@sjcrh/proteinpaint-client 2.210.0 → 2.210.1

package/dist/selectGenomeWithTklst-ZZUJ7AQ7.js

@@ -1,129 +0,0 @@
-import {
-  addGeneSearchbox,
-  first_genetrack_tolist
-} from "./chunk-55FABQU2.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-UXD6G6G4.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import "./chunk-3FEP6B5T.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VA57CUC7.js";
-import "./chunk-BK6UDL7F.js";
-import "./chunk-KIAMLQ7S.js";
-import {
-  contigNameNoChr2
-} from "./chunk-SB36AUG7.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.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-43KNTXZ5.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-ZZUJ7AQ7.js.map

package/dist/singleCellCellType-LCF2JNZ2.js

@@ -1,33 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-JDVBUIEU.js";
-import "./chunk-55FABQU2.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-UXD6G6G4.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-3FEP6B5T.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VA57CUC7.js";
-import "./chunk-BK6UDL7F.js";
-import "./chunk-KIAMLQ7S.js";
-import "./chunk-SB36AUG7.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  SearchHandler
-};
-//# sourceMappingURL=singleCellCellType-LCF2JNZ2.js.map

package/dist/singleCellCellType.unit.spec-T6DYH4BC.js

@@ -1,154 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-JDVBUIEU.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-55FABQU2.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-UXD6G6G4.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-3FEP6B5T.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VA57CUC7.js";
-import "./chunk-BK6UDL7F.js";
-import "./chunk-KIAMLQ7S.js";
-import {
-  SINGLECELL_CELLTYPE,
-  TermTypeGroups
-} from "./chunk-SB36AUG7.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.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-T6DYH4BC.js.map

package/dist/singleCellGeneExpression-2XUYTH4C.js

@@ -1,33 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-EDZJ3VNZ.js";
-import "./chunk-55FABQU2.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-UXD6G6G4.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-3FEP6B5T.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VA57CUC7.js";
-import "./chunk-BK6UDL7F.js";
-import "./chunk-KIAMLQ7S.js";
-import "./chunk-SB36AUG7.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  SearchHandler
-};
-//# sourceMappingURL=singleCellGeneExpression-2XUYTH4C.js.map

package/dist/singleCellGeneExpression.unit.spec-SMRCLOF4.js

@@ -1,148 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-EDZJ3VNZ.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-55FABQU2.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-UXD6G6G4.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-3FEP6B5T.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VA57CUC7.js";
-import "./chunk-BK6UDL7F.js";
-import "./chunk-KIAMLQ7S.js";
-import {
-  SINGLECELL_GENE_EXPRESSION
-} from "./chunk-SB36AUG7.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.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-SMRCLOF4.js.map

package/dist/singleCellNumericValue-57I33FZT.js

@@ -1,33 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-PZ2OSHBF.js";
-import "./chunk-55FABQU2.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-UXD6G6G4.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-3FEP6B5T.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-VA57CUC7.js";
-import "./chunk-BK6UDL7F.js";
-import "./chunk-KIAMLQ7S.js";
-import "./chunk-SB36AUG7.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-7X6NF7NI.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-Z2ZITHT4.js";
-import "./chunk-4OLM3KSB.js";
-import "./chunk-FXQXCOII.js";
-import "./chunk-TLT4YIG3.js";
-import "./chunk-5R63Q5KH.js";
-import "./chunk-I6Y4O3RR.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-DQC5FFGV.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  SearchHandler
-};
-//# sourceMappingURL=singleCellNumericValue-57I33FZT.js.map