@sjcrh/proteinpaint-client 2.198.0 → 2.200.0

package/dist/chunk-USFSHSCJ.js

@@ -1,477 +0,0 @@
-import {
-  rehydrateFilter
-} from "./chunk-SKMFMGCD.js";
-import {
-  findParent,
-  getFilter,
-  getFilterItemByTag,
-  getSamplelstTW
-} from "./chunk-5VOPABBA.js";
-import {
-  importPlot
-} from "./chunk-Z5U6HOE4.js";
-import {
-  StoreApi,
-  StoreBase
-} from "./chunk-M3J4MINX.js";
-import {
-  CustomError
-} from "./chunk-JNITUVXP.js";
-
-// mass/store.ts
-var idPrefix = "_MASS_AUTOID_" + Math.random().toString().slice(-6);
-var id = 0;
-var usedPlotIds = /* @__PURE__ */ new Set();
-function getId() {
-  return idPrefix + "_" + id++;
-}
-var navHeaderModes = /* @__PURE__ */ new Set([
-  "with_tabs",
-  // default, shows tabs cohort/charts/filter etc
-  "hidden",
-  // no header
-  "search_only",
-  // ?
-  "hide_search",
-  // ?
-  "with_cohortHtmlSelect",
-  // only show cohort toggle as <select>
-  "only_buttons"
-]);
-var defaultState = {
-  nav: {
-    header_mode: "with_tabs",
-    activeTab: 0
-    // -1 for no active tab and all closed
-  },
-  // will be ignored if there is no dataset termdb.selectCohort
-  // or value will be set to match a filter node that has been tagged
-  // as 'cohortfilter' in state.termfilter.filter
-  activeCohort: 0,
-  search: { isVisible: true },
-  plots: [],
-  termfilter: {
-    filter: {
-      type: "tvslst",
-      in: true,
-      join: "",
-      lst: []
-    }
-  },
-  reuse: {
-    customTermQ: {
-      byId: {},
-      // non-dictionary terms do not have a term.id,
-      // save by term.type + name?
-      byName: {}
-    }
-  },
-  groups: [],
-  // element: {name=str, filter={}}, to show in Groups tab
-  customTerms: [],
-  // element: {name=str, term={}}, able to attach more attr to object if needed
-  autoSave: true
-};
-var MassStore = class extends StoreBase {
-  constructor(opts, api) {
-    super(opts);
-    // expected class-specific props
-    this.defaultState = defaultState;
-    this.plotAdjusters = /* @__PURE__ */ new WeakMap();
-    this.app = opts.app;
-    this.api = api;
-    this.type = "store";
-    let savedState = {};
-    try {
-      const key = window.navigator.webdriver && window["SJPP_E2E_STORAGE_STATES_KEY"];
-      const savedStateStr = key && window.localStorage.getItem("SJPP_E2E_STORAGE_STATES") || "{}";
-      savedState = JSON.parse(savedStateStr)[key]?.state || {};
-    } catch (_) {
-      savedState = {};
-    }
-    this.state = this.copyMerge(this.toJson(defaultState), opts.state, savedState);
-    this.prevGeneratedId = 0;
-  }
-  static {
-    this.type = "store";
-  }
-  validateOpts(opts) {
-    const s = opts.state;
-    if (s.vocab.dslabel) {
-      if (!s.vocab.genome) throw ".state[.vocab].genome missing";
-    } else {
-      if (!Array.isArray(s.vocab.terms)) throw "vocab.terms must be an array of objects";
-    }
-    return opts;
-  }
-  validateState() {
-    if (!navHeaderModes.has(this.state.nav.header_mode)) throw "invalid state.nav.header_mode";
-  }
-  async init() {
-    try {
-      this.state.termdbConfig = await this.app.vocabApi.getTermdbConfig();
-      await this.setTermfilter();
-      await this.rehydrateGroups();
-      await this.app.vocabApi.main({
-        termfilter: JSON.parse(JSON.stringify(this.state.termfilter)),
-        termdbConfig: this.state.termdbConfig
-      });
-      const invalidPlots = [];
-      for (const [i, savedPlot] of this.state.plots.entries()) {
-        let plot;
-        try {
-          const _ = await importPlot(savedPlot.chartType);
-          plot = await _.getPlotConfig(savedPlot, this.app, this.state.activeCohort);
-        } catch (e) {
-          this.app.printError(e);
-          console.error(`getPlotConfig() failed: ${e}`);
-        }
-        if (!plot) {
-          invalidPlots.push(i);
-          continue;
-        }
-        this.state.plots[i] = plot;
-        if (!("id" in plot)) plot.id = `_AUTOID_${id++}_${i}`;
-        if (plot.mayAdjustConfig) {
-          plot.mayAdjustConfig(plot);
-          this.plotAdjusters.set(plot, plot.mayAdjustConfig);
-          delete plot.mayAdjustConfig;
-        }
-      }
-      if (invalidPlots.length) {
-        for (const i of invalidPlots) {
-          this.state.plots.splice(i, 1);
-        }
-      }
-    } catch (e) {
-      console.log("store.init() error", e);
-      throw e;
-    }
-  }
-  setId(item) {
-    item.$id = this.prevGeneratedId++;
-    if (item.$lst) {
-      for (const subitem of item.$lst) {
-        this.setId(subitem);
-      }
-    }
-  }
-  async setTermfilter() {
-    let filterUiRoot = getFilterItemByTag(this.state.termfilter.filter, "filterUiRoot");
-    if (!filterUiRoot) {
-      this.state.termfilter.filter.tag = "filterUiRoot";
-      filterUiRoot = this.state.termfilter.filter;
-    }
-    await Promise.all(rehydrateFilter(this.state.termfilter.filter, this.app.vocabApi));
-    if (!this.state.termdbConfig.selectCohort) {
-      this.state.activeCohort = -1;
-      if (this.state.activeTab === 0) this.state.activeTab = 1;
-      if (this.state.nav.header_mode === "with_cohortHtmlSelect") {
-        console.warn(`no termdbConfig.selectCohort to use for nav.header_mode = 'with_cohortHtmlSelect'`);
-        this.state.nav.header_mode = "search_only";
-      }
-    } else {
-      let cohortFilter = getFilterItemByTag(this.state.termfilter.filter, "cohortFilter");
-      if (!cohortFilter) {
-        cohortFilter = {
-          tag: "cohortFilter",
-          type: "tvs",
-          tvs: {
-            term: JSON.parse(JSON.stringify(this.state.termdbConfig.selectCohort.term)),
-            values: this.state.activeCohort == -1 ? [] : this.state.termdbConfig.selectCohort.values[this.state.activeCohort].keys.map((key) => {
-              return { key, label: key };
-            })
-          }
-        };
-        this.state.termfilter.filter = {
-          type: "tvslst",
-          in: true,
-          join: "and",
-          lst: [cohortFilter, filterUiRoot]
-        };
-      } else {
-        const sorter = (a, b) => a < b ? -1 : 1;
-        cohortFilter.tvs.values.sort((a, b) => a.key < b.key ? -1 : 1);
-        const keysStr = JSON.stringify(cohortFilter.tvs.values.map((v) => v.key).sort(sorter));
-        const i = this.state.termdbConfig.selectCohort.values.findIndex(
-          (v) => keysStr == JSON.stringify(v.keys.sort(sorter))
-        );
-        if (this.state.activeCohort !== -1 && this.state.activeCohort !== 0 && i !== this.state.activeCohort) {
-          console.log("Warning: cohortFilter will override the state.activeCohort due to mismatch");
-        }
-        this.state.activeCohort = i;
-      }
-    }
-  }
-  async rehydrateGroups() {
-    const lst = [];
-    for (const g of this.state.groups) {
-      lst.push(...rehydrateFilter(g.filter, this.app.vocabApi));
-    }
-    await Promise.all(lst);
-  }
-};
-MassStore.prototype.actions = {
-  // 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>'.
-  // Object literal may only specify known properties, and 'app_refresh' does not exist in type '(action: { [prop: string]: any; type: string; }) => void | Promise<void>'.
-  async app_refresh(action) {
-    this.state = this.copyMerge(this.toJson(this.state), action.state || {});
-    const subactionPlotIds = /* @__PURE__ */ new Set();
-    const promises = [];
-    if (action.subactions) {
-      for (const a of action.subactions) {
-        promises.push(this.actions[a.type].call(this, a));
-        if (a.type.startsWith("plot_")) subactionPlotIds.add(a.id);
-      }
-    }
-    await Promise.all(promises);
-    for (const plot of this.state.plots) {
-      const mayAdjustConfig = this.plotAdjusters.get(plot);
-      if (mayAdjustConfig && !subactionPlotIds.has(plot.id)) {
-        mayAdjustConfig(plot, action.config);
-      }
-    }
-  },
-  tab_set(action) {
-    this.state.nav.activeTab = action.activeTab;
-  },
-  cohort_set(action) {
-    this.state.activeCohort = action.activeCohort;
-    const cohort = this.state.termdbConfig.selectCohort.values[action.activeCohort];
-    const cohortFilter = getFilterItemByTag(this.state.termfilter.filter, "cohortFilter");
-    if (!cohortFilter) throw `No item tagged with 'cohortFilter'`;
-    cohortFilter.tvs.values = cohort.keys.map((key) => {
-      return { key, label: key };
-    });
-  },
-  // dispatch "plot_prep" action to produce a 'initiating' UI of this plot, for user to fill in additional details to launch the plot
-  // example: table, scatterplot which requires user to select two terms
-  async plot_prep(action) {
-    if (usedPlotIds.has(action.id)) delete action.id;
-    const plot = {
-      // rx.getComponents() relies on parsing dot-separated key names that breaks if a key has a dot,
-      // the plot.id value should be assumed to be auto-generated and to not have any non-rx usage expectations
-      id: "id" in action && !action.id.includes(".") ? action.id : getId()
-    };
-    usedPlotIds.add(plot.id);
-    if (!action.config) throw ".config{} missing for plot_prep";
-    if (action.config.chartType && Object.keys(action.config).length == 1) {
-      const _ = await importPlot(action.config.chartType);
-      const config = await _.getPlotConfig(action.config, this.app, this.state.activeCohort);
-      action.config = Object.assign(config, action.config);
-    }
-    Object.assign(plot, action.config);
-    this.state.plots.push(plot);
-  },
-  async plot_create(action) {
-    if (usedPlotIds.has(action.id)) delete action.id;
-    const _ = await importPlot(action.config.chartType);
-    const plot = await _.getPlotConfig(action.config, this.app, this.state.activeCohort);
-    if (!("id" in action) || action.id.includes(".")) action.id = getId();
-    plot.id = action.id;
-    usedPlotIds.add(plot.id);
-    if (plot.mayAdjustConfig) {
-      plot.mayAdjustConfig(plot);
-      this.plotAdjusters.set(plot, plot.mayAdjustConfig);
-      delete plot.mayAdjustConfig;
-    }
-    this.state.plots.push(plot);
-    if (plot.sections) {
-      for (const section of plot.sections) {
-        for (const p of section.plots) {
-          p.parentId = plot.id;
-          if (!p.id) p.id = getId();
-          const _2 = await importPlot(p.chartType);
-          const config = await _2.getPlotConfig(p, this.app, this.state.activeCohort);
-          this.state.plots.push(config);
-        }
-      }
-    }
-  },
-  plot_edit(action) {
-    const plot = this.state.plots.find((p) => p.id === action.id);
-    if (!plot) {
-      throw new CustomError(`missing plot config for id='${action.id}' in store.plot_edit()`, {
-        name: "MISSING_PLOT_CONFIG",
-        level: "warn"
-      });
-    }
-    this.copyMerge(plot, action.config, action.opts ? action.opts : {});
-    const mayAdjustConfig = this.plotAdjusters.get(plot);
-    if (mayAdjustConfig) mayAdjustConfig(plot, action.config);
-    if (action.config && "cutoff" in action.config) {
-      plot.cutoff = action.config.cutoff;
-    } else {
-      delete plot.cutoff;
-    }
-    if (!action.parentId && plot.parentId) action.parentId = plot.parentId;
-  },
-  plot_delete(action) {
-    const i = this.state.plots.findIndex((p) => p.id === action.id);
-    if (i !== -1) {
-      this.state.plots.splice(i, 1);
-      const plot = this.state.plots[i];
-      if (!action.parentId && plot?.parentId) action.parentId = plot.parentId;
-    }
-  },
-  plot_nestedEdits(action) {
-    const plot = this.state.plots.find((p) => p.id === action.id);
-    if (!plot) {
-      throw new CustomError(`missing plot config for id='${action.id}' in store.plot_edit_nested`, {
-        name: "MISSING_PLOT_CONFIG",
-        level: "warn"
-      });
-    }
-    for (const edit of action.edits) {
-      const lastKey = edit.nestedKeys.pop();
-      const obj = edit.nestedKeys.reduce((obj2, key) => obj2[key], plot);
-      obj[lastKey] = edit.value;
-    }
-    if (!action.parentId && plot.parentId) action.parentId = plot.parentId;
-  },
-  // TODO: delete this action? does not seem to be used
-  async plot_splice(action) {
-    for (const a of action.subactions) {
-      await this.actions[a.type].call(this, a);
-    }
-  },
-  filter_replace(action) {
-    if ("filter0" in action) {
-      this.state.termfilter.filter0 = action.filter0;
-      return;
-    }
-    const replacementFilter = action.filter ? action.filter : { type: "tvslst", join: "", in: 1, lst: [] };
-    if (!action.filter.tag) {
-      this.state.termfilter.filter = replacementFilter;
-    } else {
-      const filter = getFilterItemByTag(this.state.termfilter.filter, action.filter.tag);
-      if (!filter) throw `cannot replace missing filter with tag '${action.filter.tag}'`;
-      const parent = findParent(this.state.termfilter.filter, filter.$id);
-      if (parent == filter) {
-        this.state.termfilter.filter = replacementFilter;
-      } else {
-        const i = parent.lst.indexOf(filter);
-        parent.lst[i] = replacementFilter;
-      }
-    }
-    if (this.app.opts.app?.onFilterChange) this.app.opts.app.onFilterChange(this.state.plots);
-  },
-  cache_termq({ termId, q }) {
-    if (!termId) throw `missing termId for caching custom term.q`;
-    if (!q?.reuseId) throw `missing or empty tw.q.reuseId as cache identifier for term='${termId}'`;
-    const cache = this.state.reuse.customTermQ.byId;
-    if (!cache[termId]) cache[termId] = {};
-    cache[termId][q.reuseId] = q;
-    for (const plot of this.state.plots) {
-      if (!(plot.chartType in getTwsByChartType)) continue;
-      const twlst = getTwsByChartType[plot.chartType](plot);
-      for (const tw of twlst) {
-        if (tw?.q?.reuseId === q.reuseId) tw.q = q;
-      }
-    }
-  },
-  uncache_termq({ term, q }) {
-    if (!term.id) throw `missing term.id for uncaching custom term.q`;
-    if (!q.reuseId) throw `missing qname as uncache identifier for term.id='${term.id}'`;
-    const cache = this.state.reuse.customTermQ.byId[term.id];
-    if (!cache) throw `missing term.q cache for term.id='${term.id}`;
-    if (!(q.reuseId in cache)) console.warn(`q.reuseId='${q.cacheid}' not cached for term.id='${term.id}'`);
-    else {
-      delete cache[q.reuseId];
-      for (const plot of this.state.plots) {
-        if (!(plot.chartType in getTwsByChartType)) continue;
-        const twlst = getTwsByChartType[plot.chartType](plot);
-        for (const tw of twlst) {
-          if (tw.q.reuseId === q.reuseId) {
-            delete tw.q.reuseId;
-            delete tw.q.name;
-          }
-        }
-      }
-    }
-  },
-  add_customTerm(action) {
-    this.state.customTerms.push(action.obj);
-  },
-  delete_customTerm({ name }) {
-    const i = this.state.customTerms.findIndex((i2) => i2.name == name);
-    if (i != -1) this.state.customTerms.splice(i, 1);
-  },
-  add_group(action) {
-    if (this.state.nav.header_mode != "hidden") {
-      const group = action.obj;
-      const name = `Group ${this.state.groups.length + 1}`;
-      const samplelstTW = getSamplelstTW([group]);
-      const appGroup = {
-        name,
-        filter: getFilter(samplelstTW),
-        plotId: group.plotId
-      };
-      this.state.groups.push(appGroup);
-      this.state.nav.activeTab = 1;
-    } else if ("plotId" in action.obj) {
-      const plot = this.state.plots.find((p) => p.id == action.obj.plotId);
-      if (plot.groups) {
-        action.obj.index = plot.groups.length;
-        action.obj.name = `Group ${plot.groups.length + 1}`;
-        plot.groups.push(action.obj);
-      }
-    }
-  },
-  rename_group(action) {
-    const index = action.index;
-    const newName = action.newName;
-    if (this.state.nav.header_mode != "hidden") {
-      this.state.groups[index].name = newName;
-    } else {
-      for (const plot of this.state.plots) {
-        if (plot?.groups) {
-          plot.groups[index].name = newName;
-        }
-      }
-    }
-  },
-  change_color_group(action) {
-    const index = action.index;
-    const newColor = action.newColor;
-    if (this.state.nav.header_mode != "hidden") {
-      this.state.groups[index].color = newColor;
-    } else {
-      for (const plot of this.state.plots) {
-        if (plot?.groups) {
-          plot.groups[index].color = newColor;
-        }
-      }
-    }
-  },
-  delete_group({ name }) {
-    if (this.state.nav.header_mode != "hidden") {
-      const i = this.state.groups.findIndex((i2) => i2.name == name);
-      if (i != -1) this.state.groups.splice(i, 1);
-    } else {
-      for (const plot of this.state.plots) {
-        if (plot?.groups) {
-          const j = plot.groups.findIndex((j2) => j2.name == name);
-          if (j != -1) plot.groups.splice(j, 1);
-        }
-      }
-    }
-  }
-};
-var getNestedChartSeriesDataTws = (plot) => [plot.term0, plot.term, plot.term2].filter((d) => !!d);
-var getTwsByChartType = {
-  summary: getNestedChartSeriesDataTws,
-  survival: getNestedChartSeriesDataTws,
-  cuminc: getNestedChartSeriesDataTws,
-  regression: (plot) => [plot.outcome, ...plot.independent].filter((d) => !!d),
-  matrix: (plot) => plot.termgroups.reduce((arr, grp) => {
-    arr.push(...grp.lst);
-    return arr;
-  }, [])
-};
-var storeInit = StoreApi.getInitFxn(MassStore);
-
-export {
-  storeInit
-};
-//# sourceMappingURL=chunk-USFSHSCJ.js.map

package/dist/chunk-USFSHSCJ.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'\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\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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