@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/chunk-KVG7FTTK.js

@@ -0,0 +1,470 @@
+import {
+  rehydrateFilter
+} from "./chunk-SKMFMGCD.js";
+import {
+  findParent,
+  getFilter,
+  getFilterItemByTag,
+  getSamplelstTW
+} from "./chunk-7FEHI46K.js";
+import {
+  importPlot
+} from "./chunk-XD6BFNMR.js";
+import {
+  StoreApi,
+  StoreBase
+} from "./chunk-MVTCBVSX.js";
+import {
+  CustomError
+} from "./chunk-BEWDIM6H.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-KVG7FTTK.js.map

package/dist/chunk-LEDPPLQK.js

@@ -0,0 +1,158 @@
+import {
+  appInit
+} from "./chunk-PIACSJPH.js";
+import {
+  showErrorsWithCounter
+} from "./chunk-7FEHI46K.js";
+import {
+  mclass
+} from "./chunk-IGEQI6MR.js";
+
+// plots/disco/launch.adhoc.ts
+async function launch(arg, genomeObj, holder) {
+  const [mlst, errors] = await getMlst(arg);
+  if (errors?.length) {
+    return showErrorsWithCounter(errors, holder);
+  }
+  const opts = {
+    holder,
+    vocabApi: {
+      // api is required by plot.app.js, so create a mock one for the adhoc data
+      vocab: { terms: [] },
+      main: () => {
+        return;
+      },
+      getTermdbConfig: () => {
+        return {};
+      }
+    },
+    state: {
+      args: {
+        data: mlst,
+        genome: genomeObj
+      },
+      plots: [
+        {
+          chartType: "Disco",
+          subfolder: "disco",
+          extension: "ts",
+          /** NOTE: Users should only override the settings in the default
+           * settings.Disco:{}, not the entire settings:{} object.*/
+          overrides: { Disco: arg?.settings || {} }
+        }
+      ]
+    }
+  };
+  const plotAppApi = await appInit(opts);
+  return plotAppApi;
+}
+async function getMlst(arg) {
+  if (Array.isArray(arg.mlst)) {
+    return [arg.mlst, null];
+  }
+  const mlst = [];
+  const errors = [];
+  if (arg.snvText) parseSnvText(arg.snvText, mlst, errors);
+  if (arg.svText) parseSvText(arg.svText, mlst, errors);
+  if (arg.cnvText) parseCnvText(arg.cnvText, mlst, errors);
+  return [mlst, errors];
+}
+function parseSnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 5) {
+      errors.push("snv input not equal to 5 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 1,
+        chr: l[0],
+        position: Number(l[1]),
+        gene: l[2],
+        mname: l[3],
+        class: validateMutation(l[4], errors)
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseSvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length < 4 || l.length > 6) {
+      errors.push("sv input not equal to 4 or 6 columns");
+      continue;
+    }
+    let m;
+    try {
+      const length = l.length;
+      if (length == 4) {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          chrB: l[2],
+          posB: Number(l[3])
+        };
+      } else {
+        m = {
+          dt: 2,
+          chrA: l[0],
+          posA: Number(l[1]),
+          geneA: l[2],
+          chrB: l[3],
+          posB: Number(l[4]),
+          geneB: l[5]
+        };
+      }
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function parseCnvText(text, mlst, errors) {
+  for (const line of text.trim().split("\n")) {
+    const l = line.trim().split("	");
+    if (l.length != 4) {
+      errors.push("cnv input not equal to 4 columns");
+      continue;
+    }
+    let m;
+    try {
+      m = {
+        dt: 4,
+        chr: l[0],
+        start: Number(l[1]),
+        stop: Number(l[2]),
+        value: Number(l[3])
+      };
+    } catch (e) {
+      errors.push(e);
+      continue;
+    }
+    mlst.push(m);
+  }
+}
+function validateMutation(mutation, errors) {
+  const mut2check = mutation.toLowerCase();
+  const foundMutation = Object.values(mclass).find(
+    (m) => m.key.toLowerCase() === mut2check || m.label.toLowerCase() === mut2check
+  );
+  if (foundMutation) {
+    return foundMutation.key;
+  } else {
+    errors.push(`Invalid mutation class: ${mutation}`);
+  }
+}
+
+export {
+  launch
+};
+//# sourceMappingURL=chunk-LEDPPLQK.js.map