@sjcrh/proteinpaint-client 2.207.0 → 2.207.1

package/dist/chunk-UO5AU7IW.js

@@ -1,216 +0,0 @@
-import {
-  Tabs,
-  addGeneSearchbox,
-  make_one_checkbox,
-  make_radios
-} from "./chunk-NQDF3U2C.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import {
-  termType2label
-} from "./chunk-HZ3TCGBK.js";
-import {
-  TermTypeGroups
-} from "./chunk-IZUYLFOX.js";
-
-// termdb/handlers/pseudobulk.ts
-function isSamePseudobulkSelection(a, b) {
-  return a.type === b.type && a.assay === b.assay && a.memberId === b.memberId && a.id === b.id;
-}
-var SearchHandler = class {
-  async init(opts) {
-    const pseudobulkTerms = this.validateOpts(opts);
-    this.callback = opts.callback;
-    this.app = opts.app;
-    this.genome = opts.genomeObj;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    this.multiSelect = opts?.usecase?.target == "aggregateMatrix";
-    this.selectedTerm = void 0;
-    this.map = this.buildRenderingDataMap(pseudobulkTerms);
-    this.renderPseudobulkSearch(holder);
-  }
-  validateOpts(opts) {
-    if (!opts) throw new Error("opts is required");
-    if (!opts.app) throw new Error("opts.app is required");
-    if (!opts.holder) throw new Error("opts.holder is required");
-    if (opts.genomeObj == null || typeof opts.genomeObj !== "object") throw new Error("genomeObj is required");
-    if (!opts.callback) throw new Error("opts.callback is required");
-    const pseudobulkTerms = opts.app.vocabApi.termdbConfig?.termType2terms?.[TermTypeGroups.PSEUDOBULK];
-    if (!pseudobulkTerms) {
-      throw new Error(
-        `termType2terms[${TermTypeGroups.PSEUDOBULK}]:[] is required in termdbConfig for pseudobulk handler`
-      );
-    }
-    return pseudobulkTerms;
-  }
-  /** Builds a map from assay to memberId to terms */
-  buildRenderingDataMap(pseudobulkTerms) {
-    const map = /* @__PURE__ */ new Map();
-    for (const term of pseudobulkTerms) {
-      const { assay, memberId } = term;
-      if (!map.has(assay)) map.set(assay, /* @__PURE__ */ new Map());
-      const assayMap = map.get(assay);
-      if (!assayMap.has(memberId)) assayMap.set(memberId, []);
-      assayMap.get(memberId).push(term);
-    }
-    return map;
-  }
-  /** If more than one assay, render tabs for each assay. Member IDs within
-   * an assay are rendered as tabs when there is more than one. */
-  renderPseudobulkSearch(holder) {
-    if (!this.map || this.map.size < 1) throw new Error("map is not initialized");
-    if (this.map.size === 1) {
-      const label = termType2label(this.map.keys().next().value);
-      holder.append("div").style("padding-bottom", "10px").text("Single-cell pseudobulk " + label);
-      this.renderMemberIdsByAssay(holder.append("div"), this.map);
-      return;
-    }
-    const tabs = this.buildTabsOpts(this.map);
-    new Tabs({ holder, tabs, tabsPosition: "vertical" }).main();
-  }
-  buildTabsOpts(map) {
-    const tabs = [];
-    for (const [key, valuesMap] of map.entries()) {
-      const label = termType2label(key);
-      tabs.push({
-        label,
-        active: false,
-        callback: (_, tab) => {
-          this.renderMemberIdsByAssay(tab.contentHolder, /* @__PURE__ */ new Map([[key, valuesMap]]));
-        }
-      });
-    }
-    return tabs;
-  }
-  renderMemberIdsByAssay(holder, map) {
-    const memberIdMap = map.values().next().value;
-    holder.selectAll("*").remove();
-    this.renderTermdByMemberId(holder, memberIdMap);
-  }
-  renderTermdByMemberId(holder, memberIdMap) {
-    const layout = holder.append("div").style("display", "flex").style("align-items", "flex-start").style("gap", "30px");
-    const pseudoTermsWrapper = layout.append("div").attr("data-testid", "sjpp-pseudobulk-terms-wrapper");
-    const geneSearchWrapper = layout.append("div").attr("data-testid", "sjpp-pseudobulk-gene-search-wrapper");
-    this.renderPseudobulkTerms(pseudoTermsWrapper, memberIdMap, geneSearchWrapper);
-  }
-  renderPseudobulkTerms(holder, memberIdMap, geneSearchHolder) {
-    if (memberIdMap.size === 1) {
-      const [memberId, terms] = memberIdMap.entries().next().value;
-      if (this.multiSelect) {
-        this.renderCategoriesAsTerms(holder, terms);
-      } else this.renderCategoryRadios(holder, memberId, terms, geneSearchHolder);
-      return;
-    }
-    const memberEntries = Array.from(memberIdMap.entries());
-    const tabs = memberEntries.map(([memberId, terms]) => ({
-      label: memberId,
-      active: false,
-      testid: `sjpp-pseudobulk-member-${memberId}`,
-      callback: (_, tab) => {
-        geneSearchHolder.selectAll("*").remove();
-        tab.contentHolder.selectAll("*").remove();
-        if (this.multiSelect) this.renderCategoriesAsTerms(tab.contentHolder, terms);
-        else this.renderCategoryRadios(tab.contentHolder, memberId, terms, geneSearchHolder);
-      }
-    }));
-    new Tabs({ holder, tabs, tabsPosition: "vertical" }).main();
-  }
-  renderCategoryRadios(holder, memberId, terms, geneSearchHolder) {
-    if (!terms || terms.length < 1) throw new Error("No terms found for memberId");
-    const options = terms.map((term) => ({
-      label: term.name,
-      value: term.id,
-      checked: false,
-      testid: `sjpp-pseudobulk-category-${term.id}`
-    }));
-    make_radios({
-      holder,
-      inputName: `sjpp-pseudobulk-category-radios-${memberId}`,
-      options,
-      styles: { display: "block", padding: "3px 5px" },
-      callback: (value) => {
-        const term = terms.find((term2) => term2.id == value);
-        if (!term) throw new Error(`No pseudobulk term found for category ${value}`);
-        this.selectedTerm = term;
-        this.renderGeneSelection(geneSearchHolder);
-      }
-    });
-  }
-  renderGeneSelection(holder) {
-    holder.selectAll("*").remove();
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: this.genome,
-      row: holder,
-      searchOnly: "gene",
-      callback: () => {
-        if (!geneSearch.geneSymbol) throw new Error("No gene selected");
-        if (!this.selectedTerm) throw new Error("No pseudobulk cell type selected");
-        this.callback(createPseudobulkTerm(this.selectedTerm, geneSearch.geneSymbol));
-      }
-    });
-  }
-  /** Mimics the style and functionality of pills created in tree.js.
-   * Returns the term object(s) from termdbConfig.termType2terms.[TermTypeGroups.PSEUDOBULK]
-   * without the gene. */
-  renderCategoriesAsTerms(holder, terms) {
-    holder.style("padding", "0px 10px");
-    const isSelected = (term) => this.app.getState().selectedTerms.some((selected) => isSamePseudobulkSelection(selected, term));
-    const setSelected = async (term, selected) => {
-      const selectedTerms = this.app.getState().selectedTerms;
-      if (selectedTerms.some((selectedTerm) => isSamePseudobulkSelection(selectedTerm, term)) === selected) return;
-      const nextSelectedTerms = selected ? [...selectedTerms, term] : selectedTerms.filter((selectedTerm) => !isSamePseudobulkSelection(selectedTerm, term));
-      await this.app.dispatch({ type: "app_refresh", state: { selectedTerms: nextSelectedTerms } });
-    };
-    const selectAll = make_one_checkbox({
-      holder,
-      labeltext: "Select all",
-      divstyle: { opacity: "0.7" },
-      callback: async () => {
-        const checked = selectAll.property("checked");
-        const selectedTerms = this.app.getState().selectedTerms;
-        const nextSelectedTerms = checked ? [
-          ...selectedTerms,
-          ...terms.filter(
-            (term) => !selectedTerms.some((selected) => isSamePseudobulkSelection(selected, term))
-          )
-        ] : selectedTerms.filter(
-          (selected) => !terms.some((term) => isSamePseudobulkSelection(selected, term))
-        );
-        await this.app.dispatch({ type: "app_refresh", state: { selectedTerms: nextSelectedTerms } });
-        update();
-      }
-    });
-    const wrapper = holder.append("div").style("display", "block").style("padding", "10px 15px 0px");
-    const termRows = wrapper.selectAll(".pseudobulk-term").data(terms, (term) => term.id).join((enter) => {
-      const row = enter.append("div").attr("class", "pseudobulk-term");
-      row.append("div").attr("class", "termlabel sja_filter_tag_btn sja_tree_click_term ts_pill").style("padding", "5px 8px").style("margin", "1px 0px").style("border-radius", "6px").text((term) => term.name);
-      row.append("div").attr("class", "termcheck").style("color", "#008000").html("&check;");
-      return row;
-    });
-    termRows.select(".ts_pill").on("click", async (_, term) => {
-      await setSelected(term, !isSelected(term));
-      update();
-    });
-    const update = () => {
-      termRows.select(".ts_pill").style("background-color", (term) => isSelected(term) ? "#FFC20A80" : "#cfe2f3");
-      termRows.select(".termcheck").style("display", (term) => isSelected(term) ? "inline-block" : "none");
-      const selectedCount = terms.filter(isSelected).length;
-      selectAll.property("checked", terms.length > 0 && selectedCount === terms.length).property("indeterminate", selectedCount > 0 && selectedCount < terms.length);
-    };
-    update();
-  }
-};
-function createPseudobulkTerm(selectedTerm, gene) {
-  const category = selectedTerm.category || selectedTerm.id;
-  const name = `${selectedTerm.assay} ${category} ${gene}`;
-  return { ...selectedTerm, id: name, category, gene, name };
-}
-
-export {
-  isSamePseudobulkSelection,
-  SearchHandler,
-  createPseudobulkTerm
-};
-//# sourceMappingURL=chunk-UO5AU7IW.js.map

package/dist/chunk-UTOWZWZ5.js

@@ -1,243 +0,0 @@
-import {
-  keyupEnter
-} from "./chunk-NQDF3U2C.js";
-import {
-  get_bin_label,
-  get_bin_range_equation
-} from "./chunk-GRVO7RW4.js";
-import {
-  toStoredUnit,
-  toUserUnit
-} from "./chunk-W5J3LTYS.js";
-
-// termsetting/handlers/NumCustomBinEditor.ts
-var NumCustomBinEditor = class {
-  constructor(editHandler) {
-    this.dom = {};
-    this.editHandler = editHandler;
-    this.opts = editHandler.opts;
-    this.tw = editHandler.tw;
-    this.termsetting = editHandler.termsetting;
-  }
-  /* bin boundaries are stored in the term's own unit but entered and shown in its user-facing one.
-  both are identity functions unless the term declares valueConversion{} */
-  toDisplay(v) {
-    return toUserUnit(v, this.tw.term);
-  }
-  toStored(v) {
-    return toStoredUnit(v, this.tw.term);
-  }
-  async render(div) {
-    this.tw = this.editHandler.tw;
-    const isRemounting = !!this.dom.inputsDiv && this.editHandler.dom.binsDiv?.node().contains(this.dom.inputsDiv.node());
-    if (!isRemounting) this.q = this.getDefaultQ();
-    await this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-    if (isRemounting) return;
-    if (this.dom.inputsDiv) {
-      this.dom.inputsDiv.remove();
-      delete this.dom.inputsDiv;
-    }
-    this.dom.inputsDiv = div.append("div").style("display", "flex").style("width", "100%");
-    this.renderCustomBinInputs();
-  }
-  getBoundaryOpts() {
-    return {
-      values: this.q.lst.slice(1).map((bin) => ({ x: this.toDisplay(bin.startunbounded ? bin.stop : bin.start), isDraggable: true })),
-      // the dragged value arrives in display units, matching what the textarea holds
-      callback: (d, value) => {
-        const boundaryValues = this.q.lst.slice(1).map((d2) => "start" in d2 ? this.toDisplay(d2.start) : "");
-        boundaryValues[d.index] = value;
-        this.dom.customBinBoundaryInput.property("value", boundaryValues.join("\n"));
-        this.handleInputChange("drag");
-        return 0;
-      }
-    };
-  }
-  getDefaultQ() {
-    if (this.tw.q.mode == "discrete" && this.tw.q.type == "custom-bin") {
-      const copy = JSON.parse(JSON.stringify(this.tw.q));
-      copy.lst.forEach((bin) => {
-        if (!bin.label) bin.label = get_bin_label(bin, this.tw.q, this.tw.term.valueConversion);
-        bin.range = get_bin_range_equation(bin, this.tw.q, this.tw.term.valueConversion);
-      });
-      return copy;
-    }
-    const { min, max } = this.editHandler.handler.density_data;
-    const defaultCustomBoundary = (
-      /* when no sample is annotated by this term,
-      minvalue and maxvalue are both null
-      setting defaultCustomBoundary to arbitrary "0" will allow existing UI to work
-      but remains to be evaluated if is really okay to use 0
-      */
-      !Number.isFinite(min) || !Number.isFinite(max) ? 0 : (
-        // minvalue and maxvalue is valid number
-        max != min ? min + (max - min) / 2 : max
-      )
-    );
-    const firstBin = {
-      startunbounded: true,
-      startinclusive: false,
-      stopinclusive: false,
-      stop: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
-    };
-    const lastBin = {
-      stopunbounded: true,
-      startinclusive: true,
-      stopinclusive: false,
-      start: +defaultCustomBoundary.toFixed(this.tw.term.type == "integer" ? 0 : 2)
-    };
-    return {
-      mode: "discrete",
-      type: "custom-bin",
-      lst: [
-        // Type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' is not assignable to type 'StartUnboundedBin | FullyBoundedBin'.
-        // Property 'start' is missing in type '{ label: any; range: any; startunbounded: boolean; startinclusive: boolean; stopinclusive: boolean; stop: number; }' but required in type 'FullyBoundedBin'.
-        {
-          ...firstBin,
-          label: get_bin_label(firstBin, this.tw.q, this.tw.term.valueConversion),
-          range: get_bin_range_equation(firstBin, this.tw.q, this.tw.term.valueConversion)
-        },
-        {
-          ...lastBin,
-          label: get_bin_label(lastBin, this.tw.q, this.tw.term.valueConversion),
-          range: get_bin_range_equation(lastBin, this.tw.q, this.tw.term.valueConversion)
-        }
-        //satisfies StopUnboundedBin
-      ]
-    };
-  }
-  /******************* Functions for Numerical Custom size bins *******************/
-  renderCustomBinInputs() {
-    const q = this.q;
-    const boundaryDiv = this.dom.inputsDiv.append("div").style("margin-right", "20px");
-    this.dom.rangeAndLabelDiv = this.dom.inputsDiv.append("div");
-    boundaryDiv.append("div").style("margin-bottom", "5px").style("color", "rgb(136, 136, 136)").text("Bin boundaries");
-    this.dom.customBinBoundaryInput = boundaryDiv.append("textarea").style("width", "100px").style("height", "70px").text(
-      q.lst.slice(1).map((d) => "start" in d ? this.toDisplay(d.start) : "").join("\n")
-    ).on("change", () => this.handleInputChange()).on("keyup", async (event) => {
-      if (!keyupEnter(event) && event.key != 8 && event.key != "Enter") return;
-      if (!this.dom.inputsDiv.selectAll("input").node().value) return;
-      this.handleInputChange();
-    });
-    boundaryDiv.append("div").style("font-size", ".6em").style("margin-left", "1px").style("color", "#858585").html("Enter numeric values </br>seperated by ENTER");
-    this.renderBoundaryInputDivs();
-  }
-  renderBoundaryInputDivs() {
-    const data = this.q.lst;
-    const holder = this.dom.rangeAndLabelDiv;
-    holder.selectAll("*").remove();
-    const grid = holder.append("div").style("display", "grid").style("grid-template-columns", "auto auto").style("column-gap", "20px").style("align-items", "center");
-    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Range");
-    grid.append("div").style("margin-bottom", "3px").style("color", "rgb(136, 136, 136)").text("Bin label");
-    for (const d of data) {
-      grid.append("div").attr("name", "range").html(d.range);
-      grid.append("div").append("input").attr("type", "text").style("margin", "2px 0px").property("value", d.label).on("change", function() {
-        d.label = this.value;
-      });
-    }
-    this.dom.customBinRanges = this.dom.inputsDiv.selectAll('div[name="range"]').data(data);
-    this.dom.customBinLabelInput = this.dom.inputsDiv.selectAll("input").data(data);
-  }
-  handleInputChange(eventType = "") {
-    const self = this.tw;
-    const inputs = this.dom.inputsDiv.selectAll("input");
-    inputs.property("value", "");
-    const data = this.processCustomBinInputs();
-    if (data == void 0) {
-      return;
-    }
-    if (self.q.hiddenValues) this.tw.q.hiddenValues = self.q.hiddenValues;
-    if (this.binsChanged(data, this.q.lst)) {
-      this.q.lst = data;
-    }
-    this.renderBoundaryInputDivs();
-    if (eventType != "drag") this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-  binsChanged(data, qlst) {
-    if (data.length != qlst.length) return true;
-    if (Object.keys(data[0]).length !== Object.keys(qlst[0]).length) return true;
-    for (const [i, bin] of qlst.entries()) {
-      for (const k of Object.keys(bin)) {
-        if (bin[k] && bin[k] !== data[i][k]) {
-          return true;
-        }
-      }
-    }
-    return false;
-  }
-  processCustomBinInputs() {
-    const self = this.termsetting;
-    const startinclusive = this.editHandler.boundaryInclusion == "startinclusive";
-    const stopinclusive = this.editHandler.boundaryInclusion == "stopinclusive";
-    const inputs = this.dom.inputsDiv.node().querySelectorAll("input");
-    const inputData = this.dom.customBinBoundaryInput.property("value").split("\n").filter((d) => d != "" && !isNaN(d));
-    const trackBins = new Set(inputData);
-    if (!trackBins.size) return this.tw.q.lst;
-    const sortedBins = Array.from(trackBins).map((v) => this.toStored(Number(v))).sort((a, b) => a - b);
-    const data = [
-      // first bin: StartUnbounded type
-      {
-        startunbounded: true,
-        stop: sortedBins[0],
-        startinclusive: false,
-        stopinclusive,
-        label: inputs[0].value
-      }
-    ];
-    if (!data[0].label) data[0].label = get_bin_label(data[0], self.q, self.term.valueConversion);
-    if (!data[0].range) data[0].range = get_bin_range_equation(data[0], self.q, self.term.valueConversion);
-    for (const [i, d] of sortedBins.entries()) {
-      let bin;
-      const label = inputs[i + 1]?.value || "";
-      if (i !== trackBins.size - 1) {
-        bin = {
-          start: +d,
-          startinclusive,
-          stopinclusive,
-          stop: sortedBins[i + 1],
-          label
-          //range: ''
-        };
-      } else {
-        bin = {
-          start: +d,
-          startinclusive,
-          stopinclusive: false,
-          stopunbounded: true,
-          label
-          //range: ''
-        };
-      }
-      if (bin.label === "" || bin.label === void 0) bin.label = get_bin_label(bin, self.q, self.term.valueConversion);
-      if (bin.range === "" || bin.range === void 0)
-        bin.range = get_bin_range_equation(bin, self.q, self.term.valueConversion);
-      data.push(bin);
-    }
-    return data;
-  }
-  getEditedQ(destroyDom = true) {
-    const lst = this.processCustomBinInputs();
-    if (destroyDom) {
-      for (const name of Object.keys(this.dom)) {
-        this.dom[name].remove();
-        delete this.dom[name];
-      }
-    }
-    return {
-      mode: "discrete",
-      type: "custom-bin",
-      lst
-    };
-  }
-  undoEdits() {
-    this.q = this.getDefaultQ();
-    this.dom.inputsDiv.selectAll("*").remove();
-    this.renderCustomBinInputs();
-    this.editHandler.handler.density.setBinLines(this.getBoundaryOpts());
-  }
-};
-
-export {
-  NumCustomBinEditor
-};
-//# sourceMappingURL=chunk-UTOWZWZ5.js.map