@sjcrh/proteinpaint-client 2.205.0 → 2.206.0

package/dist/junction.unit.spec-6MAKIB3R.js

@@ -1,182 +0,0 @@
-import {
-  SearchHandler
-} from "./chunk-4AQQ3BXD.js";
-import {
-  makeJunctionCustomTerm
-} from "./chunk-JNVWSFNC.js";
-import {
-  require_tape
-} from "./chunk-PJYCTAMC.js";
-import "./chunk-J7JDCNLU.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-N635HDJ4.js";
-import "./chunk-T46FA72N.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-JYOIO5UY.js";
-import "./chunk-YN5NY3D3.js";
-import "./chunk-RN4BOWRH.js";
-import "./chunk-IK2BO37K.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.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/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-6MAKIB3R.js.map

package/dist/launch.adhoc-FAHRZFYG.js

@@ -1,37 +0,0 @@
-import {
-  launch
-} from "./chunk-D2MZT7CC.js";
-import "./chunk-5AAAH4OZ.js";
-import "./chunk-IAE3KWN5.js";
-import "./chunk-X46YA4CB.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-J7JDCNLU.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-N635HDJ4.js";
-import "./chunk-T46FA72N.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-JYOIO5UY.js";
-import "./chunk-YN5NY3D3.js";
-import "./chunk-RN4BOWRH.js";
-import "./chunk-IK2BO37K.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.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 {
-  launch
-};
-//# sourceMappingURL=launch.adhoc-FAHRZFYG.js.map

package/dist/leftlabel.sample-PDZLWLJ4.js

@@ -1,258 +0,0 @@
-import {
-  displaySampleTable,
-  getFilterName,
-  makelabel
-} from "./chunk-YHA3AYAM.js";
-import "./chunk-SKMFMGCD.js";
-import "./chunk-6JBQLOJW.js";
-import "./chunk-3MFFZRH3.js";
-import "./chunk-V2OJLJSK.js";
-import "./chunk-4FTH4L3A.js";
-import "./chunk-ABTO5QSB.js";
-import {
-  Tabs,
-  fillbar,
-  filterInit,
-  getNormalRoot,
-  renderTable
-} from "./chunk-J7JDCNLU.js";
-import "./chunk-HJ6L54YS.js";
-import "./chunk-KV4W2ACA.js";
-import "./chunk-N635HDJ4.js";
-import "./chunk-T46FA72N.js";
-import "./chunk-ELJX3QIQ.js";
-import "./chunk-EEB5VE2A.js";
-import "./chunk-6RRZRISL.js";
-import "./chunk-2KM4PRQM.js";
-import "./chunk-JYOIO5UY.js";
-import "./chunk-YN5NY3D3.js";
-import "./chunk-RN4BOWRH.js";
-import "./chunk-IK2BO37K.js";
-import "./chunk-WINIL2KN.js";
-import "./chunk-PF4DSFDR.js";
-import {
-  violinRenderer
-} from "./chunk-D6G64XPJ.js";
-import "./chunk-W5J3LTYS.js";
-import "./chunk-YLJOZP4P.js";
-import "./chunk-HDTFYTEL.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";
-
-// mds3/leftlabel.sample.js
-function makeSampleLabel(data, tk, block, laby) {
-  if (!tk.leftlabels.doms.samples) {
-    tk.leftlabels.doms.samples = makelabel(tk, block, laby);
-  }
-  if (data.sampleTotalNumber) {
-    tk.leftlabels.doms.samples.attr("class", "sja_clbtext2").style("opacity", 1).text(`${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? "s" : ""}`).attr("data-testid", "sjpp_mds3tk_samples_label").on("click", async (event) => {
-      tk.menutip.clear().showunder(event.target);
-      await mayShowSummary(tk, block);
-      const buttonrow = tk.menutip.d.append("div").style("margin", "10px");
-      menu_listSamples(buttonrow, data, tk, block);
-    });
-  } else {
-    tk.leftlabels.doms.samples.text("No samples").attr("class", "").style("opacity", 0.5).on("click", null);
-  }
-}
-function makeSampleFilterLabel(data, tk, block, laby) {
-  if (!tk.leftlabels.doms.filterObj) {
-    tk.leftlabels.doms.filterObj = makelabel(tk, block, laby);
-    tk.leftlabels.doms.filterObj.attr("data-testid", "sjpp_mds3tk_leftlabel_samplefilter");
-  }
-  tk.leftlabels.doms.filterObj.text(getFilterName(tk.filterObj)).on("click", async (event) => {
-    tk.menutip.clear().showunder(event.target);
-    const arg = {
-      holder: tk.menutip.d.append("div").style("margin", "10px"),
-      vocabApi: tk.mds.termdb.vocabApi,
-      callback: (f) => {
-        tk.filterObj = f;
-        tk.load();
-      }
-    };
-    mayAddGetCategoryArgs(arg, block);
-    filterInit(arg).main(tk.filterObj);
-  });
-}
-function mayAddGetCategoryArgs(arg, block) {
-  if (block.usegm) {
-    arg.getCategoriesArguments = { currentGeneNames: [block.usegm.name] };
-  } else {
-    arg.getCategoriesArguments = { rglst: structuredClone(block.rglst) };
-  }
-}
-async function mayShowSummary(tk, block) {
-  if (!tk.mds.variant2samples.twLst) {
-    return;
-  }
-  const div = tk.menutip.d.append("div").style("margin", "10px");
-  const wait = div.append("div").text("Loading...");
-  try {
-    const { summary } = await tk.mds.getSamples({ isSummary: true });
-    tk.leftlabels.__samples_data = summary;
-    wait.remove();
-    await showSummary4terms(summary, div.append("div").attr("data-testid", "sja_mds3samplesummarydiv"), tk, block);
-  } catch (e) {
-    wait.text(`Error: ${e.message || e}`);
-    if (e.stack) console.log(e.stack);
-  }
-}
-async function showSummary4terms(data, div, tk, block) {
-  const tabs = [];
-  for (const { termid, numbycategory } of data) {
-    tabs.push({
-      label: tk.mds.variant2samples.twLst.find((i) => i.term.id == termid).term.name + (numbycategory ? `<span style="font-size:.8em;float:right;margin-left: 5px;">n=${numbycategory.length}</span>` : ""),
-      keydownCallback: function(event) {
-        setTimeout(() => {
-          const tr = this.contentHolder.select("tbody").select("tr").node();
-          if (!tr) return;
-          tr.focus();
-        }, 100);
-      }
-    });
-  }
-  new Tabs({
-    holder: div,
-    tabsPosition: "vertical",
-    linePosition: "right",
-    tabs
-  }).main();
-  for (const [i, d] of data.entries()) {
-    const holder = tabs[i].contentHolder.style("padding-left", "20px");
-    if (d.numbycategory) {
-      holder.append("div").text("Click a category to create new track.").style("margin-bottom", "10px").style("font-size", ".8em").style("opacity", 0.5);
-      showSummary4oneTerm(d.termid, holder, d.numbycategory, tk, block);
-      continue;
-    }
-    if (d.density_data) {
-      if (!Number.isFinite(d.density_data.min) || !Number.isFinite(d.density_data.max)) {
-        holder.append("div").text("No data");
-        continue;
-      }
-      holder.append("div").text("Select a range to create new track.").style("margin-bottom", "10px").style("font-size", ".8em").style("opacity", 0.5);
-      showDensity4oneTerm(d.termid, holder, d, tk, block);
-      continue;
-    }
-    throw "unknown summary data";
-  }
-}
-function showSummary4oneTerm(termid, div, numbycategory, tk, block) {
-  const tw = tk.mds.variant2samples.twLst.find((i) => i.term.id == termid);
-  if (!tw) throw "showSummary4oneTerm(): tw not found from variant2samples.twLst";
-  const rows = [];
-  for (const [category_key, count, total] of numbycategory) {
-    const sk = category_key.replace(/\s/g, "-");
-    const row = [
-      { value: tw.term.values?.[category_key]?.label || category_key },
-      { html: total == void 0 ? "" : fillbar(null, { f: count / total, v1: count, v2: total }) },
-      {
-        html: `<span data-testid=sjpp-mds3tk-samsumcatmutcount-${sk}>${count}</span>
-			${total ? ` <span style="font-size:.8em">/ <span data-testid=sjpp-mds3tk-samsumcattotalcount-${sk}>` + total + "</span></span>" : ""}`
-      }
-    ];
-    rows.push(row);
-  }
-  renderTable({
-    div,
-    rows,
-    columns: [
-      {
-        nowrap: true
-        // to force all category values to show in one line without wrap. otherwise they wrap and column width appears fixed
-      },
-      {},
-      {}
-    ],
-    showHeader: false,
-    singleMode: true,
-    noRadioBtn: true,
-    noButtonCallback: (i) => {
-      clickCategory(numbycategory[i][0]);
-    }
-  });
-  async function clickCategory(category) {
-    tk.menutip.clear();
-    const term = await tk.mds.termdb.vocabApi.getterm(termid);
-    if (!term.values || Object.keys(term.values).length == 0) {
-      term.values = {};
-      for (const c of numbycategory) {
-        term.values[c[0]] = { label: c[0], samplecount: c[1] };
-      }
-    }
-    const tvs = {
-      type: "tvs",
-      tvs: { term, values: [{ key: category }] }
-    };
-    createSubTk(tk, block, tvs);
-  }
-}
-function getNewFilter(tk, tvs) {
-  if (tk.filterObj) {
-    return getNormalRoot({
-      type: "tvslst",
-      join: "and",
-      in: true,
-      lst: [tk.filterObj, tvs]
-    });
-  }
-  return {
-    type: "tvslst",
-    in: true,
-    join: "",
-    lst: [tvs]
-  };
-}
-async function showDensity4oneTerm(termid, div, data, tk, block) {
-  const term = await tk.mds.termdb.vocabApi.getterm(termid);
-  const callback = async (range) => {
-    tk.menutip.clear();
-    const tvs = {
-      type: "tvs",
-      tvs: { term, ranges: [{ start: range.range_start, stop: range.range_end }] }
-    };
-    createSubTk(tk, block, tvs);
-  };
-  const vr = new violinRenderer({
-    holder: div,
-    rd: data.density_data,
-    width: 400,
-    height: 100,
-    radius: 8,
-    callback,
-    scaleFactor: term.valueConversion ? term.valueConversion.scaleFactor : 1
-  });
-  vr.render();
-}
-function createSubTk(tk, block, tvs) {
-  const tk2 = block.block_addtk_template(tk.duplicateTk(getNewFilter(tk, tvs)));
-  tk2.subtk = true;
-  block.tk_load(tk2);
-}
-function menu_listSamples(buttonrow, data, tk, block) {
-  buttonrow.append("div").text(`List ${data.sampleTotalNumber} sample${data.sampleTotalNumber > 1 ? "s" : ""}`).attr("class", "sja_menuoption sja_mds3_slb_sampletablebtn").attr("data-testid", "sjpp-mds3-list-samples-option").on("click", async () => {
-    tk.menutip.clear();
-    const wait = tk.menutip.d.append("div").text("Loading...").style("margin", "15px");
-    try {
-      const { samples } = await tk.mds.getSamples();
-      await displaySampleTable(samples, {
-        div: tk.menutip.d,
-        tk,
-        block
-      });
-      wait.remove();
-    } catch (e) {
-      wait.text(e.message || e);
-      console.log(e);
-    }
-  });
-}
-export {
-  makeSampleFilterLabel,
-  makeSampleLabel
-};
-//# sourceMappingURL=leftlabel.sample-PDZLWLJ4.js.map

package/dist/legacyDataset-27L4DMCL.js

@@ -1,117 +0,0 @@
-import {
-  schemeCategory20
-} from "./chunk-V2OJLJSK.js";
-import {
-  stratinput
-} from "./chunk-PF4DSFDR.js";
-import {
-  ordinal,
-  stratify_default
-} from "./chunk-HDTFYTEL.js";
-import "./chunk-Q5RDQNIT.js";
-import "./chunk-HS5PO5ZQ.js";
-
-// src/legacyDataset.js
-function validate_oldds(ds) {
-  if (ds.geneexpression) {
-    if (ds.geneexpression.maf) {
-      try {
-        ds.geneexpression.maf.get = new Function(...ds.geneexpression.maf.get);
-      } catch (e) {
-        return "invalid Javascript for get() of expression.maf of " + ds.label;
-      }
-    }
-  }
-  if (ds.cohort) {
-    if (ds.cohort.raw && ds.cohort.tosampleannotation) {
-      if (!ds.cohort.key4annotation) {
-        return "cohort.tosampleannotation in use by .key4annotation missing of " + ds.label;
-      }
-      if (!ds.cohort.annotation) {
-        ds.cohort.annotation = {};
-      }
-      let nosample = 0;
-      for (const a of ds.cohort.raw) {
-        const sample = a[ds.cohort.tosampleannotation.samplekey];
-        if (sample) {
-          const b = {};
-          for (const k in a) {
-            b[k] = a[k];
-          }
-          ds.cohort.annotation[sample] = b;
-        } else {
-          nosample++;
-        }
-      }
-      if (nosample) return nosample + " rows has no sample name from sample annotation of " + ds.label;
-      delete ds.cohort.tosampleannotation;
-    }
-    if (ds.cohort.levels) {
-      if (ds.cohort.raw) {
-        const nodes = stratinput(ds.cohort.raw, ds.cohort.levels);
-        ds.cohort.root = stratify_default()(nodes);
-        ds.cohort.root.sum((i) => i.value);
-      }
-    }
-    if (ds.cohort.raw) {
-      delete ds.cohort.raw;
-    }
-    ds.cohort.suncolor = ordinal(schemeCategory20);
-  }
-  if (ds.snvindel_attributes) {
-    for (const at of ds.snvindel_attributes) {
-      if (at.get) {
-        try {
-          at.get = new Function(...at.get);
-        } catch (e) {
-          return "invalid Javascript for getter of " + JSON.stringify(at);
-        }
-      } else if (at.lst) {
-        for (const at2 of at.lst) {
-          if (at2.get) {
-            try {
-              at2.get = new Function(...at2.get);
-            } catch (e) {
-              return "invalid Javascript for getter of " + JSON.stringify(at2);
-            }
-          }
-        }
-      }
-    }
-  }
-  if (ds.stratify) {
-    if (!Array.isArray(ds.stratify)) {
-      return "stratify is not an array in " + ds.label;
-    }
-    for (const strat of ds.stratify) {
-      if (!strat.label) {
-        return "stratify method lacks label in " + ds.label;
-      }
-      if (strat.bycohort) {
-        if (!ds.cohort) {
-          return "stratify method " + strat.label + " using cohort but no cohort in " + ds.label;
-        }
-      } else {
-        if (!strat.attr1) {
-          return "stratify method " + strat.label + " not using cohort but no attr1 in " + ds.label;
-        }
-        if (!strat.attr1.label) {
-          return ".attr1.label missing in " + strat.label + " in " + ds.label;
-        }
-        if (!strat.attr1.k) {
-          return ".attr1.k missing in " + strat.label + " in " + ds.label;
-        }
-      }
-    }
-  }
-  if (ds.url4variant) {
-    for (const u of ds.url4variant) {
-      u.makelabel = new Function(...u.makelabel);
-      u.makeurl = new Function(...u.makeurl);
-    }
-  }
-}
-export {
-  validate_oldds
-};
-//# sourceMappingURL=legacyDataset-27L4DMCL.js.map