@sjcrh/proteinpaint-client 2.211.0 → 2.211.1-0

package/dist/importPlot-FQ65CZRI.js

@@ -1,8 +0,0 @@
-import {
-  importPlot
-} from "./chunk-FSWBNSQD.js";
-import "./chunk-HS5PO5ZQ.js";
-export {
-  importPlot
-};
-//# sourceMappingURL=importPlot-FQ65CZRI.js.map

package/dist/isoformExpression-BFCLGD2U.js

@@ -1,35 +0,0 @@
-import {
-  SearchHandler,
-  filterIsoforms
-} from "./chunk-NGWU4QLU.js";
-import "./chunk-K7HFOAR7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-FSWBNSQD.js";
-import "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-GP4VLNMZ.js";
-import "./chunk-6AFMWQXZ.js";
-import "./chunk-CME6DYDH.js";
-import "./chunk-57Z4VYLM.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-6XKAOSQE.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,
-  filterIsoforms
-};
-//# sourceMappingURL=isoformExpression-BFCLGD2U.js.map

package/dist/isoformExpression.unit.spec-KYI4HI7U.js

@@ -1,237 +0,0 @@
-import {
-  SearchHandler,
-  filterIsoforms
-} from "./chunk-NGWU4QLU.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-K7HFOAR7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-FSWBNSQD.js";
-import "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-GP4VLNMZ.js";
-import "./chunk-6AFMWQXZ.js";
-import "./chunk-CME6DYDH.js";
-import {
-  ISOFORM_EXPRESSION
-} from "./chunk-57Z4VYLM.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-6XKAOSQE.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/isoformExpression.unit.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-function mockGm(isoform) {
-  return { isoform, chr: "chr1", start: 0, stop: 100, exon: [[0, 100]] };
-}
-(0, import_tape.default)("\n", function(test) {
-  test.comment("-***- termdb/handlers/isoformExpression -***-");
-  test.end();
-});
-(0, import_tape.default)("selectIsoform() should call callback with configured unit from termdbConfig", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {
-          isoformExpression: { unit: "TPM" }
-        }
-      }
-    }
-  };
-  handler.selectIsoform("ENST00000269305", "TP53");
-  test.equal(selected?.isoform, "ENST00000269305", "Should pass selected isoform");
-  test.equal(selected?.gene, "TP53", "Should pass gene");
-  test.equal(selected?.name, "ENST00000269305 TPM", "Should include configured unit in term name");
-  test.equal(selected?.type, ISOFORM_EXPRESSION, "Should set type to isoformExpression");
-  test.end();
-});
-(0, import_tape.default)("selectIsoform() should use default unit when not configured", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {}
-      }
-    }
-  };
-  handler.selectIsoform("ENST00000269305", "TP53");
-  test.equal(selected?.isoform, "ENST00000269305", "Should pass selected isoform");
-  test.equal(selected?.name, "ENST00000269305 TPM", "Should use default unit TPM");
-  test.equal(selected?.type, ISOFORM_EXPRESSION, "Should set type to isoformExpression");
-  test.end();
-});
-(0, import_tape.default)("selectCollection() should create a custom termCollection from multiple isoforms", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {
-          isoformExpression: { unit: "TPM" }
-        }
-      }
-    }
-  };
-  handler.selectCollection([mockGm("ENST00000256078"), mockGm("ENST00000311936")], "KRAS");
-  test.equal(selected?.type, "termCollection", "Should set type to termCollection");
-  test.equal(selected?.isCustom, true, "Should set isCustom flag");
-  test.equal(selected?.memberType, "numeric", "Should set memberType to numeric");
-  test.equal(selected?.name, "KRAS Isoforms (TPM)", "Should include gene and unit in name");
-  test.equal(selected?.isleaf, true, "Should set isleaf");
-  test.ok(selected?.propsByTermId.ENST00000256078.color, "Should assign the first isoform a color");
-  test.ok(selected?.propsByTermId.ENST00000311936.color, "Should assign the second isoform a color");
-  test.notEqual(
-    selected?.propsByTermId.ENST00000256078.color,
-    selected?.propsByTermId.ENST00000311936.color,
-    "Should assign distinct member colors"
-  );
-  test.equal(selected?.termlst?.length, 2, "Should have 2 member terms");
-  const mt = selected.termlst[0];
-  test.equal(mt.id, "ENST00000256078", "Member term id should be the isoform ID");
-  test.equal(mt.name, "ENST00000256078", "Member term name should be the isoform ID");
-  test.equal(mt.type, "isoformExpression", "Member term type should be isoformExpression");
-  test.equal(mt.isoform, "ENST00000256078", "Member term should carry isoform field");
-  test.end();
-});
-(0, import_tape.default)("selectCollection() should use default unit when not configured", (test) => {
-  const handler = new SearchHandler();
-  let selected;
-  handler.callback = (t) => {
-    selected = t;
-  };
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {}
-      }
-    }
-  };
-  handler.selectCollection([mockGm("ENST00000256078"), mockGm("ENST00000311936")], "KRAS");
-  test.equal(selected?.name, "KRAS Isoforms (TPM)", "Should use default unit TPM");
-  test.end();
-});
-(0, import_tape.default)("selectCollection() renders fraction choices when requested", (test) => {
-  const handler = new SearchHandler();
-  const holder = select_default("body").append("div");
-  let selected;
-  handler.callback = (term) => {
-    selected = term;
-  };
-  handler.app = {
-    vocabApi: { termdbConfig: { queries: { isoformExpression: { unit: "TPM" } } } }
-  };
-  handler.termCollectionSelectionMode = "fraction";
-  handler.dom = { errDiv: holder.append("div"), isoformDiv: holder.append("div") };
-  handler.selectCollection([mockGm("ENST00000256078"), mockGm("ENST00000311936")], "KRAS");
-  test.ok(holder.text().includes("Denominator"), "renders denominator choices");
-  holder.select('[data-testid="sjpp-term-collection-fraction-select"]').node().click();
-  test.equal(selected?.type, "TermCollectionTWFraction", "returns a fraction wrapper");
-  test.deepEqual(
-    selected?.q.denominators,
-    ["ENST00000256078", "ENST00000311936"],
-    "defaults every isoform as a denominator"
-  );
-  test.deepEqual(selected?.q.numerators, ["ENST00000256078"], "defaults only the first isoform as numerator");
-  test.equal(selected?.term.termlst.length, 2, "retains every isoform on the collection term");
-  holder.remove();
-  test.end();
-});
-(0, import_tape.default)("showIsoforms multi-select: single isoform calls selectIsoform, multiple calls selectCollection", (test) => {
-  const handler = new SearchHandler();
-  const calls = [];
-  handler.app = {
-    vocabApi: {
-      termdbConfig: {
-        queries: {
-          isoformExpression: { unit: "TPM" }
-        }
-      }
-    }
-  };
-  handler.selectIsoform = (isoform, gene) => {
-    calls.push({ method: "selectIsoform", args: { isoform, gene } });
-  };
-  handler.selectCollection = (gms, gene) => {
-    calls.push({ method: "selectCollection", args: { gms, gene } });
-  };
-  const onMultiSelect1 = (selected) => {
-    if (selected.length === 1) handler.selectIsoform(selected[0].isoform, "TP53");
-    else handler.selectCollection(selected, "TP53");
-  };
-  onMultiSelect1([mockGm("ENST00000269305")]);
-  test.equal(calls.length, 1, "Should have one call");
-  test.equal(calls[0].method, "selectIsoform", "Single isoform should call selectIsoform");
-  const onMultiSelect2 = (selected) => {
-    if (selected.length === 1) handler.selectIsoform(selected[0].isoform, "KRAS");
-    else handler.selectCollection(selected, "KRAS");
-  };
-  onMultiSelect2([mockGm("ENST00000256078"), mockGm("ENST00000311936")]);
-  test.equal(calls.length, 2, "Should have two calls total");
-  test.equal(calls[1].method, "selectCollection", "Multiple isoforms should call selectCollection");
-  test.equal(calls[1].args.gms.length, 2, "Should pass both gene models");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should return only ENST isoforms present in availableItems", (test) => {
-  const gmlst = [mockGm("ENST00000269305"), mockGm("ENST00000413465"), mockGm("NM_000546"), mockGm("ENST00000359597")];
-  const availableItems = ["ENST00000269305", "ENST00000359597"];
-  const result = filterIsoforms(gmlst, availableItems);
-  test.equal(result.length, 2, "Should return 2 matching isoforms");
-  test.equal(result[0].isoform, "ENST00000269305", "First match correct");
-  test.equal(result[1].isoform, "ENST00000359597", "Second match correct");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should exclude non-ENST isoforms even if in availableItems", (test) => {
-  const gmlst = [mockGm("NM_000546"), mockGm("NR_176326"), mockGm("ENST00000269305")];
-  const availableItems = ["NM_000546", "ENST00000269305"];
-  const result = filterIsoforms(gmlst, availableItems);
-  test.equal(result.length, 1, "Should only return ENST isoform");
-  test.equal(result[0].isoform, "ENST00000269305", "Should be the ENST match");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should return all ENST isoforms when availableItems is empty", (test) => {
-  const gmlst = [mockGm("ENST00000269305"), mockGm("ENST00000413465"), mockGm("NM_000546")];
-  const result = filterIsoforms(gmlst, []);
-  test.equal(result.length, 2, "Should return all ENST isoforms when no filter");
-  test.equal(result[0].isoform, "ENST00000269305", "First ENST correct");
-  test.equal(result[1].isoform, "ENST00000413465", "Second ENST correct");
-  test.end();
-});
-(0, import_tape.default)("filterIsoforms() should return empty array when no ENST isoforms match", (test) => {
-  const gmlst = [mockGm("ENST00000269305"), mockGm("ENST00000413465")];
-  const availableItems = ["ENST00000999999"];
-  const result = filterIsoforms(gmlst, availableItems);
-  test.equal(result.length, 0, "Should return empty when no matches");
-  test.end();
-});
-//# sourceMappingURL=isoformExpression.unit.spec-KYI4HI7U.js.map

package/dist/junction-BKH6RWOP.js

@@ -1,36 +0,0 @@
-import {
-  SearchHandler,
-  getJunctionCustomTerms
-} from "./chunk-QDNUIS2Y.js";
-import "./chunk-2WKGE7BO.js";
-import "./chunk-K7HFOAR7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-FSWBNSQD.js";
-import "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-GP4VLNMZ.js";
-import "./chunk-6AFMWQXZ.js";
-import "./chunk-CME6DYDH.js";
-import "./chunk-57Z4VYLM.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-6XKAOSQE.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,
-  getJunctionCustomTerms
-};
-//# sourceMappingURL=junction-BKH6RWOP.js.map

package/dist/junction.unit.spec-MQIHKSNE.js

@@ -1,182 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-QDNUIS2Y.js";
-import {
-  makeJunctionCustomTerm
-} from "./chunk-2WKGE7BO.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-K7HFOAR7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-FSWBNSQD.js";
-import "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-GP4VLNMZ.js";
-import "./chunk-6AFMWQXZ.js";
-import "./chunk-CME6DYDH.js";
-import "./chunk-57Z4VYLM.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-6XKAOSQE.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/junction.unit.spec.ts
-var import_tape = __toESM(require_tape(), 1);
-function makeJunction(id) {
-  return {
-    type: "junction",
-    id,
-    name: `Name ${id}`,
-    chr: "chr1",
-    start: 100,
-    stop: 200,
-    strand: "+",
-    info: {}
-  };
-}
-function getOpts(holder, dslabel, customTerms = [], callback = (_term) => {
-}, termCollectionSelectionMode) {
-  const state = { customTerms };
-  return {
-    holder,
-    callback,
-    termCollectionSelectionMode,
-    genomeObj: { name: "hg38" },
-    app: {
-      vocabApi: {
-        vocab: { dslabel },
-        state,
-        async deleteCustomTermById(id) {
-          const index = state.customTerms.findIndex((term) => term.id === id);
-          if (index !== -1) state.customTerms.splice(index, 1);
-        }
-      }
-    }
-  };
-}
-(0, import_tape.default)("\n", (test) => {
-  test.comment("-***- termdb/handlers/junction -***-");
-  test.end();
-});
-(0, import_tape.default)("init() shows the empty-state message", async (test) => {
-  const holder = select_default("body").append("div");
-  const handler = new SearchHandler();
-  await handler.init(getOpts(holder, "junction-handler-empty"));
-  test.ok(holder.text().includes("Junctions selected from genome browser"), "shows the empty-state instructions");
-  holder.remove();
-  test.end();
-});
-(0, import_tape.default)("ungrouped junctions render as selectable pills and can be deleted", async (test) => {
-  const holder = select_default("body").append("div");
-  const handler = new SearchHandler();
-  let selected;
-  const dslabel = "junction-handler-ungrouped";
-  const customTerms = [makeJunctionCustomTerm([makeJunction("junction-1")])];
-  await handler.init(
-    getOpts(holder, dslabel, customTerms, (term) => {
-      selected = term;
-    })
-  );
-  const pill = holder.select(".ts_pill");
-  test.equal(pill.text(), "Name junction-1", "renders the junction name in a pill");
-  pill.node().click();
-  test.equal(selected?.id, "junction-1", "selects the individual junction");
-  holder.select('[data-testid="sjpp-junction-delete"]').node().click();
-  await new Promise((resolve) => setTimeout(resolve, 0));
-  test.equal(holder.selectAll(".ts_pill").size(), 0, "removes the deleted junction pill");
-  test.ok(holder.text().includes("Junctions selected from genome browser"), "restores the empty state");
-  holder.remove();
-  test.end();
-});
-(0, import_tape.default)("event junctions render as one pill that selects and deletes the term collection", async (test) => {
-  const holder = select_default("body").append("div");
-  const handler = new SearchHandler();
-  let selected;
-  const dslabel = "junction-handler-event";
-  const customTerms = [makeJunctionCustomTerm([makeJunction("junction-1"), makeJunction("junction-2")], "Event A")];
-  await handler.init(
-    getOpts(holder, dslabel, customTerms, (term) => {
-      selected = term;
-    })
-  );
-  const pills = holder.selectAll(".ts_pill");
-  test.equal(pills.size(), 1, "renders one pill for the event and no member junction pills");
-  test.equal(pills.text(), "Event A", "uses the event label as the pill text");
-  test.ok(holder.text().includes("junction-1"), "lists the first junction ID");
-  test.ok(holder.text().includes("junction-2"), "lists the second junction ID");
-  pills.node().click();
-  test.equal(selected?.type, "termCollection", "selects a term collection");
-  test.equal(selected?.memberType, "numeric", "creates a numeric collection");
-  test.equal(selected?.name, "Event A", "uses the event label as the collection name");
-  test.deepEqual(selected?.termIds, ["junction-1", "junction-2"], "includes all event junction IDs");
-  test.ok(selected?.propsByTermId["junction-1"].color, "assigns the first junction a color");
-  test.ok(selected?.propsByTermId["junction-2"].color, "assigns the second junction a color");
-  test.notEqual(
-    selected?.propsByTermId["junction-1"].color,
-    selected?.propsByTermId["junction-2"].color,
-    "assigns distinct member colors"
-  );
-  holder.select('[data-testid="sjpp-junction-delete"]').node().click();
-  await new Promise((resolve) => setTimeout(resolve, 0));
-  test.equal(holder.selectAll(".ts_pill").size(), 0, "removes the complete event choice");
-  holder.remove();
-  test.end();
-});
-(0, import_tape.default)("init() only shows state-backed junction custom terms", async (test) => {
-  const holder = select_default("body").append("div");
-  const handler = new SearchHandler();
-  const customTerms = [
-    makeJunctionCustomTerm([makeJunction("active-junction")]),
-    { id: "other-custom-term", name: "Other", tw: { term: { type: "float", id: "other", name: "Other" } } }
-  ];
-  await handler.init(getOpts(holder, "active", customTerms));
-  test.equal(holder.selectAll(".ts_pill").size(), 1, "renders only one matching junction term");
-  test.equal(holder.select(".ts_pill").text(), "Name active-junction", "renders the state-backed junction");
-  holder.remove();
-  test.end();
-});
-(0, import_tape.default)("event junction renders fraction choices when requested", async (test) => {
-  const holder = select_default("body").append("div");
-  const handler = new SearchHandler();
-  let selected;
-  const customTerms = [makeJunctionCustomTerm([makeJunction("junction-1"), makeJunction("junction-2")], "Event A")];
-  await handler.init(
-    getOpts(
-      holder,
-      "junction-handler-fraction",
-      customTerms,
-      (term) => {
-        selected = term;
-      },
-      "fraction"
-    )
-  );
-  holder.select(".ts_pill").node().click();
-  test.ok(holder.text().includes("Denominator"), "renders denominator choices for the event collection");
-  holder.select('[data-testid="sjpp-term-collection-fraction-select"]').node().click();
-  test.equal(selected?.type, "TermCollectionTWFraction", "returns a fraction wrapper");
-  test.deepEqual(selected?.q.denominators, ["junction-1", "junction-2"], "defaults both junctions as denominators");
-  test.deepEqual(selected?.q.numerators, ["junction-1"], "defaults only the first junction as numerator");
-  test.equal(selected?.term.termlst.length, 2, "retains both junction members");
-  holder.remove();
-  test.end();
-});
-//# sourceMappingURL=junction.unit.spec-MQIHKSNE.js.map

package/dist/launch.adhoc-AHTCA2BP.js

@@ -1,37 +0,0 @@
-import {
-  launch
-} from "./chunk-OC2FSBFB.js";
-import "./chunk-SQGAWR2L.js";
-import "./chunk-V7UVHM57.js";
-import "./chunk-X46YA4CB.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-K7HFOAR7.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-FSWBNSQD.js";
-import "./chunk-7XZA2XR2.js";
-import "./chunk-DD3DWHUY.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-GP4VLNMZ.js";
-import "./chunk-6AFMWQXZ.js";
-import "./chunk-CME6DYDH.js";
-import "./chunk-57Z4VYLM.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-6XKAOSQE.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 {
-  launch
-};
-//# sourceMappingURL=launch.adhoc-AHTCA2BP.js.map