@sjcrh/proteinpaint-client 2.222.0 → 2.223.0

package/dist/selectGenomeWithTklst-E6TV7BOQ.js

@@ -0,0 +1,125 @@
+import {
+  addGeneSearchbox,
+  first_genetrack_tolist
+} from "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import {
+  contigNameNoChr2
+} from "./chunk-WJLRU5OF.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";
+
+// src/selectGenomeWithTklst.js
+var tip = new Menu({ padding: "" });
+var variantFlankingSize = 60;
+async function init(arg, holder, genomes) {
+  holder.style("margin", "40px 20px 20px 20px");
+  const formdiv = holder.append("div");
+  formdiv.append("p").text("To launch view, press ENTER at gene search.").style("opacity", 0.3);
+  const blockholder = holder.append("div");
+  const genomeselect = addGenomeSelect(formdiv, genomes).on("change", makeGeneSearch);
+  let coordInput, genome;
+  const geneInputSpan = formdiv.append("span").style("margin-left", "10px");
+  const submitBtn = formdiv.append("button").style("display", "none").style("margin-top", "20px").style("padding", "10px 15px").style("border-radius", "30px").text("Launch ProteinPaint").on("click", submit);
+  makeGeneSearch();
+  function makeGeneSearch() {
+    geneInputSpan.selectAll("*").remove();
+    const s = genomeselect.node();
+    genome = genomes[s.options[s.selectedIndex].innerHTML];
+    const opt = {
+      genome,
+      tip,
+      row: geneInputSpan,
+      allowVariant: true,
+      /* only show submit button if valid coord is found
+      this is deal with a defect with genesearch.js
+      that pasting coordinate in <input> without hitting enter
+      will not trigger coord parsing
+      */
+      callback: () => submitBtn.style("display", "block")
+    };
+    coordInput = addGeneSearchbox(opt);
+  }
+  async function submit() {
+    try {
+      formdiv.remove();
+      const par = {
+        nobox: 1,
+        genome,
+        holder: blockholder,
+        tklst: arg.selectGenomeWithTklst
+      };
+      const ci = coordInput;
+      if (ci.chr) {
+        const [nocount, hascount] = contigNameNoChr2(genome, [ci.chr]);
+        if (nocount + hascount == 0) throw "Invalid chromosome name: " + ci.chr;
+        const chr = nocount ? "chr" + ci.chr : ci.chr;
+        if (Number.isInteger(ci.pos)) {
+          if (!ci.ref) throw "Reference allele missing from variant string";
+          if (!ci.alt) throw "Alternative allele missing from variant string";
+          par.chr = chr;
+          par.start = ci.pos - variantFlankingSize;
+          par.stop = ci.pos + variantFlankingSize;
+          for (const tk of par.tklst) {
+            if (tk.type == "bam") {
+              tk.variants = [
+                {
+                  chr,
+                  pos: ci.pos - 1,
+                  // convert 1-based to 0-based
+                  ref: ci.ref,
+                  alt: ci.alt
+                }
+              ];
+            }
+          }
+        } else {
+          if (!Number.isInteger(ci.start) || !Number.isInteger(ci.stop)) throw "non-integer start/stop";
+          par.chr = chr;
+          par.start = ci.start;
+          par.stop = ci.stop;
+        }
+      } else {
+        const d = genome.defaultcoord;
+        par.chr = d.chr;
+        par.start = d.start;
+        par.stop = d.stop;
+      }
+      first_genetrack_tolist(genome, par.tklst);
+      const _ = await import("./block-MIBFGU6V.js");
+      new _.Block(par);
+    } catch (e) {
+      window.alert(e.message || e);
+    }
+  }
+}
+function addGenomeSelect(div, genomes) {
+  const select = div.append("select");
+  for (const gn in genomes) {
+    select.append("option").text(gn);
+  }
+  return select;
+}
+export {
+  init
+};
+//# sourceMappingURL=selectGenomeWithTklst-E6TV7BOQ.js.map

package/dist/singleCellCellType-CA4MPJFG.js

@@ -0,0 +1,29 @@
+import {
+  SearchHandler
+} from "./chunk-OJ6IPUZC.js";
+import "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.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
+};
+//# sourceMappingURL=singleCellCellType-CA4MPJFG.js.map

package/dist/singleCellCellType.unit.spec-NE34HWRM.js

@@ -0,0 +1,150 @@
+import {
+  SearchHandler
+} from "./chunk-OJ6IPUZC.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import {
+  SINGLECELL_CELLTYPE,
+  TermTypeGroups
+} from "./chunk-WJLRU5OF.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";
+
+// termdb/handlers/test/singleCellCellType.unit.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+function getHolder() {
+  return select_default("body").append("div");
+}
+function getUsecase(plotName = "Plot A") {
+  return {
+    target: "sampleScatter",
+    detail: "term",
+    specialCase: {
+      config: { name: plotName }
+    }
+  };
+}
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- termdb/handlers/singleCellCellType -***-");
+  test.end();
+});
+(0, import_tape.default)("validateOpts() should require callback, termType2terms, and specialCase.config.name", (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  test.throws(
+    () => handler.validateOpts({
+      holder,
+      app: { vocabApi: { termdbConfig: { termType2terms: {} } } },
+      usecase: getUsecase("Plot A")
+    }),
+    /callback is required/,
+    "Should throw when callback is missing"
+  );
+  test.throws(
+    () => handler.validateOpts({
+      holder,
+      callback: () => {
+      },
+      app: { vocabApi: { termdbConfig: {} } },
+      usecase: getUsecase("Plot A")
+    }),
+    /termType2terms is required in termdbConfig for singleCellCellType handler/,
+    "Should throw when termType2terms is missing"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("init() should render only terms matching usecase plot and call callback on click", async (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  let selectedTerm;
+  const scctTerms = [
+    { id: "t1", name: "Myeloid", type: SINGLECELL_CELLTYPE, plot: "Plot A" },
+    { id: "t2", name: "Lymphoid", type: SINGLECELL_CELLTYPE, plot: "Plot A" },
+    { id: "t3", name: "Nonmatching", type: SINGLECELL_CELLTYPE, plot: "Plot B" }
+  ];
+  await handler.init({
+    holder,
+    callback: (t) => {
+      selectedTerm = t;
+    },
+    app: {
+      vocabApi: {
+        termdbConfig: {
+          termType2terms: {
+            [TermTypeGroups.SINGLECELL_CELLTYPE]: scctTerms
+          }
+        }
+      }
+    },
+    usecase: getUsecase("Plot A")
+  });
+  const labels = holder.selectAll(".termlabel");
+  test.equal(labels.size(), 2, "Should render only two matching terms for Plot A");
+  test.deepEqual(
+    labels.nodes().map((n) => n.textContent),
+    ["Myeloid", "Lymphoid"],
+    "Should render labels in the filtered order"
+  );
+  const firstLabel = labels.nodes()[0];
+  firstLabel.click();
+  test.equal(selectedTerm?.id, "t1", "Should pass clicked term object to callback");
+  test.equal(selectedTerm?.type, SINGLECELL_CELLTYPE, "Callback term type should be singleCellCellType");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("init() should render sayerror when termType2terms key is missing for singleCellCellType", async (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  await handler.init({
+    holder,
+    callback: () => {
+    },
+    app: {
+      vocabApi: {
+        termdbConfig: {
+          termType2terms: {
+            [TermTypeGroups.DICTIONARY_VARIABLES]: []
+          }
+        }
+      }
+    },
+    usecase: getUsecase("Plot A")
+  });
+  const errorDiv = holder.select(".sja_errorbar").node();
+  test.ok(errorDiv, "Should render an error message when singleCellCellType terms are missing");
+  test.ok(
+    holder.text().includes(
+      `termType2terms[${TermTypeGroups.SINGLECELL_CELLTYPE}]:[] is required in termdbConfig for singleCellCellType handler`
+    ),
+    "Should show expected configuration error text"
+  );
+  test.equal(holder.selectAll(".termlabel").size(), 0, "Should not render term labels when config is missing");
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+//# sourceMappingURL=singleCellCellType.unit.spec-NE34HWRM.js.map

package/dist/singleCellGeneExpression-A5C7TKTF.js

@@ -0,0 +1,29 @@
+import {
+  SearchHandler
+} from "./chunk-LCUVGK27.js";
+import "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.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
+};
+//# sourceMappingURL=singleCellGeneExpression-A5C7TKTF.js.map

package/dist/singleCellGeneExpression.unit.spec-NX2JMJ5C.js

@@ -0,0 +1,144 @@
+import {
+  SearchHandler
+} from "./chunk-LCUVGK27.js";
+import {
+  require_tape
+} from "./chunk-PJYCTAMC.js";
+import "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import {
+  SINGLECELL_GENE_EXPRESSION
+} from "./chunk-WJLRU5OF.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";
+
+// termdb/handlers/test/singleCellGeneExpression.unit.spec.ts
+var import_tape = __toESM(require_tape(), 1);
+function getHolder() {
+  return select_default("body").append("div");
+}
+function getUsecase(sample = { id: "sample-A" }) {
+  return {
+    target: "sampleScatter",
+    detail: "term",
+    specialCase: {
+      config: { sample }
+    }
+  };
+}
+(0, import_tape.default)("\n", function(test) {
+  test.comment("-***- termdb/handlers/singleCellGeneExpression -***-");
+  test.end();
+});
+(0, import_tape.default)("validateOpts() should require callback, app, holder, genomeObj, and usecase.specialCase.config.sample", (test) => {
+  const handler = new SearchHandler();
+  const holder = getHolder();
+  test.throws(
+    () => handler.validateOpts({
+      holder,
+      app: { vocabApi: { termdbConfig: { queries: { singleCell: { geneExpression: {} } } } } },
+      genomeObj: {},
+      usecase: getUsecase()
+    }),
+    /callback is required/,
+    "Should throw when callback is missing"
+  );
+  test.throws(
+    () => handler.validateOpts({
+      holder,
+      callback: () => {
+      },
+      genomeObj: {},
+      usecase: getUsecase()
+    }),
+    /app is required/,
+    "Should throw when app is missing"
+  );
+  test.throws(
+    () => handler.validateOpts({
+      callback: () => {
+      },
+      app: { vocabApi: { termdbConfig: {} } },
+      genomeObj: {},
+      usecase: getUsecase()
+    }),
+    /holder is required/,
+    "Should throw when holder is missing"
+  );
+  test.throws(
+    () => handler.validateOpts({
+      holder,
+      callback: () => {
+      },
+      app: { vocabApi: { termdbConfig: {} } },
+      usecase: getUsecase()
+    }),
+    /genomeObj is required/,
+    "Should throw when genomeObj is missing"
+  );
+  if (test["_ok"]) holder.remove();
+  test.end();
+});
+(0, import_tape.default)("selectGene() should throw when no gene is selected", async (test) => {
+  const handler = new SearchHandler();
+  handler.app = { vocabApi: { termdbConfig: {} } };
+  handler.callback = () => {
+  };
+  try {
+    await handler.selectGene(void 0, { id: "sample-A" });
+    test.fail("Should throw when no gene is selected");
+  } catch (e) {
+    test.match(String(e), /No gene selected/, "Should throw expected message when gene is missing");
+  }
+  test.end();
+});
+(0, import_tape.default)("selectGene() should call callback with configured unit and default unit fallback", async (test) => {
+  const handler = new SearchHandler();
+  const sample = { id: "sample-A", type: "tumor" };
+  let selected;
+  handler.callback = (t) => {
+    selected = t;
+  };
+  handler.app = {
+    vocabApi: {
+      termdbConfig: {
+        queries: {
+          singleCell: {
+            geneExpression: { unit: "log2 CPM" }
+          }
+        }
+      }
+    }
+  };
+  await handler.selectGene("TP53", sample);
+  test.equal(selected?.gene, "TP53", "Should pass selected gene");
+  test.equal(selected?.name, "TP53 log2 CPM", "Should include configured unit in term name");
+  test.equal(selected?.type, SINGLECELL_GENE_EXPRESSION, "Should set type to singleCellGeneExpression");
+  test.deepEqual(selected?.sample, sample, "Should pass through selected sample");
+  handler.app = { vocabApi: { termdbConfig: { queries: { singleCell: { geneExpression: {} } } } } };
+  await handler.selectGene("GATA3", sample);
+  test.equal(selected?.name, "GATA3 Gene Expression", "Should use default unit when config unit is not provided");
+  test.end();
+});
+//# sourceMappingURL=singleCellGeneExpression.unit.spec-NX2JMJ5C.js.map

package/dist/singleCellNumericValue-4BEKA732.js

@@ -0,0 +1,29 @@
+import {
+  SearchHandler
+} from "./chunk-6HC6RVNT.js";
+import "./chunk-JP4IU7DO.js";
+import "./chunk-HJ6L54YS.js";
+import "./chunk-IRAB3OI7.js";
+import "./chunk-CNFTQSNE.js";
+import "./chunk-RIHO7ZD5.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-4TJO2DGU.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-MHWYRNGA.js";
+import "./chunk-JHLF2ZC2.js";
+import "./chunk-WJLRU5OF.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
+};
+//# sourceMappingURL=singleCellNumericValue-4BEKA732.js.map