@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-M3EBH2WK.js

@@ -1,194 +0,0 @@
-import {
-  sample_match_termvaluesetting
-} from "./chunk-OTCYJP7G.js";
-import {
-  isDictionaryType
-} from "./chunk-SOED2SLH.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// plots/matrix/matrix.data.js
-var matrix_data_exports = {};
-__export(matrix_data_exports, {
-  applyLegendValueFilter: () => applyLegendValueFilter,
-  getMatrixRequestOpts: () => getMatrixRequestOpts,
-  mayRequireToken: () => mayRequireToken,
-  setData: () => setData
-});
-function mayRequireToken(tokenMessage = "") {
-  const message = tokenMessage || this.state.tokenVerificationMessage;
-  if (!message && this.state.hasVerifiedToken) {
-    this.dom.errdiv.style("display", "none").html();
-    this.dom.controls.style("display", this.opts.controls ? "inline-block" : "");
-    this.dom.svg.style("display", "");
-    return false;
-  } else {
-    this.dom.errdiv.style("display", "").html(message || "Requires login");
-    this.dom.controls.style("display", "none");
-    this.dom.svg.style("display", "none");
-    return true;
-  }
-}
-function getMatrixRequestOpts(state, config) {
-  const terms = [];
-  const termgroups = this.chartType == "hierCluster" ? config.termgroups.filter((grp) => grp.type != "hierCluster") : config.termgroups;
-  for (const grp of termgroups) {
-    terms.push(...getNormalizedTwLstCopy(grp.lst));
-  }
-  if (config.divideBy) terms.push(normalizeTwForRequest(structuredClone(config.divideBy)));
-  const opts = {
-    terms,
-    filter: state.filter,
-    filter0: state.filter0,
-    maxGenes: state.config.settings.matrix.maxGenes,
-    /*********** quick fix
-    when the flag is true, set artificially large number to ensure all genes are sent in one query
-    this avoids changing getAnnotatedSampleData()
-    additional non-matrix app that calls getAnnotatedSampleData will NEED THE SAME FIX
-    */
-    termsPerRequest: this.app.vocabApi.termdbConfig.queries?.snvindel?.byisoform?.processTwsInOneQuery ? 1e3 : 1
-  };
-  if (this.chartType == "hierCluster") {
-    opts.isHierCluster = 1;
-  }
-  return opts;
-}
-function getNormalizedTwLstCopy(twlst) {
-  const lst = [];
-  for (const tw of twlst) {
-    if (tw.type && tw.constructor.name != "Object") lst.push(tw);
-    else lst.push(normalizeTwForRequest(tw));
-  }
-  lst.forEach(normalizeTwForRequest);
-  lst.sort(sortTwLst);
-  return lst;
-}
-function normalizeTwForRequest(_tw) {
-  const tw = structuredClone(_tw);
-  if (!tw?.term) return;
-  delete tw.term.category2samplecount;
-  if (isDictionaryType(tw.term.type) && tw.term.type !== "samplelst") delete tw.term.values;
-  return tw;
-}
-function sortTwLst(twa, twb) {
-  const a = twa?.$id || twa.term?.id || twa?.term?.name;
-  const b = twb?.$id || twb.term?.id || twb?.term?.name;
-  return a < b ? -1 : 1;
-}
-async function setData(_data) {
-  const opts = this.currRequestOpts?.matrix || this.getMatrixRequestOpts(this.state, this.config);
-  this.numTerms = opts.terms.length;
-  opts.loadingDiv = this.chartType != "hierCluster" && this.dom.loadingDiv;
-  opts.signal = this.api.getAbortSignal();
-  const data = await this.app.vocabApi.getAnnotatedSampleData(opts, _data);
-  this.data = data;
-  this.origData = structuredClone(this.data);
-  this.sampleIdMap = {};
-  for (const d of this.data.lst) {
-    this.sampleIdMap[d.sample] = d._ref_.label;
-  }
-}
-function applyLegendValueFilter() {
-  const self = this;
-  if (!self.config.legendValueFilter.lst.length && !self.config.legendGrpFilter.lst.length) return;
-  for (const grpFilter of self.config.legendGrpFilter.lst) {
-    if (grpFilter.dt) {
-      const filteredOutCats = /* @__PURE__ */ new Set();
-      for (const oneSampleData of self.origData.lst) {
-        for (const annoForOneTerm of Object.values(oneSampleData)) {
-          if (annoForOneTerm.values) {
-            const newValues = [];
-            for (const v of annoForOneTerm.values) {
-              if (!(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))) {
-                newValues.push(v);
-              } else {
-                filteredOutCats.add(v.class);
-              }
-            }
-            annoForOneTerm.values = newValues;
-          }
-        }
-      }
-      grpFilter.filteredOutCats = [...filteredOutCats];
-      for (const oneSampleData of Object.values(self.origData.samples)) {
-        for (const annoForOneTerm of Object.values(oneSampleData)) {
-          if (annoForOneTerm.values)
-            annoForOneTerm.values = annoForOneTerm.values.filter(
-              (v) => !(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))
-            );
-        }
-      }
-    }
-  }
-  const geneVariant$ids = Object.values(self.data.refs.byTermId).filter((v) => v.term?.type == "geneVariant").map((v) => v.$id);
-  const data = { samples: {}, lst: [], refs: self.data.refs };
-  const onlyHardFilter = structuredClone(self.config.legendValueFilter);
-  onlyHardFilter.lst = onlyHardFilter.lst.filter(
-    (l) => !l.tvs.legendFilterType || l.tvs.legendFilterType !== "geneVariant_soft"
-  );
-  for (const row of self.origData.lst) {
-    const include = sample_match_termvaluesetting(row, onlyHardFilter, geneVariant$ids);
-    if (include || self.chartType == "hierCluster") {
-      data.samples[row.sample] = row;
-      data.lst.push(row);
-    }
-  }
-  for (const valFilter of self.config.legendValueFilter.lst) {
-    if (valFilter.tvs.legendFilterType !== "geneVariant_soft") continue;
-    const tvsV = valFilter.tvs.values[0];
-    const filteredOutCats = /* @__PURE__ */ new Set();
-    for (const oneSampleData of data.lst) {
-      for (const annoForOneTerm of Object.values(oneSampleData)) {
-        if (annoForOneTerm.values) {
-          const newValues = [];
-          for (const v of annoForOneTerm.values) {
-            if (!(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))) {
-              newValues.push(v);
-            } else {
-              filteredOutCats.add(v.class);
-            }
-          }
-          annoForOneTerm.values = newValues;
-        }
-      }
-    }
-    valFilter.filteredOutCats = [...filteredOutCats];
-    for (const oneSampleData of Object.values(data.samples)) {
-      for (const annoForOneTerm of Object.values(oneSampleData)) {
-        if (annoForOneTerm.values)
-          annoForOneTerm.values = annoForOneTerm.values.filter(
-            (v) => !(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))
-          );
-      }
-    }
-  }
-  if (self.chartType !== "hierCluster" && geneVariant$ids.length && self.app.vocabApi.vocab?.dslabel == "GDC")
-    remove_empty_sample(data, geneVariant$ids);
-  self.data = data;
-}
-function remove_empty_sample(data) {
-  for (const oneSampleData of data.lst) {
-    let removeSample = true;
-    for (const [key, annoForOneTerm] of Object.entries(oneSampleData)) {
-      if (!annoForOneTerm.values) continue;
-      const annoType = data.refs.byTermId[key].term.type;
-      if (annoType != "geneVariant") continue;
-      if (annoForOneTerm.values.length) removeSample = false;
-    }
-    if (removeSample) {
-      data.lst = data.lst.filter((dl) => dl.sample !== oneSampleData.sample);
-      delete data.samples[parseInt(oneSampleData.sample)];
-    }
-  }
-  return data;
-}
-
-export {
-  mayRequireToken,
-  getMatrixRequestOpts,
-  setData,
-  applyLegendValueFilter,
-  matrix_data_exports
-};
-//# sourceMappingURL=chunk-M3EBH2WK.js.map

package/dist/chunk-MFLKXGQC.js

@@ -1,228 +0,0 @@
-import {
-  appInit
-} from "./chunk-KLV7RCJM.js";
-import {
-  getDefaultViolinSettings
-} from "./chunk-VEXSAWKT.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-
-// plots/regression.inputs.values.table.js
-var row_hover_bgcolor = "#fff6dc";
-var InputValuesTable = class {
-  constructor(opts) {
-    this.opts = opts;
-    this.input = opts.input;
-    setRenderers(this);
-    this.setDOM(opts.holder);
-  }
-  main() {
-    try {
-      const term = this.input.term;
-      if (!term || !this.input.termStatus) {
-        this.dom.holder.style("display", "none");
-        this.dom.loading_div.style("display", "none");
-        return;
-      } else if (term) {
-        this.dom.holder.style("display", "block");
-        this.dom.loading_div.style("display", "block");
-        this.updateValueCount();
-        this.dom.loading_div.style("display", "none");
-        this.render();
-        return;
-      }
-    } catch (e) {
-      this.dom.loading_div.style("display", "none");
-      throw e;
-    }
-  }
-  updateValueCount() {
-    const i = this.input;
-    try {
-      if (i.pill && i.pill.validateQ) {
-        i.pill.validateQ({
-          term: i.term.term,
-          q: i.term.q,
-          sampleCounts: i.termStatus.sampleCounts
-        });
-      }
-    } catch (e) {
-      i.term.error = e;
-    }
-  }
-};
-function setRenderers(self) {
-  self.setDOM = (holder) => {
-    self.dom = {
-      holder: holder.style("margin", "10px").style("font-size", ".8em").style("text-align", "left").style("color", "#999"),
-      loading_div: holder.append("div").text("Loading..").style("display", "none"),
-      top_info_div: holder.append("div").style("padding-bottom", "5px"),
-      violin_div: holder.append("div").style("color", "black").style("padding-top", "5px"),
-      table_div: holder.append("table").style("margin", "5px 0px 15px 0px").style("border-collapse", "collapse").style("color", "black"),
-      bottom_info_div: holder.append("div"),
-      excluded_div: holder.append("table").style("display", "none").style("margin", "5px 10px").style("border-collapse", "collapse")
-    };
-  };
-  self.render = async () => {
-    const input = self.input;
-    renderTopInfo(input);
-    await renderValuesTable(input);
-    renderBottomInfo(input);
-    renderExcludedValues(input);
-  };
-  function renderTopInfo(input) {
-    if (input.termStatus.topInfoStatus?.length) {
-      self.dom.top_info_div.style("display", "block").html(input.termStatus.topInfoStatus.join("<br>"));
-    } else {
-      self.dom.top_info_div.style("display", "none");
-    }
-  }
-  async function renderValuesTable(input) {
-    if (input.term.q.mode == "continuous" || input.term.q.mode == "spline") {
-      self.dom.violin_div.style("display", "block");
-      self.dom.table_div.style("display", "none");
-      if (self.plotAppApi) {
-        const action = {
-          type: "app_refresh",
-          state: {
-            termfilter: {
-              filter: self.input.parent.parent.filter
-            }
-          },
-          subactions: [
-            {
-              type: "plot_edit",
-              id: self.violinApi.id,
-              config: {
-                term: input.term
-              }
-            }
-          ]
-        };
-        self.plotAppApi.dispatch(action);
-      } else {
-        const opts = {
-          holder: self.dom.violin_div,
-          vocabApi: self.input.parent.app.vocabApi,
-          state: {
-            vocab: {
-              genome: self.input.parent.app.vocabApi.genome,
-              dslabel: self.input.parent.app.vocabApi.dslabel
-            },
-            termfilter: {
-              filter: self.input.parent.parent.filter
-            },
-            plots: [
-              {
-                chartType: "violin",
-                term: input.term,
-                settings: {
-                  violin: getDefaultViolinSettings(null, {
-                    svgw: 350,
-                    axisHeight: 25,
-                    rightMargin: 10,
-                    datasymbol: "rug",
-                    radius: 8,
-                    plotThickness: 80
-                  })
-                }
-              }
-            ]
-          },
-          // global options for plotAppApi
-          // opts.violin will apply to all violin plots within the plotApp
-          // rx will pass options by component type, which are not tracked in state
-          // examples are callbacks, event listeners, etc
-          violin: {
-            mode: "minimal"
-          }
-        };
-        self.plotAppApi = await appInit(opts);
-        const plotId = self.plotAppApi.getState().plots[0].id;
-        self.violinApi = self.plotAppApi.getComponents(`plots.${plotId}`);
-      }
-    } else {
-      self.dom.violin_div.style("display", "none");
-      const data = input.termStatus.sampleCounts;
-      if (!data || !data.length) {
-        self.dom.table_div.style("display", "none");
-        return;
-      }
-      self.dom.table_div.style("display", "block");
-      const l = self.input.orderedLabels;
-      const sortFxn = l && l.length ? (a, b) => l.indexOf(a.label) - l.indexOf(b.label) : (a, b) => b.samplecount - a.samplecount;
-      const tr_data = data.sort(sortFxn);
-      const maxCount = Math.max(...tr_data.map((v) => v.samplecount), 0);
-      tr_data.forEach((v) => v.bar_width_frac = Number((1 - (maxCount - v.samplecount) / maxCount).toFixed(4)));
-      self.dom.table_div.selectAll("tr").remove();
-      const trs = self.dom.table_div.selectAll("tr").data(tr_data, (b) => b.key);
-      trs.enter().append("tr").each(trEnter);
-    }
-  }
-  function renderBottomInfo(input) {
-    if (input.termStatus.bottomSummaryStatus) {
-      self.dom.bottom_info_div.style("display", "block").html(input.termStatus.bottomSummaryStatus);
-    } else {
-      self.dom.bottom_info_div.style("display", "none");
-    }
-  }
-  function renderExcludedValues(input) {
-    const data = input.termStatus.excludeCounts;
-    if (!data || !data.length) {
-      self.dom.excluded_div.style("display", "none");
-      return;
-    }
-    self.dom.excluded_div.style("display", "block").selectAll("tr").remove();
-    const trs = self.dom.excluded_div.selectAll("tr").data(data, (b) => b.key);
-    trs.enter().append("tr").each(trEnter);
-    self.dom.excluded_div.selectAll("td").style("color", "#999");
-  }
-  function trEnter(item) {
-    const tr = select_default(this);
-    const input = this.parentNode.__data__;
-    const t = input.term;
-    const maxBarWidth = 150;
-    tr.style("text-align", "left").style("cursor", input.termStatus.allowToSelectRefGrp ? "pointer" : "default");
-    const tdSpacing = "1px 10px 1px 0px";
-    tr.append("td").style("padding", tdSpacing).style("text-align", "left").style("color", "black").text(item.samplecount !== void 0 ? "n=" + item.samplecount : "");
-    tr.append("td").style("padding", tdSpacing).style("text-align", "left").style("color", "black").text(item.label);
-    const bar_td = tr.append("td").style("padding", tdSpacing);
-    const barWidth = maxBarWidth * item.bar_width_frac;
-    bar_td.append("div").style("margin", tdSpacing).style("width", barWidth + "px").style("height", "15px").style("background-color", "#ddd");
-    addTrBehavior({ input, item, tr, rendered: false });
-  }
-  function addTrBehavior({ input, item, tr, rendered }) {
-    if (!item.bar_width_frac) return;
-    const t = input.term;
-    const hover_flag = input.termStatus.allowToSelectRefGrp;
-    let ref_text;
-    if (rendered) {
-      tr.style("background", "white");
-      ref_text = select_default(tr.node().lastChild).select("div").style("display", item.key === t.refGrp && hover_flag ? "inline-block" : "none").style("border", item.key === t.refGrp && hover_flag ? "1px solid #bbb" : "");
-    } else if (input.term.q.mode != "cutoff") {
-      const reference_td = tr.append("td").style("padding", "1px 5px").style("text-align", "left");
-      ref_text = reference_td.append("div").style("display", item.key === t.refGrp && hover_flag ? "inline-block" : "none").style("padding", "2px 10px").style("border", item.key === t.refGrp && hover_flag ? "1px solid #bbb" : "").style("border-radius", "10px").style("color", "#999").style("font-size", ".7em").text("REFERENCE");
-      if (hover_flag) {
-        tr.on("mouseover", () => {
-          if (t.refGrp !== item.key) {
-            tr.style("background", row_hover_bgcolor);
-            ref_text.style("display", "inline-block").style("border", "").text("Set as reference");
-          } else tr.style("background", "white");
-        }).on("mouseout", () => {
-          tr.style("background", "white");
-          if (t.refGrp !== item.key) ref_text.style("display", "none");
-        }).on("click", () => {
-          t.refGrp = item.key;
-          ref_text.style("border", "1px solid #bbb").text("REFERENCE");
-          self.opts.callback(t);
-        });
-      }
-    }
-  }
-}
-
-export {
-  InputValuesTable
-};
-//# sourceMappingURL=chunk-MFLKXGQC.js.map

package/dist/chunk-MHTDDCB7.js

@@ -1,142 +0,0 @@
-import {
-  runproteinpaint
-} from "./chunk-KQKC2KYW.js";
-
-// test/front.helpers.js
-var serverData = /* @__PURE__ */ Object.create(null);
-function getRunPp(appname = "", defaultArgs = {}, _host = "http://localhost:3000") {
-  const host = window.testHost || _host;
-  const arg = {
-    host: window.testHost || _host,
-    noheader: 1,
-    nobox: true,
-    debug: 1,
-    norecover: true
-  };
-  if (appname == "mass" || appname == "termdb") {
-    defaultArgs.debounceInterval = 0;
-  }
-  if (appname) arg[appname] = defaultArgs;
-  else copyMerge(arg, defaultArgs);
-  const argStr = JSON.stringify(arg);
-  return function runpp(overrides = {}) {
-    const argCopy = JSON.parse(argStr);
-    if (appname) copyMerge(argCopy[appname], overrides);
-    else copyMerge(argCopy, overrides);
-    if (appname && defaultArgs.fetchOpts) {
-      argCopy[appname].fetchOpts = defaultArgs.fetchOpts;
-    }
-    return runproteinpaint(Object.assign(argCopy, { serverData }));
-  };
-}
-function copyMerge(base, ...args) {
-  const target = typeof base == "string" ? JSON.parse(base) : base;
-  for (const arg of args) {
-    if (arg) {
-      const source = typeof base == "string" ? JSON.parse(JSON.stringify(arg)) : arg;
-      for (const key in source) {
-        if (!target[key] || Array.isArray(target[key]) || typeof target[key] !== "object") target[key] = source[key];
-        else copyMerge(target[key], source[key]);
-      }
-    }
-  }
-  return target;
-}
-function rideInit(opts = {}) {
-  const self = new Ride(opts);
-  const rideApi = {
-    // ride on the default event bus
-    to(callback, sub = {}) {
-      self.addToThen(callback, Object.assign({}, opts, sub));
-      return rideApi;
-    },
-    use(triggerFxn, sub = {}) {
-      self.addUseThen(triggerFxn, Object.assign({}, opts, sub));
-      return rideApi;
-    },
-    change(sub = {}) {
-      Object.assign(opts, sub);
-      return rideApi;
-    },
-    // run callback without using bus, with or without timeout
-    run(callback, after = 0) {
-      self.addRunThen(callback, after, opts);
-      return rideApi;
-    },
-    // close the event bus
-    done(test) {
-      if (opts.bus) self.resolved.then(() => opts.bus.on(opts.eventType, null));
-      self.resolved.then(() => {
-        test.end();
-        if (!opts.preserve && test._ok && opts.arg.Inner.app && typeof opts.arg.Inner.app.destroy == "function") {
-          opts.arg.Inner.app.destroy();
-        }
-      }).catch(console.log);
-      return rideApi;
-    }
-  };
-  return Object.freeze(rideApi);
-}
-var Ride = class {
-  // mutable but private access props and methods
-  // when used inside rideInit()
-  constructor(opts) {
-    this.validateOpts(opts);
-    this.resolved = Promise.resolve();
-  }
-  validateOpts(opts) {
-    try {
-      if (opts.eventType && !opts.bus) {
-        if (!opts.arg) throw "must specify opts.bus or opts.arg for rideInit() argument";
-        opts.bus = opts.arg;
-      }
-      if (opts.bus) {
-        if (typeof opts.eventType !== "string") throw "invalid default.eventType";
-        opts.bus.on(opts.eventType, null);
-        return opts;
-      }
-    } catch (e) {
-      console.log(e);
-    }
-  }
-  addToThen(callback, opts) {
-    this.resolved = this.resolved.then(async (triggerFxn) => {
-      opts.bus.on(opts.eventType, null);
-      return new Promise(async (resolve, reject) => {
-        opts.bus.on(opts.eventType, async () => {
-          await sleep(opts.wait);
-          callback(opts.arg);
-          resolve();
-        });
-        if (triggerFxn) await triggerFxn();
-      });
-    });
-  }
-  // prepare a trigger function for use in the pattern
-  // rideInit().use(triggerFxn).to(...)
-  //
-  // .use() enables setting a different opts.arg to be used for triggerFxn
-  //
-  addUseThen(triggerFxn, opts) {
-    this.resolved = this.resolved.then(async (prevTriggerFxn) => {
-      if (typeof prevTriggerFxn == "function") await prevTriggerFxn();
-      await sleep(isNaN(opts.wait) ? 0 : opts.wait);
-      return () => triggerFxn(opts.arg);
-    });
-  }
-  addRunThen(callback, after, opts) {
-    this.resolved = this.resolved.then(async () => {
-      await sleep(typeof after == "number" ? after : 0);
-      callback(opts.arg);
-    });
-  }
-};
-function sleep(ms) {
-  return new Promise((resolve) => setTimeout(resolve, ms));
-}
-
-export {
-  getRunPp,
-  rideInit
-};
-//# sourceMappingURL=chunk-MHTDDCB7.js.map