@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-4KRGCOTL.js.map

@@ -0,0 +1,7 @@
+{
+  "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'\nimport { CustomError } from '#shared/helpers.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 carereg. 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\n// will be used to track plotId's that have already been used, so that plot_prep() and\n// plot_create() will avoid conflicts from having a plotId that's used by different plots\nconst usedPlotIds = new Set()\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\tplotAdjusters = new WeakMap()\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\tlet savedState = {}\n\t\ttry {\n\t\t\t// only automatically detect and recover saved state when webdriver is detected\n\t\t\tconst key = window.navigator.webdriver && window['SJPP_E2E_STORAGE_STATES_KEY']\n\t\t\tconst savedStateStr = (key && window.localStorage.getItem('SJPP_E2E_STORAGE_STATES')) || '{}'\n\t\t\tsavedState = JSON.parse(savedStateStr)[key]?.state || {}\n\t\t\t// console.log(107, 'mass/store savedState', key, savedState)\n\t\t} catch (_) {\n\t\t\t// okay to ignore error of not being able to recover state\n\t\t\tsavedState = {}\n\t\t}\n\t\tthis.state = this.copyMerge(this.toJson(defaultState), opts.state, savedState)\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++}_${i}`\n\t\t\t\tif (plot.mayAdjustConfig) {\n\t\t\t\t\tplot.mayAdjustConfig(plot)\n\t\t\t\t\tthis.plotAdjusters.set(plot, plot.mayAdjustConfig)\n\t\t\t\t\tdelete plot.mayAdjustConfig\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (invalidPlots.length) {\n\t\t\t\tfor (const i of invalidPlots) {\n\t\t\t\t\tthis.state.plots.splice(i, 1)\n\t\t\t\t}\n\t\t\t}\n\t\t} catch (e) {\n\t\t\tconsole.log('store.init() error', e)\n\t\t\tthrow e\n\t\t}\n\t}\n\n\tsetId(item) {\n\t\titem.$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\tconst mayAdjustConfig = this.plotAdjusters.get(plot)\n\t\t\tif (mayAdjustConfig && !subactionPlotIds.has(plot.id)) {\n\t\t\t\t// assume that mayAdjustConfig() is not async\n\t\t\t\tmayAdjustConfig(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\tif (usedPlotIds.has(action.id)) delete action.id // prevent potential conflicts\n\n\t\tconst plot = {\n\t\t\t// rx.getComponents() relies on parsing dot-separated key names that breaks if a key has a dot,\n\t\t\t// the plot.id value should be assumed to be auto-generated and to not have any non-rx usage expectations\n\t\t\tid: 'id' in action && !action.id.includes('.') ? action.id : getId()\n\t\t}\n\t\tusedPlotIds.add(plot.id)\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\tif (usedPlotIds.has(action.id)) delete action.id // prevent potential conflicts\n\n\t\tconst _ = await importPlot(action.config.chartType)\n\t\tconst plot = await _.getPlotConfig(action.config, this.app, this.state.activeCohort)\n\t\t// rx.getComponents() relies on parsing dot-separated key names that breaks if a key has a dot,\n\t\t// the plot.id value should be assumed to be auto-generated and to not have any non-rx usage expectations\n\t\tif (!('id' in action) || action.id.includes('.')) action.id = getId()\n\t\tplot.id = action.id\n\t\tusedPlotIds.add(plot.id)\n\n\t\tif (plot.mayAdjustConfig) {\n\t\t\tplot.mayAdjustConfig(plot)\n\t\t\tthis.plotAdjusters.set(plot, plot.mayAdjustConfig)\n\t\t\tdelete plot.mayAdjustConfig\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 carereg 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) {\n\t\t\t// plot may have been deleted from closing the plot sandbox or another reason,\n\t\t\t// assume this action is stale and not an error\n\t\t\tthrow new CustomError(`missing plot config for id='${action.id}' in store.plot_edit()`, {\n\t\t\t\tname: 'MISSING_PLOT_CONFIG',\n\t\t\t\tlevel: 'warn'\n\t\t\t})\n\t\t}\n\t\tthis.copyMerge(plot, action.config, action.opts ? action.opts : {})\n\t\tconst mayAdjustConfig = this.plotAdjusters.get(plot)\n\t\tif (mayAdjustConfig) mayAdjustConfig(plot, action.config)\n\n\t\tif (action.config && 'cutoff' in action.config) {\n\t\t\tplot.cutoff = action.config.cutoff\n\t\t} else {\n\t\t\tdelete plot.cutoff\n\t\t}\n\n\t\t// action.parentId may be used in reactsTo() code\n\t\tif (!action.parentId && plot.parentId) action.parentId = plot.parentId\n\t},\n\n\tplot_delete(this: MassStore, action) {\n\t\tconst i = this.state.plots.findIndex(p => p.id === action.id)\n\t\tif (i !== -1) {\n\t\t\tthis.state.plots.splice(i, 1)\n\t\t\t// action.parentId may be used in reactsTo() code\n\t\t\tconst plot = this.state.plots[i]\n\t\t\tif (!action.parentId && plot?.parentId) action.parentId = plot.parentId\n\t\t}\n\t},\n\n\tplot_nestedEdits(this: MassStore, action) {\n\t\tconst plot = this.state.plots.find(p => p.id === action.id)\n\t\tif (!plot) {\n\t\t\t// plot may have been deleted from closing the plot sandbox or another reason,\n\t\t\t// assume this action is stale and not an error\n\t\t\tthrow new CustomError(`missing plot config for id='${action.id}' in store.plot_edit_nested`, {\n\t\t\t\tname: 'MISSING_PLOT_CONFIG',\n\t\t\t\tlevel: 'warn'\n\t\t\t})\n\t\t}\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\tconst i = action.obj.id ? 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+  "names": ["_", "obj", "id", "i", "j"]
+}

package/dist/chunk-4WF3XDQP.js

@@ -0,0 +1,220 @@
+// ../shared/utils/dist/src/termCollection.js
+function validateTermCollectionTerm(term) {
+  if (!Array.isArray(term?.termlst) || !term.termlst.length)
+    throw new Error("termCollection requires nonempty term.termlst[]");
+  const memberIds = /* @__PURE__ */ new Set();
+  const types = /* @__PURE__ */ new Set();
+  for (const t of term.termlst) {
+    if (typeof t.id != "string" || !t.id) throw new Error("member term id not non-empty string");
+    if (typeof t.type != "string" || !t.type) throw new Error("member term type not non-empty string");
+    if (memberIds.has(t.id)) throw new Error(`duplicate member term id '${t.id}'`);
+    memberIds.add(t.id);
+    types.add(t.type == "integer" || t.type == "float" ? "numDict" : t.type);
+  }
+  if (types.size > 1) throw new Error("termCollection.termlst[] not allowed to mix multiple term types");
+  return memberIds;
+}
+function validateFractionMembers(numerators, denominators, memberIds) {
+  if (!Array.isArray(denominators) || !denominators.length) throw new Error("fraction requires nonempty denominators[]");
+  if (!Array.isArray(numerators) || !numerators.length) throw new Error("fraction requires nonempty numerators[]");
+  if (new Set(denominators).size !== denominators.length) throw new Error("fraction denominators[] contains duplicates");
+  if (new Set(numerators).size !== numerators.length) throw new Error("fraction numerators[] contains duplicates");
+  for (const id of denominators) {
+    if (typeof id != "string" || !id) throw new Error("fraction denominator id not non-empty string");
+    if (!memberIds.has(id)) throw new Error(`fraction denominator '${id}' is not a collection member`);
+  }
+  for (const id of numerators) {
+    if (typeof id != "string" || !id) throw new Error("fraction numerator id not non-empty string");
+    if (!denominators.includes(id)) throw new Error(`fraction numerator '${id}' is not included in denominators[]`);
+  }
+}
+var FRACTION_TW_TYPE = "TermCollectionTWFraction";
+function isFractionTw(tw) {
+  return tw?.type === FRACTION_TW_TYPE && tw?.term?.type === "termCollection";
+}
+function getFractionTvsTerm(tw) {
+  if (!isFractionTw(tw)) throw new Error("not a fraction termCollection tw");
+  const term = structuredClone(tw.term);
+  const memberIds = term.termlst?.length ? validateTermCollectionTerm(term) : new Set(term.termIds || []);
+  const denominators = tw.q?.denominators?.length ? [...tw.q.denominators] : [...memberIds];
+  const numerators = tw.q?.numerators?.length ? [...tw.q.numerators] : [...denominators];
+  validateFractionMembers(numerators, denominators, memberIds);
+  term.numerators = numerators;
+  term.denominators = denominators;
+  return term;
+}
+function validateTermCollectionFraction(q, term) {
+  const memberIds = validateTermCollectionTerm(term);
+  validateFractionMembers(q?.numerators, q?.denominators, memberIds);
+  if (q.mode === "discrete" && q.type !== "regular-bin" && q.type !== "custom-bin")
+    throw new Error("discrete fraction termCollection requires regular-bin or custom-bin q.type");
+}
+
+// ../shared/utils/dist/src/filter.js
+function getFilteredSamples(sampleAnno, filter) {
+  setDatasetAnnotations(filter);
+  const samples = /* @__PURE__ */ new Set();
+  for (const anno of sampleAnno) {
+    if (samples.has(anno.sample)) continue;
+    const data = anno.s || anno.data;
+    if (data && sample_match_termvaluesetting(data, filter)) {
+      samples.add(anno.sample);
+    }
+  }
+  return samples;
+}
+function sample_match_termvaluesetting(row, filter, _term = null, sample = null) {
+  const lst = filter.type == "tvslst" ? filter.lst : [filter];
+  let numberofmatchedterms = 0;
+  for (const item of lst) {
+    if ("type" in item && item.type == "tvslst") {
+      if (sample_match_termvaluesetting(row, item, _term, sample)) {
+        numberofmatchedterms++;
+      }
+    } else {
+      const itemCopy = JSON.parse(JSON.stringify(item));
+      const t = itemCopy.tvs;
+      if (_term && t.term) {
+        if (!(_term.name == t.term.name && _term.type == t.term.type)) {
+          numberofmatchedterms++;
+          continue;
+        }
+      }
+      let samplevalue;
+      if (_term && !t.term) {
+        if (t.term$type && t.term$type !== _term.type) {
+          numberofmatchedterms++;
+          continue;
+        }
+        t.term = _term;
+        samplevalue = typeof row === "object" && t.term.id in row ? row[t.term.id] : row;
+      } else if (sample && t.term.$id) {
+        samplevalue = sample[t.term.$id].value;
+      } else {
+        samplevalue = t.term.id in row ? row[t.term.id] : row;
+      }
+      setDatasetAnnotations(itemCopy);
+      let thistermmatch;
+      if (t.term.type == "categorical") {
+        if (samplevalue === void 0) continue;
+        thistermmatch = t.valueset.has(samplevalue);
+      } else if (t.term.type == "integer" || t.term.type == "float") {
+        if (samplevalue === void 0) continue;
+        for (const range of t.ranges) {
+          if ("value" in range) {
+            thistermmatch = samplevalue === range.value;
+            if (thistermmatch) break;
+          } else if (samplevalue == range.name) {
+            thistermmatch = true;
+            break;
+          } else {
+            if (t.term.values) {
+              const v = t.term.values[samplevalue.toString()];
+              if (v && v.uncomputable) {
+                continue;
+              }
+            }
+            let left, right;
+            if (range.startunbounded) {
+              left = true;
+            } else if ("start" in range) {
+              if (range.startinclusive) {
+                left = samplevalue >= range.start;
+              } else {
+                left = samplevalue > range.start;
+              }
+            }
+            if (range.stopunbounded) {
+              right = true;
+            } else if ("stop" in range) {
+              if (range.stopinclusive) {
+                right = samplevalue <= range.stop;
+              } else {
+                right = samplevalue < range.stop;
+              }
+            }
+            thistermmatch = left && right;
+          }
+          if (thistermmatch) break;
+        }
+      } else if (t.term.type == "condition") {
+        const key = getPrecomputedKey(t);
+        const anno = samplevalue && samplevalue[key];
+        if (anno) {
+          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
+        }
+      } else if (t.term.type == "geneVariant") {
+        const svalues = samplevalue.values || [samplevalue];
+        for (const sv of svalues) {
+          thistermmatch = t.values.find(
+            (v) => v.dt == sv.dt && (!v.origin || sv.origin == v.origin) && (!v.mclasslst || v.mclasslst.includes(sv.class))
+          ) && true;
+          if (thistermmatch) break;
+        }
+      } else {
+        throw "unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]";
+      }
+      if (t.isnot) {
+        thistermmatch = !thistermmatch;
+      }
+      if (thistermmatch) numberofmatchedterms++;
+    }
+    if (filter.join == "or") {
+      if (numberofmatchedterms && filter.in) return true;
+      if (!numberofmatchedterms && !filter.in) return true;
+    }
+  }
+  if (!("in" in filter)) filter.in = true;
+  return filter.in == (numberofmatchedterms == lst.length);
+}
+function setDatasetAnnotations(item, ds = null) {
+  if (item.type == "tvslst") {
+    for (const subitem of item.lst) {
+      setDatasetAnnotations(subitem, ds);
+    }
+  } else {
+    if (ds && typeof ds.setAnnoByTermId == "function") {
+      ds.setAnnoByTermId(item.tvs.term.id);
+    }
+    if (item.tvs.term.type == "categorical") {
+      const tvsAny = item.tvs;
+      tvsAny.valueset = new Set(tvsAny.values.map((i) => i.key));
+    }
+  }
+}
+function getPrecomputedKey(q) {
+  const precomputedKey = q.bar_by_children && q.value_by_max_grade ? "childrenAtMaxGrade" : q.bar_by_children && q.value_by_most_recent ? "childrenAtMostRecent" : q.bar_by_children && q.value_by_computable_grade ? "children" : q.bar_by_grade && q.value_by_max_grade ? "maxGrade" : q.bar_by_grade && q.value_by_most_recent ? "mostRecentGrades" : q.bar_by_grade && q.value_by_computable_grade ? "computableGrades" : "";
+  if (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`;
+  return precomputedKey;
+}
+function getWrappedTvslst(lst = [], join = "", $id = null) {
+  const filter = {
+    type: "tvslst",
+    in: true,
+    join,
+    lst
+  };
+  if ($id !== null) filter.$id = $id;
+  return filter;
+}
+function getTvsDenominators(term) {
+  if (Array.isArray(term?.denominators) && term.denominators.length) return term.denominators;
+  return (term?.termlst || []).map((t) => t.id);
+}
+function validateTermCollectionTvs(term) {
+  const memberIds = validateTermCollectionTerm(term);
+  if (!term.numerators) return;
+  validateFractionMembers(term.numerators, getTvsDenominators(term), memberIds);
+}
+
+export {
+  isFractionTw,
+  getFractionTvsTerm,
+  validateTermCollectionFraction,
+  getFilteredSamples,
+  sample_match_termvaluesetting,
+  getWrappedTvslst,
+  getTvsDenominators,
+  validateTermCollectionTvs
+};
+//# sourceMappingURL=chunk-4WF3XDQP.js.map

package/dist/chunk-4WF3XDQP.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/utils/src/termCollection.ts", "../../shared/utils/src/filter.ts"],
+  "sourcesContent": ["import type { TermCollectionQFraction } from '#types'\n\ntype CollectionMemberLike = {\n\tid?: string\n\tname?: string\n\ttype?: string\n}\n\nexport type CollectionTermLike = {\n\ttermlst: CollectionMemberLike[]\n\t/** numerator/denominator member ids of a filter tvs, mirroring q.numerators[]/q.denominators[]\n\tof a fraction tw. only used by validateTermCollectionTvs() */\n\tnumerators?: string[]\n\tdenominators?: string[]\n}\n\n/** Validate the term obj of a termCollection, shared by the fraction tw and the filter tvs.\nReturns the set of member term ids, for validating id arrays e.g. numerators. */\nexport function validateTermCollectionTerm(term: CollectionTermLike): Set<string> {\n\tif (!Array.isArray(term?.termlst) || !term.termlst.length)\n\t\tthrow new Error('termCollection requires nonempty term.termlst[]')\n\tconst memberIds: Set<string> = new Set()\n\tconst types: Set<string> = new Set() // term types of member terms\n\tfor (const t of term.termlst) {\n\t\tif (typeof t.id != 'string' || !t.id) throw new Error('member term id not non-empty string') // id required for validating id arrays e.g. numerators\n\t\tif (typeof t.type != 'string' || !t.type) throw new Error('member term type not non-empty string')\n\t\tif (memberIds.has(t.id)) throw new Error(`duplicate member term id '${t.id}'`)\n\t\tmemberIds.add(t.id)\n\n\t\t// allow integer/float to be mixed in one collection\n\t\ttypes.add(t.type == 'integer' || t.type == 'float' ? 'numDict' : t.type)\n\t}\n\tif (types.size > 1) throw new Error('termCollection.termlst[] not allowed to mix multiple term types')\n\treturn memberIds\n}\n\n/** Validate the numerator/denominator member selection of a fraction, shared by the q{} of a\nfraction tw and the term of a filter tvs. Both lists are member term ids of the collection.\nmemberIds is returned by validateTermCollectionTerm() */\nexport function validateFractionMembers(numerators: string[], denominators: string[], memberIds: Set<string>): void {\n\tif (!Array.isArray(denominators) || !denominators.length) throw new Error('fraction requires nonempty denominators[]')\n\tif (!Array.isArray(numerators) || !numerators.length) throw new Error('fraction requires nonempty numerators[]')\n\tif (new Set(denominators).size !== denominators.length) throw new Error('fraction denominators[] contains duplicates')\n\tif (new Set(numerators).size !== numerators.length) throw new Error('fraction numerators[] contains duplicates')\n\tfor (const id of denominators) {\n\t\tif (typeof id != 'string' || !id) throw new Error('fraction denominator id not non-empty string')\n\t\tif (!memberIds.has(id)) throw new Error(`fraction denominator '${id}' is not a collection member`)\n\t}\n\tfor (const id of numerators) {\n\t\tif (typeof id != 'string' || !id) throw new Error('fraction numerator id not non-empty string')\n\t\t// no need to test against memberIds: denominators[] is already a subset of it\n\t\tif (!denominators.includes(id)) throw new Error(`fraction numerator '${id}' is not included in denominators[]`)\n\t}\n}\n\n/** tw.type of a termCollection that resolves to one numeric value per sample, the fraction\nof the numerator members over the denominator ones */\nexport const FRACTION_TW_TYPE = 'TermCollectionTWFraction'\n\n/** True when a tw is a fraction termCollection */\nexport function isFractionTw(tw: any): boolean {\n\treturn tw?.type === FRACTION_TW_TYPE && tw?.term?.type === 'termCollection'\n}\n\n/** Build the tvs.term for filtering on a fraction termCollection, e.g. from a clicked bar\nor a brushed violin. The member selection of a tw lives in q{}, but a tvs is standalone:\nthe server filter and the filter ui both read numerators[]/denominators[] from tvs.term.\nReturns a copy, so that editing the filter later does not mutate the plot term.\n@param tw a filled fraction termCollection tw\n@throws Error if the tw or its member selection is invalid */\nexport function getFractionTvsTerm(tw: any): CollectionTermLike {\n\tif (!isFractionTw(tw)) throw new Error('not a fraction termCollection tw')\n\tconst term = structuredClone(tw.term)\n\t// a min copy tw may carry termIds[] instead of the full termlst[]\n\tconst memberIds = term.termlst?.length ? validateTermCollectionTerm(term) : new Set<string>(term.termIds || [])\n\tconst denominators = tw.q?.denominators?.length ? [...tw.q.denominators] : [...memberIds]\n\tconst numerators = tw.q?.numerators?.length ? [...tw.q.numerators] : [...denominators]\n\tvalidateFractionMembers(numerators, denominators, memberIds)\n\tterm.numerators = numerators\n\tterm.denominators = denominators\n\treturn term\n}\n\n/** Validate the member selection and binning discriminator for a fraction term collection. */\nexport function validateTermCollectionFraction(q: TermCollectionQFraction, term: CollectionTermLike): void {\n\tconst memberIds = validateTermCollectionTerm(term)\n\tvalidateFractionMembers(q?.numerators, q?.denominators, memberIds)\n\tif (q.mode === 'discrete' && q.type !== 'regular-bin' && q.type !== 'custom-bin')\n\t\tthrow new Error('discrete fraction termCollection requires regular-bin or custom-bin q.type')\n}\n", "import type { Filter, Tvs } from '#types'\nimport { validateTermCollectionTerm, validateFractionMembers, type CollectionTermLike } from './termCollection.js'\n\n/**\n * Sample annotation structure\n */\nexport interface SampleAnnotation {\n\tsample: string | number\n\ts?: Record<string, any>\n\tdata?: Record<string, any>\n}\n\n/**\n * Dataset with annotation functionality\n */\nexport interface Dataset {\n\tsetAnnoByTermId?: (termId: string) => void\n}\n\n/**\n * Filters an array of sample annotations and returns a Set of matching sample names\n * @param sampleAnno Array of sample annotations\n * @param filter Nested filter structure as used in the termdbapp\n * @returns Set of sample names that match the filter\n */\nexport function getFilteredSamples(sampleAnno: SampleAnnotation[], filter: Filter): Set<string | number> {\n\tsetDatasetAnnotations(filter)\n\n\tconst samples = new Set<string | number>()\n\tfor (const anno of sampleAnno) {\n\t\tif (samples.has(anno.sample)) continue\n\t\tconst data = anno.s || anno.data\n\t\tif (data && sample_match_termvaluesetting(data, filter)) {\n\t\t\tsamples.add(anno.sample)\n\t\t}\n\t}\n\treturn samples\n}\n\n/**\n * Given a value from a sample's annotation of a term, return true if a value matches the filter\n * @param row Sample annotation data\n * @param filter Filter structure or single tvs item\n * @param _term Optional term to filter by\n * @param sample Optional sample data\n * @returns True if the sample matches the filter\n */\nexport function sample_match_termvaluesetting(\n\trow: any,\n\tfilter: Filter,\n\t_term: any = null,\n\tsample: any = null\n): boolean {\n\tconst lst = filter.type == 'tvslst' ? filter.lst : [filter]\n\tlet numberofmatchedterms = 0\n\n\t/* for AND, require all terms to match */\n\tfor (const item of lst) {\n\t\tif ('type' in item && item.type == 'tvslst') {\n\t\t\tif (sample_match_termvaluesetting(row, item, _term, sample)) {\n\t\t\t\tnumberofmatchedterms++\n\t\t\t}\n\t\t} else {\n\t\t\tconst itemCopy = JSON.parse(JSON.stringify(item))\n\t\t\tconst t = itemCopy.tvs\n\n\t\t\tif (_term && t.term) {\n\t\t\t\tif (!(_term.name == t.term.name && _term.type == t.term.type)) {\n\t\t\t\t\t// for an filter from \"this.config.legendValueFilter\", if the filter is not for the tw\n\t\t\t\t\t// (not the same type and name), ignore the filter.\n\t\t\t\t\tnumberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tlet samplevalue\n\t\t\tif (_term && !t.term) {\n\t\t\t\tif (t.term$type && t.term$type !== _term.type) {\n\t\t\t\t\t//when the filter is not for the term being tested, ignore the filter\n\t\t\t\t\tnumberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tt.term = _term\n\t\t\t\tsamplevalue = typeof row === 'object' && t.term.id in row ? row[t.term.id] : row\n\t\t\t} else if (sample && t.term.$id) {\n\t\t\t\tsamplevalue = sample[t.term.$id].value\n\t\t\t} else {\n\t\t\t\tsamplevalue = t.term.id in row ? row[t.term.id] : row\n\t\t\t}\n\t\t\tsetDatasetAnnotations(itemCopy)\n\t\t\tlet thistermmatch\n\n\t\t\tif (t.term.type == 'categorical') {\n\t\t\t\tif (samplevalue === undefined) continue // this sample has no anno for this term, do not count\n\t\t\t\tthistermmatch = t.valueset.has(samplevalue)\n\t\t\t} else if (t.term.type == 'integer' || t.term.type == 'float') {\n\t\t\t\tif (samplevalue === undefined) continue // this sample has no anno for this term, do not count\n\t\t\t\tfor (const range of t.ranges) {\n\t\t\t\t\tif ('value' in range) {\n\t\t\t\t\t\tthistermmatch = samplevalue === range.value\n\t\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t\t} else if (samplevalue == range.name) {\n\t\t\t\t\t\tthistermmatch = true\n\t\t\t\t\t\tbreak\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// actual range\n\t\t\t\t\t\tif (t.term.values) {\n\t\t\t\t\t\t\tconst v = t.term.values[samplevalue.toString()]\n\t\t\t\t\t\t\tif (v && v.uncomputable) {\n\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tlet left, right\n\t\t\t\t\t\tif (range.startunbounded) {\n\t\t\t\t\t\t\tleft = true\n\t\t\t\t\t\t} else if ('start' in range) {\n\t\t\t\t\t\t\tif (range.startinclusive) {\n\t\t\t\t\t\t\t\tleft = samplevalue >= range.start\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tleft = samplevalue > range.start\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (range.stopunbounded) {\n\t\t\t\t\t\t\tright = true\n\t\t\t\t\t\t} else if ('stop' in range) {\n\t\t\t\t\t\t\tif (range.stopinclusive) {\n\t\t\t\t\t\t\t\tright = samplevalue <= range.stop\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tright = samplevalue < range.stop\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthistermmatch = left && right\n\t\t\t\t\t}\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'condition') {\n\t\t\t\tconst key = getPrecomputedKey(t)\n\t\t\t\tconst anno = samplevalue && samplevalue[key]\n\t\t\t\tif (anno) {\n\t\t\t\t\tthistermmatch = Array.isArray(anno)\n\t\t\t\t\t\t? t.values.find((d: any) => anno.includes(d.key))\n\t\t\t\t\t\t: t.values.find((d: any) => d.key == anno)\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'geneVariant') {\n\t\t\t\t/*\n\t\t\t\tsamplevalue.values here can be an array or only one of the entries \n\t\t\t\t[\n\t\t\t\t\t{ dt: 1, class: 'WT', _SAMPLEID_: 21, origin: 'germline' },\n\t\t\t\t\t{ dt: 1, class: 'WT', _SAMPLEID_: 21, origin: 'somatic' },\n\t\t\t\t\t{ dt: 2, class: 'Blank', _SAMPLEID_: 21 },\n\t\t\t\t\t{ dt: 4, class: 'WT', _SAMPLEID_: 21 }\n\t\t\t\t]\n\t\t\t\t*/\n\t\t\t\t/* tvs.values is an array that stores classes (for each available dt) that have/haven't been crossed out by the user at this round of edit-and-apply, e.g.\n          [\n            {dt: 1, mclassLst: ['WT'], mclassExcludeLst: ['Blank'], origin: 'germline'}\n            {dt: 1, mclassLst: ['Blank', 'WT', 'M'], mclassExcludeLst:[], origin:'somatic'},\n            {dt: 2, mclassLst: ['Blank', 'WT'], mclassExcludeLst:[]}\n            {dt: 4, mclassLst: ['WT', 'CNV_loss'], mclassExcludeLst:[]}\n          ]\n        */\n\t\t\t\tconst svalues = samplevalue.values || [samplevalue]\n\t\t\t\tfor (const sv of svalues) {\n\t\t\t\t\tthistermmatch =\n\t\t\t\t\t\tt.values.find(\n\t\t\t\t\t\t\t(v: any) =>\n\t\t\t\t\t\t\t\tv.dt == sv.dt &&\n\t\t\t\t\t\t\t\t(!v.origin || sv.origin == v.origin) &&\n\t\t\t\t\t\t\t\t(!v.mclasslst || v.mclasslst.includes(sv.class))\n\t\t\t\t\t\t) && true\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tthrow 'unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]'\n\t\t\t}\n\n\t\t\tif (t.isnot) {\n\t\t\t\tthistermmatch = !thistermmatch\n\t\t\t}\n\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t}\n\n\t\t// if one tvslst is matched with an \"or\" (Set UNION), then sample is okay\n\t\tif (filter.join == 'or') {\n\t\t\tif (numberofmatchedterms && filter.in) return true\n\t\t\tif (!numberofmatchedterms && !filter.in) return true\n\t\t}\n\t}\n\t// for join=\"and\" (Set intersection)\n\tif (!('in' in filter)) (filter as any).in = true // casting to any avoids tsc err despite it's typed!\n\treturn filter.in == (numberofmatchedterms == lst.length)\n}\n\n/**\n * Recursively processes filter items and sets dataset annotations\n * @param item Filter item to process\n * @param ds Optional dataset with annotation functionality\n */\nexport function setDatasetAnnotations(item: Filter | { type: 'tvs'; tvs: Tvs }, ds: Dataset | null = null): void {\n\tif (item.type == 'tvslst') {\n\t\tfor (const subitem of item.lst) {\n\t\t\tsetDatasetAnnotations(subitem, ds)\n\t\t}\n\t} else {\n\t\tif (ds && typeof ds.setAnnoByTermId == 'function') {\n\t\t\tds.setAnnoByTermId(item.tvs.term.id)\n\t\t}\n\t\tif (item.tvs.term.type == 'categorical') {\n\t\t\tconst tvsAny = item.tvs as any\n\t\t\ttvsAny.valueset = new Set(tvsAny.values.map((i: any) => i.key))\n\t\t}\n\t}\n}\n\n/**\n * Gets the precomputed key for a condition term based on bar_by and value_by settings\n */\nfunction getPrecomputedKey(q: any): string {\n\tconst precomputedKey =\n\t\tq.bar_by_children && q.value_by_max_grade\n\t\t\t? 'childrenAtMaxGrade'\n\t\t\t: q.bar_by_children && q.value_by_most_recent\n\t\t\t? 'childrenAtMostRecent'\n\t\t\t: q.bar_by_children && q.value_by_computable_grade\n\t\t\t? 'children'\n\t\t\t: q.bar_by_grade && q.value_by_max_grade\n\t\t\t? 'maxGrade'\n\t\t\t: q.bar_by_grade && q.value_by_most_recent\n\t\t\t? 'mostRecentGrades'\n\t\t\t: q.bar_by_grade && q.value_by_computable_grade\n\t\t\t? 'computableGrades'\n\t\t\t: ''\n\tif (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`\n\treturn precomputedKey\n}\n\n/**\n * Joins a list of filters into the first filter with \"and\", returns joined filter\n * Used by caller app to join hidden filters into a visible filter\n * @param lst List of filters to join\n * @returns The joined filter\n */\nexport function filterJoin(lst: Filter[]): Filter | undefined {\n\tif (!lst || lst.length == 0) return\n\tlet f = JSON.parse(JSON.stringify(lst[0]))\n\tif (lst.length == 1) return f\n\t// more than 1 item, will join\n\tif (f.lst.length < 2) {\n\t\tif (f.join !== '') throw 'filter.join must be an empty string \"\" when filter.lst.length < 2'\n\t\tf.join = 'and'\n\t} else if (f.join == 'or') {\n\t\t// f is \"or\", wrap it with another root layer of \"and\"\n\t\tf = {\n\t\t\ttype: 'tvslst',\n\t\t\tjoin: 'and',\n\t\t\tin: true,\n\t\t\tlst: [f]\n\t\t}\n\t} else if (f.join != 'and') {\n\t\tthrow 'filter.join must be either \"and\" or \"or\" when .lst length > 1'\n\t}\n\t// now, f.join should be \"and\"\n\t// if the argument lst[0].join == \"and\",\n\t// then the f.in boolean value is reused\n\tfor (let i = 1; i < lst.length; i++) {\n\t\tconst f2 = JSON.parse(JSON.stringify(lst[i]))\n\t\tif (f2.join == 'or') f.lst.push(f2)\n\t\telse f.lst.push(...f2.lst)\n\t}\n\t// if f ends up single-tvs item (from joining single tvs to empty filter), need to set join to '' per filter spec\n\tif (f.lst.length == 1 && f.lst[0].type == 'tvs') {\n\t\tf.join = ''\n\t}\n\treturn f\n}\n\n/**\n * Creates a wrapped tvslst (term value settings list) filter object\n * @param lst List of filter items\n * @param join Join operation (and/or)\n * @param $id Optional filter ID\n * @returns Wrapped filter object\n */\nexport function getWrappedTvslst(lst: Filter['lst'] = [], join: string = '', $id: string | null = null): Filter {\n\tconst filter: Filter = {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin,\n\t\tlst\n\t}\n\tif ($id !== null) filter.$id = $id\n\treturn filter\n}\n\nexport function getTvsDenominators(term: any): string[] {\n\t/* Denominator term ids of a termCollection tvs, which reduces the collection to a\n\tpercentage. term.denominators[] is explicit, matching q.denominators[] of a fraction\n\ttermCollection tw. Filters saved before term.denominators[] existed implied the\n\tdenominator from term.termlst[], which was pruned to the selected members. */\n\tif (Array.isArray(term?.denominators) && term.denominators.length) return term.denominators\n\treturn (term?.termlst || []).map(t => t.id)\n}\n\n/**\n * Validates the term obj of a termCollection tvs, and its fraction member selection\n * @param term tvs.term of a termCollection. term.numerators[] is optional: a tvs may brush\n * on a single member instead of the numerator/denominator fraction. When present, it is\n * validated against the denominators from getTvsDenominators()\n * @throws Error if validation fails\n */\nexport function validateTermCollectionTvs(term: CollectionTermLike): void {\n\tconst memberIds = validateTermCollectionTerm(term)\n\tif (!term.numerators) return // not filtering on a fraction, nothing more to validate\n\tvalidateFractionMembers(term.numerators, getTvsDenominators(term), memberIds)\n}\n"],
+  "mappings": 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+  "names": []
+}

package/dist/chunk-5DMVORBB.js

@@ -0,0 +1,98 @@
+import {
+  keyupEnter
+} from "./chunk-TKW5TW4Z.js";
+import {
+  require_debounce
+} from "./chunk-LSEFWW72.js";
+import {
+  Menu
+} from "./chunk-HYOEWQ5P.js";
+import {
+  dofetch,
+  dofetch3
+} from "./chunk-JVPWIVDT.js";
+import {
+  __toESM
+} from "./chunk-HFNDKYVF.js";
+
+// src/gene.js
+var import_debounce = __toESM(require_debounce(), 1);
+var tip;
+function gene_searchbox(p) {
+  if (!tip) {
+    tip = new Menu({ padding: "" });
+    tip.d.style("z-index", 1e3);
+  }
+  const input = p.div.append("input").attr("placeholder", "Search gene").style("width", p.width || "100px");
+  const printdiv = p.resultdiv || (p.tip ? p.tip.d : tip.d);
+  function fold() {
+    if (p.resultdiv) {
+      p.resultdiv.selectAll("*").remove();
+    } else if (p.tip) {
+      p.tip.hide();
+    } else {
+      tip.hide();
+    }
+  }
+  input.on("keyup", (event) => {
+    const str = event.target.value;
+    if (str.length <= 1) {
+      fold();
+      return;
+    }
+    if (keyupEnter(event)) {
+      const hitgene = printdiv.select(".sja_menuoption");
+      if (hitgene.size() > 0) {
+        p.callback(hitgene.text());
+        fold();
+      }
+      return;
+    }
+    debouncer();
+  });
+  input.node().focus();
+  function genesearch() {
+    dofetch("genelookup", { genome: p.genome, input: input.property("value") }).then((data) => {
+      if (data.error) throw data.error;
+      if (!data.hits) throw ".hits[] missing";
+      if (p.resultdiv) {
+        p.resultdiv.selectAll("*").remove();
+      } else if (p.tip) {
+        p.tip.clear().showunder(input.node());
+      } else {
+        tip.clear().showunder(input.node());
+      }
+      for (const name of data.hits) {
+        printdiv.append("div").attr("class", "sja_menuoption").text(name).on("click", () => {
+          p.callback(name);
+          fold();
+        });
+      }
+    }).catch((err) => {
+      printdiv.append("div").text(err.message || err);
+      if (err.stack) console.log(err.stack);
+    });
+  }
+  const debouncer = (0, import_debounce.debounce)(genesearch, 300);
+}
+function findgenemodel_bysymbol(genome, str) {
+  return dofetch3("genelookup", {
+    body: {
+      deep: 1,
+      input: str,
+      genome
+    }
+  }).then((data) => {
+    if (data.error) throw data.error;
+    if (!data.gmlst || data.gmlst.length == 0) return null;
+    return data.gmlst;
+  }).catch((e) => {
+    throw e;
+  });
+}
+
+export {
+  gene_searchbox,
+  findgenemodel_bysymbol
+};
+//# sourceMappingURL=chunk-5DMVORBB.js.map