@sjcrh/proteinpaint-client 2.181.0 → 2.182.1

package/dist/chunk-BHVDOW3W.js

@@ -1,470 +0,0 @@
-import {
-  rehydrateFilter
-} from "./chunk-SKMFMGCD.js";
-import {
-  findParent,
-  getFilter,
-  getFilterItemByTag,
-  getSamplelstTW
-} from "./chunk-XZZLEHWC.js";
-import {
-  importPlot
-} from "./chunk-CJJ6LDZM.js";
-import {
-  StoreApi,
-  StoreBase
-} from "./chunk-MVTCBVSX.js";
-import {
-  CustomError
-} from "./chunk-TV74I3Y5.js";
-
-// mass/store.ts
-var idPrefix = "_MASS_AUTOID_" + Math.random().toString().slice(-6);
-var id = 0;
-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) {
-    const plot = {
-      id: "id" in action ? action.id : getId()
-    };
-    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) {
-    const _ = await importPlot(action.config.chartType);
-    const plot = await _.getPlotConfig(action.config, this.app, this.state.activeCohort);
-    if (!("id" in action)) action.id = getId();
-    plot.id = action.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-BHVDOW3W.js.map

package/dist/chunk-BNN32RI2.js

@@ -1,36 +0,0 @@
-import {
-  addGeneSearchbox
-} from "./chunk-XZZLEHWC.js";
-import {
-  Menu
-} from "./chunk-2SRMRC6L.js";
-import {
-  TermTypes
-} from "./chunk-2UWHV2SB.js";
-
-// termdb/handlers/geneExpression.ts
-var SearchHandler = class {
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => this.selectGene(geneSearch.geneSymbol)
-    });
-  }
-  async selectGene(gene) {
-    const unit = this.app.vocabApi.termdbConfig.queries.geneExpression?.unit || "Gene Expression";
-    const name = `${gene} ${unit}`;
-    if (!gene) throw new Error("No gene selected");
-    this.callback({ gene, name, type: TermTypes.GENE_EXPRESSION });
-  }
-};
-
-export {
-  SearchHandler
-};
-//# sourceMappingURL=chunk-BNN32RI2.js.map

package/dist/chunk-BNN32RI2.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../termdb/handlers/geneExpression.ts"],
-  "sourcesContent": ["import { Menu, addGeneSearchbox } from '#dom'\nimport { TermTypes } from '#shared/terms.js'\n\nexport class SearchHandler {\n\tcallback: any\n\tapp: any\n\tinit(opts) {\n\t\tthis.callback = opts.callback\n\t\tthis.app = opts.app\n\t\tconst holder = opts.holder.append('div').style('padding', '10px 0px')\n\t\tconst geneSearch = addGeneSearchbox({\n\t\t\ttip: new Menu({ padding: '0px' }),\n\t\t\tgenome: opts.genomeObj,\n\t\t\trow: holder,\n\t\t\tsearchOnly: 'gene',\n\t\t\tcallback: () => this.selectGene(geneSearch.geneSymbol)\n\t\t})\n\t}\n\n\tasync selectGene(gene) {\n\t\tconst unit = this.app.vocabApi.termdbConfig.queries.geneExpression?.unit || 'Gene Expression'\n\t\tconst name = `${gene} ${unit}`\n\t\tif (!gene) throw new Error('No gene selected')\n\t\tthis.callback({ gene, name, type: TermTypes.GENE_EXPRESSION })\n\t}\n}\n"],
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-  "names": []
-}