@sjcrh/proteinpaint-client 2.225.0 → 2.226.0

package/dist/pseudbulk.unit.spec-VPZWNTIA.js

@@ -0,0 +1,82 @@
+import {
+  SearchHandler,
+  createPseudobulkTerm
+} from "./chunk-USGUVW5Q.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import "./chunk-DPWSIN62.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KZ54E2FU.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-6V7ITU5F.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-KUOXZIH4.js";
+import "./chunk-T2W4JHWJ.js";
+import "./chunk-2N345NXD.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import {
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// termdb/handlers/test/pseudbulk.unit.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- termdb/handlers/pseudobulk -***-");
+  test.end();
+});
+(0, import_tape.default)("buildRenderingDataMap() groups terms by assay and memberId", function(test) {
+  const handler = new SearchHandler();
+  const terms = [
+    { id: "t1", name: "A", assay: "geneExpression", memberId: "CD4" },
+    { id: "t2", name: "B", assay: "geneExpression", memberId: "CD4" },
+    { id: "t3", name: "C", assay: "geneExpression", memberId: "CD8" },
+    { id: "t4", name: "D", assay: "cellType", memberId: "Myeloid" }
+  ];
+  const map = handler.buildRenderingDataMap(terms);
+  test.equal(map.size, 2, "creates one top-level key per assay");
+  test.ok(map.has("geneExpression"), "contains geneExpression assay");
+  test.ok(map.has("cellType"), "contains cellType assay");
+  const geneExpressionMap = map.get("geneExpression");
+  test.equal(geneExpressionMap.size, 2, "creates one nested key per memberId within assay");
+  test.equal(geneExpressionMap.get("CD4").length, 2, "groups multiple terms under same assay/memberId");
+  test.equal(geneExpressionMap.get("CD8")[0].id, "t3", "stores the correct term under another memberId");
+  const cellTypeMap = map.get("cellType");
+  test.equal(cellTypeMap.size, 1, "cellType assay has one memberId");
+  test.equal(cellTypeMap.get("Myeloid")[0].id, "t4", "stores term under expected cellType memberId");
+  test.end();
+});
+(0, import_tape.default)("buildRenderingDataMap() returns an empty map for empty input", function(test) {
+  const handler = new SearchHandler();
+  const map = handler.buildRenderingDataMap([]);
+  test.equal(map.size, 0, "empty input produces empty map");
+  test.end();
+});
+(0, import_tape.default)("createPseudobulkTerm() creates one term for one cell type and gene", function(test) {
+  const selectedTerm = {
+    id: "blast",
+    name: "Blast",
+    type: "pseudobulk",
+    assay: "geneExpression",
+    memberId: "Cell Type"
+  };
+  const term = createPseudobulkTerm(selectedTerm, "TP53");
+  test.equal(term.id, "geneExpression blast TP53", "sets a unique term.id");
+  test.equal(term.category, "blast", "sets term.category");
+  test.equal(term.gene, "TP53", "sets term.gene");
+  test.equal(term.name, "geneExpression blast TP53", "sets term.name");
+  test.notOk("genes" in term, "does not add the obsolete genes array");
+  test.end();
+});
+//# sourceMappingURL=pseudbulk.unit.spec-VPZWNTIA.js.map

package/dist/pseudobulk-RUXGZ7OY.js

@@ -0,0 +1,31 @@
+import {
+  SearchHandler,
+  createPseudobulkTerm
+} from "./chunk-USGUVW5Q.js";
+import "./chunk-DPWSIN62.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KZ54E2FU.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-6V7ITU5F.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-KUOXZIH4.js";
+import "./chunk-T2W4JHWJ.js";
+import "./chunk-2N345NXD.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  SearchHandler,
+  createPseudobulkTerm
+};
+//# sourceMappingURL=pseudobulk-RUXGZ7OY.js.map

package/dist/qualitative-3AVR4GRX.js

@@ -0,0 +1,34 @@
+import {
+  QualCustomGS,
+  QualPredefinedGS,
+  QualValues,
+  QualitativeBase
+} from "./chunk-DPWSIN62.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KZ54E2FU.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-6V7ITU5F.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-KUOXZIH4.js";
+import "./chunk-T2W4JHWJ.js";
+import "./chunk-2N345NXD.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+export {
+  QualCustomGS,
+  QualPredefinedGS,
+  QualValues,
+  QualitativeBase
+};
+//# sourceMappingURL=qualitative-3AVR4GRX.js.map

package/dist/qualitative-5QNBKDOZ.js

@@ -0,0 +1,241 @@
+import {
+  HandlerBase,
+  require_debounce
+} from "./chunk-DPWSIN62.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-KZ54E2FU.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-6V7ITU5F.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-KUOXZIH4.js";
+import "./chunk-T2W4JHWJ.js";
+import "./chunk-2N345NXD.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import {
+  __toESM
+} from "./chunk-HS5PO5ZQ.js";
+
+// termsetting/handlers/qualitative.ts
+var import_debounce = __toESM(require_debounce(), 1);
+var GroupSet = class extends HandlerBase {
+  constructor(opts) {
+    super(opts);
+    this.defaultMaxGrpNum = 5;
+    this.minGrpNum = 3;
+    //{groups: any[], values: any[]}
+    this.dom = {};
+    this.termsetting = opts.termsetting;
+    this.tw = opts.termsetting.tw;
+    this.dom.holder = opts.holder || this.termsetting.dom.tip.d;
+    this.data = { groups: [], values: [], filters: [] };
+  }
+  getPillStatus() {
+    this.tw = this.termsetting.tw;
+    return this.tw.getStatus(this.termsetting.usecase);
+  }
+  async showEditMenu() {
+    const self = this.termsetting;
+    const holder = this.dom.holder;
+    this.dom.loadingDiv = holder.append("div").style("margin", "15px").text("Getting categories...");
+    this.dom.menuWrapper = holder.append("div");
+    const body = self.opts.getBodyParams?.() || {};
+    const data = await self.vocabApi.getCategories(self.term, self.filter, body);
+    this.dom.loadingDiv.style("display", "none");
+    this.category2samplecount = data.lst;
+    this.tw = this.termsetting.tw;
+    this.data = this.tw.getGroups(this.category2samplecount);
+    await this.initGrpSetUI();
+  }
+  async initGrpSetUI() {
+    const self = this.termsetting;
+    this.maxGrpNum = this.data.values.length >= this.defaultMaxGrpNum ? this.defaultMaxGrpNum + 1 : this.data.values.length;
+    self.dom.tip.showunder(self.dom.holder.node());
+    await this.showDraggables();
+  }
+  async showDraggables() {
+    const self = this.termsetting;
+    this.dom.menuWrapper.style("padding", "10px");
+    this.dom.actionDiv = this.dom.menuWrapper.append("div").attr("class", "sjpp-group-actions").style("padding", "0px 10px 10px 0px");
+    const findNewGrps = this.data.groups.filter((g) => g.name.startsWith("New Group"));
+    let newGrpNum = findNewGrps.length > 0 ? findNewGrps[findNewGrps.length - 1].name.replace(`New Group `, "") : 0;
+    const q = this.tw.q;
+    this.dom.actionDiv.addGroup = this.dom.actionDiv.append("button").classed("sjpp_grpset_addGrp_btn", true).style("display", "inline-block").style("text-align", "center").style("cursor", q.mode == "binary" ? "default" : "pointer").property("disabled", q.mode == "binary" ? true : this.data.groups.length >= this.maxGrpNum).text("Add Group").on("click", async () => {
+      newGrpNum++;
+      this.data.groups.push({
+        currentIdx: this.data.groups.length,
+        type: "values",
+        name: `New Group${newGrpNum != 1 ? ` ${newGrpNum}` : ""}`
+      });
+      const group = this.data.groups[this.data.groups.length - 1];
+      await this.initGroupDiv(group);
+      await this.update();
+    });
+    this.dom.actionDiv.applyBtn = this.dom.actionDiv.append("button").classed("sjpp_grpset_apply_btn", true).style("display", self.opts.hideApply ? "none" : "inline-block").style("text-align", "center").style("float", "right").style("cursor", "pointer").text("Apply").on("click", () => {
+      this.processDraggables();
+      self.dom.tip.hide();
+      self.api.runCallback();
+    });
+    this.dom.menuWrapper.append("div").style("display", "block").style("margin", "5px 2px").style("font-size", ".6em").style("color", "#999").text("Drag-and-drop to assign categories to groups.");
+    this.dom.grpsWrapper = this.dom.menuWrapper.append("div").classed("sjpp-groups-wrapper", true);
+    this.dom.includedWrapper = this.dom.grpsWrapper.append("div").classed("sjpp-groups-include", true).classed("sjpp-group-edit-div", true).style("display", "flex");
+    this.dom.excludedWrapper = this.dom.grpsWrapper.append("div").classed("sjpp-groups-exclude", true).classed("sjpp-group-edit-div", true).classed("sjpp-drag-drop-div", true);
+    const excludedGroup = this.data.groups.find((d) => d.currentIdx === 0);
+    delete excludedGroup.wrapper;
+    await this.initGroupDiv(excludedGroup);
+    const handler = this;
+    await this.dom.includedWrapper.selectAll("div").data(this.data.groups.filter((d) => d.currentIdx != 0)).enter().append("div").classed("sjpp-drag-drop-div", true).style("border", "1px solid #efefef").style("display", "block").style("padding", "10px").style("vertical-align", "top").each(async function(group) {
+      group.wrapper = select_default(this);
+      await handler.initGroupDiv(group);
+    });
+  }
+  processDraggables() {
+    const self = this.termsetting;
+    const editedGrpset = this.draggedItem || this.editedName || this.removedGrp;
+    if (!editedGrpset) return;
+    const customset = { groups: [] };
+    for (const group of this.data.groups) {
+      if (group.type != "values" && group.type != "QualTWValues" && group.type != "QualTWValues")
+        throw `group.type='${group.type}' is not recognized`;
+      const customgroup = { name: group.name, type: "values", uncomputable: group.uncomputable };
+      const groupValues = this.data.values.filter((v) => v.group == group.currentIdx).map((v) => {
+        return { key: v.key, label: v.label, samplecount: v.samplecount };
+      });
+      customgroup.values = groupValues;
+      customset.groups.push(customgroup);
+    }
+    Object.assign(self.q, {
+      type: "custom-groupset",
+      customset
+    });
+  }
+  async initGroupDiv(group) {
+    const wrapper = group.currentIdx === 0 ? this.dom.excludedWrapper : this.dom.includedWrapper;
+    if (!group.type) group.type = "values";
+    if (!group.wrapper)
+      group.wrapper = wrapper.append("div").classed("sjpp-drag-drop-div", true).style("border", "1px solid #efefef").style("display", "block").style("padding", "10px").style("vertical-align", "top");
+    group.wrapper.on("drop", (event) => {
+      const itemData = this.draggedItem.node().__data__;
+      if (itemData.group === group.currentIdx) return;
+      group.draggables.node().appendChild(this.draggedItem.node());
+      this.draggedItem.style("transition-property", "background-color").style("transition-duration", "1s").style("background-color", "#fff2cc");
+      this.data.values.find((v) => v === itemData).group = group.currentIdx;
+      event.preventDefault();
+      event.stopPropagation();
+    }).on("dragleave", (event) => {
+      event.preventDefault();
+      event.stopPropagation();
+      group.wrapper.style("background-color", "#fff");
+    }).on("dragend", (event) => {
+      event.preventDefault();
+      event.stopPropagation();
+      group.wrapper.style("background-color", "#fff");
+    }).on("dragover", (event) => {
+      event.preventDefault();
+      event.stopPropagation();
+      group.wrapper.style(
+        "background-color",
+        group.currentIdx !== this.draggedItem.node().__data__.group ? "#cfe2f3" : "#fff"
+      );
+    }).on("dragenter", (event) => {
+      if (this.draggedItem.node().__data__.group === group.currentIdx) return;
+      event.preventDefault();
+      event.stopPropagation();
+      group.wrapper.style(
+        "background-color",
+        group.currentIdx !== this.draggedItem.node().__data__.group ? "#cfe2f3" : "#fff"
+      );
+    });
+    if (group.currentIdx === 0) {
+      group.title = group.wrapper.append("div").style("display", "inline-block").style("padding", "3px 10px").style("text-align", "left").style("font-size", ".6em").style("text-transform", "uppercase").style("color", "#999").text(group.name);
+    } else {
+      group.dragActionDiv = group.wrapper.append("div").style("display", "flex").style("align-items", "center");
+      group.input = group.dragActionDiv.append("input").attr("size", 12).attr("value", group.name).style("margin", "5px").style("margin-left", "8px").style("display", "inline-block").style("font-size", ".8em").style("width", "87%").on("keyup", () => {
+        (0, import_debounce.debounce)(this.onKeyUp(group), 1e3);
+      });
+      group.inputMessage = group.dragActionDiv.append("span").style("color", "red").style("font-size", "0.7em").text("NOT unique").style("display", "none");
+      group.destroyBtn = group.dragActionDiv.append("button").style("display", "inline-block").style("padding", "0px 4px").property("disabled", this.data.groups.length <= this.minGrpNum).text("x").on("click", async () => {
+        if (this.data.groups.length <= this.minGrpNum) return;
+        this.data.groups = this.data.groups.filter((d) => d.currentIdx != group.currentIdx);
+        await this.removeGroup(group);
+      });
+    }
+    group.draggables = group.wrapper.append("div").classed("sjpp-drag-list-div", true);
+    await this.addItems(group);
+  }
+  async addItems(group) {
+    const handler = this;
+    await group.draggables.selectAll("div").data(this.data.values.filter((d) => d.group == group.currentIdx)).enter().append("div").attr("draggable", "true").attr("class", "sjpp-drag-item").style("margin", "3px").style("cursor", "default").style("padding", "3px 10px").style("border-radius", "5px").style("color", (d) => d.samplecount == 0 ? "#777" : "black").text((d) => `${d.label}${d.samplecount !== void 0 ? ` (n=${d.samplecount})` : ""}`).style("background-color", "#eee").each(function() {
+      const itemNode = select_default(this).on("dragstart", function() {
+        itemNode.style("background-color", "#fff2cc");
+        handler.draggedItem = itemNode;
+      }).on("mouseenter", function() {
+        itemNode.style("background-color", "#fff2cc");
+      }).on("mouseleave", function() {
+        itemNode.style("background-color", "#eee");
+      });
+    });
+  }
+  async removeGroup(group) {
+    this.removedGrp = true;
+    const itemsNum = group.wrapper.selectAll(".sjpp-drag-item").nodes();
+    if (itemsNum.length === 0) {
+      group.wrapper.remove();
+    } else {
+      group.input.remove();
+      group.destroyBtn.remove();
+      group.wrapper.remove();
+      for (const v of this.data.values) {
+        if (v.group == group.currentIdx) v.group = 0;
+      }
+    }
+    await this.update();
+  }
+  async update() {
+    this.dom.actionDiv.addGroup.property("disabled", this.data.groups.length >= this.maxGrpNum);
+    for (const [i, grp] of this.data.groups.entries()) {
+      if (i === 0) continue;
+      if (grp.currentIdx != i) {
+        this.data.values.filter((v) => v.group == grp.currentIdx).forEach((v) => v.group = i);
+        this.data.filters.filter((f) => f.group == grp.currentIdx).forEach((f) => f.group = i);
+        grp.currentIdx = i;
+      }
+    }
+    this.dom.grpsWrapper.selectAll(".sjpp-drag-drop-div").data(this.data.groups).each(async (group) => {
+      if (group.currentIdx !== 0) {
+        group.input.node().value = group.name;
+        group.destroyBtn.property("disabled", this.data.groups.length <= this.minGrpNum);
+      }
+      await this.addItems(group);
+    });
+  }
+  async onKeyUp(group) {
+    if (group.name == group.input.node().value) return;
+    this.editedName = true;
+    const match = this.data.groups.filter((g) => g.name == group.input.node().value);
+    if (match.length > 0) {
+      this.dom.actionDiv.applyBtn.property("disabled", true);
+      group.inputMessage.style("display", "block");
+    } else {
+      this.dom.actionDiv.applyBtn.property("disabled", false);
+      group.inputMessage.style("display", "none");
+      this.data.groups[group.currentIdx].name = group.input.node().value.trim();
+    }
+  }
+};
+export {
+  GroupSet
+};
+//# sourceMappingURL=qualitative-5QNBKDOZ.js.map