
-        test.end();
-        if (!opts.preserve && test._ok && opts.arg.Inner.app && typeof opts.arg.Inner.app.destroy == "function") {
-          opts.arg.Inner.app.destroy();
-        }
-      }).catch(console.log);
-      return rideApi;
-    }
-  };
-  return Object.freeze(rideApi);
-}
-var Ride = class {
-  // mutable but private access props and methods
-  // when used inside rideInit()
-  constructor(opts) {
-    this.validateOpts(opts);
-    this.resolved = Promise.resolve();
-  }
-  validateOpts(opts) {
-    try {
-      if (opts.eventType && !opts.bus) {
-        if (!opts.arg) throw "must specify opts.bus or opts.arg for rideInit() argument";
-        opts.bus = opts.arg;
-      }
-      if (opts.bus) {
-        if (typeof opts.eventType !== "string") throw "invalid default.eventType";
-        opts.bus.on(opts.eventType, null);
-        return opts;
-      }
-    } catch (e) {
-      console.log(e);
-    }
-  }
-  addToThen(callback, opts) {
-    this.resolved = this.resolved.then(async (triggerFxn) => {
-      opts.bus.on(opts.eventType, null);
-      return new Promise(async (resolve, reject) => {
-        opts.bus.on(opts.eventType, async () => {
-          await sleep(opts.wait);
-          callback(opts.arg);
-          resolve();
-        });
-        if (triggerFxn) await triggerFxn();
-      });
-    });
-  }
-  // prepare a trigger function for use in the pattern
-  // rideInit().use(triggerFxn).to(...)
-  //
-  // .use() enables setting a different opts.arg to be used for triggerFxn
-  //
-  addUseThen(triggerFxn, opts) {
-    this.resolved = this.resolved.then(async (prevTriggerFxn) => {
-      if (typeof prevTriggerFxn == "function") await prevTriggerFxn();
-      await sleep(isNaN(opts.wait) ? 0 : opts.wait);
-      return () => triggerFxn(opts.arg);
-    });
-  }
-  addRunThen(callback, after, opts) {
-    this.resolved = this.resolved.then(async () => {
-      await sleep(typeof after == "number" ? after : 0);
-      callback(opts.arg);
-    });
-  }
-};
-function sleep(ms) {
-  return new Promise((resolve) => setTimeout(resolve, ms));
-}
-
-export {
-  getRunPp,
-  rideInit
-};
-//# sourceMappingURL=chunk-XATIKUGU.js.map